{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33889524", "kind": "science-record", "revision": 7, "content_hash": "sha256:0db6af1624135c9af44934c07dac3685f359fdb1b1bec5ab9c9a5f86006a3052", "created_at": "2026-11-01T15:41:33Z", "updated_at": "2026-11-01T21:25:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A signature of estimate-stromal-immune score-based genes associated with the prognosis of lung adenocarcinoma.", "doi": "10.21037/tlcr-21-223", "pmid": "33889524", "authors": ["Qianli Ma", "Yang Chen", "Fei Xiao", "Yang Hao", "Zhiyi Song", "Jin Zhang", "Katsuhiro Okuda", "Sang-Won Um", "Mario Silva", "Yoshihisa Shimada", "Chaozeng Si", "Chaoyang Liang"], "journal": "Translational lung cancer research", "year": 2021, "abstract": "BACKGROUND: Immune and stromal component evaluation is necessary to establish accurate prognostic markers for the prediction of clinical outcomes in lung adenocarcinoma (LUAD). We aimed to develop a gene signature based on the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE)-stromal-immune score in LUAD.\nMETHODS: The transcriptomic profiles of patients with LUAD were obtained from The Cancer Genome Atlas (TCGA), and the immune and stromal scores were derived using the ESTIMATE algorithm. The prognostic signature genes were selected from the differentially expressed genes (DEGs) using the robust partial likelihood-based cox proportional hazards regression method. The negative log-likelihood and the Akaike Information Criterion (AIC) were used to identify the optimal gene signature. The validation was carried out in 2 independent datasets from the Gene Expression Omnibus (GSE68571 and GSE72094).\nRESULTS: Patients with high ESTIMATE, stromal, and immune scores had better overall survivals (P=0.0035, P=0.066, and P=0.0077). The expression of thirty-seven genes was related to ESTIMATE-stromal-immune score. A risk stratification model was developed based on a gene signature containing CD74, JCHAIN, and PTGDS. The ESTIMATE-stromal-immune risk score was revealed to be a prognostic factor (P=0.009) after multivariate analysis. Four groups were classified based on this risk stratification model, yielding increasing survival outcomes (log-rank test, P=0.0051). This risk stratification model and other clinicopathological factors were combined to generate a nomogram. The calibration curves showed perfect agreement between the nomogram-predicted outcomes and those actually observed. Similar observations were made in 2 independent cohorts.\nCONCLUSIONS: The gene signature based on the ESTIMATE-stromal-immune score could predict the prognosis of patients with LUAD.", "claims": [{"id": "claim-method", "statement": "The Kaplan–Meier estimator was used to estimate the patients’ overall survival. The derivation cohort was divided into 2 groups based on their ESTIMATE, stromal, and immune scores: maximally selected rank statistics were employed to identify the optimal score cutoff for classifying patients by each score. The R package “maxstat” was used during identification (16). Log-rank tests were used to compare the survival outcomes of the 2 groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33889524", "locator": "sections[6] \"Relationship of estimate-stromal-immune scores and prognosis\" paragraph 2", "quote": "The Kaplan–Meier estimator was used to estimate the patients’ overall survival. The derivation cohort was divided into 2 groups based on their ESTIMATE, stromal, and immune scores: maximally selected rank statistics were employed to identify the optimal score cutoff for classifying patients by each score. The R package “maxstat” was used during identification (16). Log-rank tests were used to compare the survival outcomes of the 2 groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "❖ Derivation cohort: 514 LUAD samples from The Cancer Genome Atlas (TCGA);❖ Validation cohorts: external validation was operated in two independent cohorts from the Gene Expression Omnibus (GEO) database:96 LUAD samples from GSE68571 database;442 LUAD samples from GSE72094 database. Clinicopathological data for the corresponding patients were obtained including age, sex, pathologic stage, and survival outcome.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33889524", "locator": "sections[3] \"Population\" paragraphs 1-4", "quote": "❖ Derivation cohort: 514 LUAD samples from The Cancer Genome Atlas (TCGA);❖ Validation cohorts: external validation was operated in two independent cohorts from the Gene Expression Omnibus (GEO) database:96 LUAD samples from GSE68571 database;442 LUAD samples from GSE72094 database. Clinicopathological data for the corresponding patients were obtained including age, sex, pathologic stage, and survival outcome."}], "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:33889524"], "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:GSE68571"], "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:GSE68571"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33889524", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tlcr-21-223", "sha256": "sha256:216ea8519ce015fcd86333ba8c716a43643e283cc06c253dfed69ff69c7d8364", "bytes": 46806, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tlcr-21-223", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8044489", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE68571", "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=GSE68571", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68571", "version": null, "note": "❖ Derivation cohort: 514 LUAD samples from The Cancer Genome Atlas (TCGA);❖ Validation cohorts: external validation was operated in two independent cohorts from the Gene Expression Omnibus (GEO) database:96 LUAD samples from GSE68571 database;442 LUAD samples from GSE72094 database. Clinicopathological data for the corresponding patients were obtained including age, sex, pathologic stage, and survival outcome.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "❖ Derivation cohort: 514 LUAD samples from The Cancer Genome Atlas (TCGA);❖ Validation cohorts: external validation was operated in two independent cohorts from the Gene Expression Omnibus (GEO) database:96 LUAD samples from GSE68571 database;442 LUAD samples from GSE72094 database. 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Clinicopathological data for the corresponding patients were obtained including age, sex, pathologic stage, and survival outcome.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "❖ Derivation cohort: 514 LUAD samples from The Cancer Genome Atlas (TCGA);❖ Validation cohorts: external validation was operated in two independent cohorts from the Gene Expression Omnibus (GEO) database:96 LUAD samples from GSE68571 database;442 LUAD samples from GSE72094 database. 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null, "sha256": "sha256:f67647fc8e32045f62ddeed9685217814ce0f607f450f726966f1c5985994521", "bytes": 3043, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#t1", "version": null, "note": "Clinicopathologic characteristics of patients in different risk groups", "structure": {"pmcid": "PMC8044489", "section_index": 9, "section_title": "Gene signature and risk evaluation model", "row_count": 43, "column_count": 7}, "table": {"label": "Table 1", "caption": "Clinicopathologic characteristics of patients in different risk groups", "rows": [["Characteristics", "Whole cohort (n=514)", "Risk score =0 (n=124)", "Risk score =1 (n=130)", "Risk score =2 (n=139)", "Risk score =3 (n=121)", "P value"], ["Age [median (IQR)]", "66.00 [59.00, 72.25]", "68.50 [61.00, 74.00]", "68.00 [60.00, 74.25]", "65.00 [57.00, 71.50]", "62.00 [56.50, 70.00]", "<0.001"], ["Gender (%)", "", "", "", "", "", "0.006"], ["Female", "274 (53.6)", "82 (66.1)", "68 (52.7)", "71 (51.4)", "53 (44.2)", ""], ["Male", "237 (46.4)", "42 (33.9)", "61 (47.3)", "67 (48.6)", "67 (55.8)", ""], ["Stage (%)", "", "", "", "", "", "<0.001"], ["I", "275 (54.3)", "85 (70.2)", "73 (57.5)", "60 (43.5)", "57 (47.5)", ""], ["II", "121 (23.9)", "29 (24.0)", "28 (22.0)", "29 (21.0)", "35 (29.2)", ""], ["III", "84(16.6)", "6 (5.0)", "18 (14.2)", "40 (29.0)", "20 (16.7)", ""], ["IV", "26 (5.1)", "1 (0.8)", "8 (6.3)", "9 (6.5)", "8 (6.7)", ""], ["Survival (%)", "", "", "", "", "", "0.023"], ["Alive", "327 (63.6)", "92 (74.2)", "84 (64.6)", "81 (58.3)", "70 (57.9)", ""], ["Dead", "187 (36.4)", "32 (25.8)", "46 (35.4)", "58 (41.7)", "51 (42.1)", ""], ["Stage (%)*", "", "", "", "", "", "<0.001"], ["i", "274 (53.6)", "85 (68.5)", "73 (56.6)", "60 (43.5)", "56 (46.7)", ""], ["ii", "120 (23.5)", "29 (23.4)", "28 (21.7)", "28 (20.3)", "35 (29.2)", ""], ["iii", "84 (16.4)", "6 (4.8)", "18 (14.0)", "40 (29.0)", "20 (16.7)", ""], ["iv", "26 (5.1)", "1 (0.8)", "8 (6.2)", "9 (6.5)", "8 (6.7)", ""], ["M (%)*", "", "", "", "", "", "0.322"], ["M0", "343 (67.1)", "83 (66.9)", "83 (64.3)", "93 (67.4)", "84 (70.0)", ""], ["M1", "25 (4.9)", "1 (0.8)", "7 (5.4)", "9 (6.5)", "8 (6.7)", ""], ["Mx", "139 (27.2)", "38 (30.6)", "39 (30.2)", "35 (25.4)", "27 (22.5)", ""], ["N (%)*", "", "", "", "", "", "<0.001"], ["N0", "328 (64.2)", "91 (73.4)", "87 (67.4)", "74 (53.6)", "76 (63.3)", ""], ["N1", "95 (18.6)", "24 (19.4)", "21 (16.3)", "22 (15.9)", "28 (23.3)", ""], ["N2", "74 (14.5)", "4 (3.2)", "15 (11.6)", "39 (28.3)", "16 (13.3)", ""], ["N3", "2 (0.4)", "1 (0.8)", "0 (0.0)", "1 (0.7)", "0 (0.0)", ""], ["Nx", "11 (2.2)", "3 (2.4)", "6 (4.7)", "2 [1–4]", "0 (0.0)", ""], ["T (%)", "", "", "", "", "", "0.002"], ["T1", "168 (32.9)", "55 (44.4)", "51 (39.5)", "35 (25.4)", "27 (22.5)", ""], ["T2", "276 (54.0)", "60 (48.4)", "61 (47.3)", "87 (63.0)", "68 (56.7)", ""], ["T3", "45 (8.8)", "6 (4.8)", "11 (8.5)", "9 (6.5)", "19 (15.8)", ""], ["T4", "19 (3.7)", "3 (2.4)", "4 (3.1)", "6 (4.3)", "6 (5.0)", ""], ["Tx", "3 (0.6)", "0 (0.0)", "2 [1–6]", "1 (0.7)", "0 (0.0)", ""], ["Estimate score (%)", "", "", "", "", "", "<0.001"], ["High", "257 (50.0)", "111 (89.5)", "82 (63.1)", "49 (35.3)", "15 (12.4)", ""], ["Low", "257 (50.0)", "13 (10.5)", "48 (36.9)", "90 (64.7)", "106 (87.6)", ""], ["Immune score (%)", "", "", "", "", "", "<0.001"], ["High", "453 (88.1)", "124 (100.0)", "128 (98.5)", "122 (87.8)", "79 (65.3)", ""], ["Low", "61 (11.9)", "0 (0.0)", "2 [1–5]", "17 (12.2)", "42 (34.7)", ""], ["Stromal score (%)", "", "", "", "", "", "0.003"], ["High", "26 (5.1)", "13 (10.5)", "8 (6.2)", "4 (2.9)", "1 (0.8)", ""], ["Low", "488 (94.9)", "111 (89.5)", "122 (93.8)", "135 (97.1)", "120 (99.2)", ""]], "row_count": 43, "column_count": 7, "numeric_cells": 176, "header_rows": 1, "locator": "section[9]/table-wrap[1]#t1"}}, {"id": "asset:table:pmid:33889524:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8bbd5f59df1dc5288edecd72950a11cdc96bc0d9b2a7d08e26ae76ca30b9036e", "bytes": 957, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#t2", "version": null, "note": "Prognostic gene signature selection based on a robust likelihood- based survival model", "structure": {"pmcid": "PMC8044489", "section_index": 15, "section_title": "Gene signature based on the estimate, stromal, and immune scores and risk stratification model for LUAD", "row_count": 20, "column_count": 4}, "table": {"label": "Table 2", "caption": "Prognostic gene signature selection based on a robust likelihood- based survival model", "rows": [["Gene Symbol", "Negative log-likelihood", "AIC", "Forward selection"], ["CD74", "973.92", "1,949.83", "Y"], ["JCHAIN", "971", "1,946", "Y"], ["PTGDS", "969.98", "1,945.96", "Y"], ["HLA-DRA", "969.95", "1,947.9", "-"], ["HLA-DRB5", "969.07", "1,948.13", "-"], ["HLA-DOA", "968.91", "1,949.82", "-"], ["C7", "968.89", "1,951.78", "-"], ["PTPRC", "968.89", "1,953.77", "-"], ["HLA-DQA1", "968.7", "1,955.39", "-"], ["HLA-DMB", "966.91", "1,953.81", "-"], ["CHIT1", "966.85", "1,955.7", "-"], ["CPA3", "965.89", "1,955.78", "-"], ["CSF2RB", "965.89", "1,957.78", "-"], ["HLA-DPB1", "965.86", "1,959.72", "-"], ["CD79A", "965.06", "1,960.13", "-"], ["S100P", "963.13", "1,958.25", "-"], ["HLA-DQB2", "962.83", "1,959.66", "-"], ["HLA-DRB1", "962.72", "1,961.45", "-"], ["CD52", "962.65", "1,963.31", "-"]], "row_count": 20, "column_count": 4, "numeric_cells": 42, "header_rows": 1, "locator": "section[15]/table-wrap[1]#t2"}}, {"id": "asset:table:pmid:33889524:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:eaf0f4aa7f92d9f49209ffd1e285bf66102264abd90f3ff45cf88dc91eeb0e23", "bytes": 576, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#t3", "version": null, "note": "Multivariate Cox regression analyses of risk factors for overall survival", "structure": {"pmcid": "PMC8044489", "section_index": 16, "section_title": "Relationship of estimate-stromal-immune score-based risk group with overall survival in patients with LUAD", "row_count": 7, "column_count": 5}, "table": {"label": "Table 3", "caption": "Multivariate Cox regression analyses of risk factors for overall survival", "rows": [["Characteristics", "", "Hazard ratio", "95% Cl", "P value"], ["Risk Score", "1 vs. 0", "1.31", "(0.82–2.11)", "0.262"], ["", "2 vs. 0", "1.41", "(0.88–2.24)", "0.151"], ["", "3 vs. 0", "1.84", "(1.16–2.91)", "0.009"], ["Stage", "II vs. 1", "2.42", "(1.68–3.48)", "<0.001"], ["", "III vs. 1", "3.42", "(2.30–5.08)", "<0.001"], ["", "IV vs. 1", "3.53", "(2.02–6.18)", "<0.001"]], "row_count": 7, "column_count": 5, "numeric_cells": 25, "header_rows": 1, "locator": "section[16]/table-wrap[1]#t3"}}], "gaps": ["asset:data:geo:GSE68571 not downloaded", "asset:data:geo:GSE68571 licence not read", "asset:data:geo:GSE72094 not downloaded", "asset:data:geo:GSE72094 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The Kaplan–Meier estimator was used to estimate the patients’ overall survival. The derivation cohort was divided into 2 groups based on their ESTIMATE, stromal, and immune scores: maximally selected rank statistics were employed to identify the optimal score cutoff for classifying patients by each score. The R package “maxstat” was used during identification (16). Log-rank tests were used to compare the survival outcomes of the 2 groups."}}, {"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": "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 proportional hazards"}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE68571", "GSE72094"], "resolved_accessions": ["GSE68571", "GSE72094"], "statements": ["❖ Derivation cohort: 514 LUAD samples from The Cancer Genome Atlas (TCGA);❖ Validation cohorts: external validation was operated in two independent cohorts from the Gene Expression Omnibus (GEO) database:96 LUAD samples from GSE68571 database;442 LUAD samples from GSE72094 database. Clinicopathological data for the corresponding patients were obtained including age, sex, pathologic stage, and survival outcome."], "basis": "The paper names GSE68571, GSE72094 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": ["logrank_test"], "assets": ["source:pmid:33889524", "data:geo:GSE68571", "asset:table:pmid:33889524:1", "asset:table:pmid:33889524:2", "asset:table:pmid:33889524:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE68571"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 35589, "completion_tokens": 2100, "cached_tokens": 12040}}, "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:33889524", "type": "paper", "label": "pmid:33889524"}, {"id": "source:pmid:33889524", "type": "manuscript", "label": "PMID 33889524 full text"}, {"id": "data:geo:GSE68571", "type": "dataset", "label": "GEO GSE68571"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33889524", "type": "paper", "label": "pmid:33889524"}, {"id": "source:pmid:33889524", "type": "manuscript", "label": "PMID 33889524 full text"}, {"id": "data:geo:GSE68571", "type": "dataset", "label": "GEO GSE68571"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33889524", "type": "extraction", "used": ["source:pmid:33889524"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE68571", "type": "accession_resolution", "used": ["data:geo:GSE68571"], "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:33889524", "parent_hash": "sha256:2724793c8eba878f5db20e1041d7ff8aa9399caf19595bfd518507f70d195ce6", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE68571 licence not read", "asset:data:geo:GSE68571 not downloaded", "asset:data:geo:GSE72094 licence not read", "asset:data:geo:GSE72094 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": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Kaplan–Meier estimator was used to estimate the patients’ overall survival. The derivation cohort was divided into 2 groups based on their ESTIMATE, stromal, and immune scores: maximally selected rank statistics were employed to identify the optimal score cutoff for classifying patients by each score. The R package “maxstat” was used during identification (16). Log-rank tests were used to compare the survival outcomes of the 2 groups."], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T00:38:29+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}