{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33330025", "kind": "science-record", "revision": 7, "content_hash": "sha256:63388493418c41227c5ecc47835239908b896e765ee4e30913a41e2eb706835d", "created_at": "2026-11-01T15:41:19Z", "updated_at": "2026-11-01T22:02:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CD8+ T Cell Co-Expressed Genes Correlate With Clinical Phenotype and Microenvironments of Urothelial Cancer.", "doi": "10.3389/fonc.2020.553399", "pmid": "33330025", "authors": ["Yutao Wang", "Kexin Yan", "Jiaxing Lin", "Yang Liu", "Jianfeng Wang", "Xuejie Li", "Xinxin Li", "Zhixiong Hua", "Zhenhua Zheng", "Jianxiu Shi", "Siqing Sun", "Jianbin Bi"], "journal": "Frontiers in oncology", "year": 2020, "abstract": "PURPOSE: To identify immune-related co-expressed genes that promote CD8+ T cell infiltration in bladder cancer, and to explore the interactions among relevant genes in the tumor microenvironment.\nMETHOD: We obtained bladder cancer gene matrix and clinical information data from TCGA, GSE32894 and GSE48075. The \"estimate\" package was used to calculate tumor purity and immune score. The CIBERSORT algorithm was used to assess CD8+ T cell proportions. Weighted gene co-expression network analysis was used to identify the co-expression modules with CD8+ T cell proportions and bladder tumor purity. Subsequently, we performed correlation analysis among angiogenesis factors, angiogenesis inhibitors, immune inflammatory responses, and CD8+ T cell related genes in tumor microenvironment.\nRESULTS: A CD8+ T cell related co-expression network was identified. Eight co-expressed genes (PSMB8, PSMB9, PSMB10, PSME2, TAP1, IRF1, FBOX6, ETV7) were identified as CD8+ T cell-related genes that promoted infiltration of CD8+ T cells, and were enriched in the MHC class I tumor antigen presentation process. The proteins level encoded by these genes (PSMB10, PSMB9, PSMB8, TAP1, IRF1, and FBXO6) were lower in the high clinical grade patients, which suggested the clinical phenotype correlation both in mRNA and protein levels. These factors negatively correlated with angiogenesis factors and positively correlated with angiogenesis inhibitors. PD-1 and PD-L1 positively correlated with these genes which suggested PD-1 expression level positively correlated with the biological process composed by these co-expression genes. In the high expression group of these genes, inflammation and immune response were more intense, and the tumor purity was lower, suggesting that these genes were immune protective factors that improved the prognosis in patients with bladder cancer.\nCONCLUSION: These co-expressed genes promote high levels of infiltration of CD8+ T cells in an immunoproteasome process involved in MHC class I molecules. The mechanism might provide new pathways for treatment of patients who are insensitive to PD-1 immunotherapy due to low degrees of CD8+ T cell infiltration.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier survival analysis was applied to generate overall survival curves and the log-rank test was used to calculate the significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33330025", "locator": "sections[11] \"Statistical Analysis\" paragraph 2", "quote": "Kaplan–Meier survival analysis was applied to generate overall survival curves and the log-rank test was used to calculate the significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: The datasets TCGA-BLCA for this study can be found in the [The Cancer Genome Atlas] [http://cancergenome.nih.gov/)].The datasets GSE32894 and GSE48075 for this study can be found in the [GEO] [http://www.ncbi.nlm.nih.gov/geo/].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33330025", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: The datasets TCGA-BLCA for this study can be found in the [The Cancer Genome Atlas] [http://cancergenome.nih.gov/)].The datasets GSE32894 and GSE48075 for this study can be found in the [GEO] [http://www.ncbi.nlm.nih.gov/geo/]."}], "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:33330025"], "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:GSE32894"], "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:GSE32894"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33330025", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2020.553399", "sha256": "sha256:3047d746ab872b0974bd5a878d8a941a778471dbaded39971cd110fadae7b6d5", "bytes": 32713, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2020.553399", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7713665", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE32894", "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=GSE32894", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32894", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: The datasets TCGA-BLCA for this study can be found in the [The Cancer Genome Atlas] [http://cancergenome.nih.gov/)].The datasets GSE32894 and GSE48075 for this study can be found in the [GEO] [http://www.ncbi.nlm.nih.gov/geo/].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. 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This data can be found here: The datasets TCGA-BLCA for this study can be found in the [The Cancer Genome Atlas] [http://cancergenome.nih.gov/)].The datasets GSE32894 and GSE48075 for this study can be found in the [GEO] [http://www.ncbi.nlm.nih.gov/geo/].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: The datasets TCGA-BLCA for this study can be found in the [The Cancer Genome Atlas] [http://cancergenome.nih.gov/)].The datasets GSE32894 and GSE48075 for this study can be found in the [GEO] [http://www.ncbi.nlm.nih.gov/geo/].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1167333", "GSM1167334", "GSM1167335", "GSM1167336", "GSM1167337", "GSM1167338", "GSM1167339", "GSM1167340", "GSM1167341", "GSM1167342", "GSM1167343", "GSM1167344", "GSM1167345", "GSM1167346", "GSM1167347", "GSM1167348", "GSM1167349", "GSM1167350", "GSM1167351", "GSM1167352", "GSM1167353", "GSM1167354", "GSM1167355", "GSM1167356", "GSM1167357", "GSM1167358", "GSM1167359", "GSM1167360", "GSM1167361", "GSM1167362", "GSM1167363", "GSM1167364", "GSM1167365", "GSM1167366", "GSM1167367", "GSM1167368", "GSM1167369", "GSM1167370", "GSM1167371", "GSM1167372", "GSM1167373", "GSM1167374", "GSM1167375", "GSM1167376", "GSM1167377", "GSM1167378", "GSM1167379", 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"6.27E-08"], ["FBXO6", "green yellow", "0.408", "6.46E-08"], ["PSMB10", "green yellow", "0.408", "6.57E-08"], ["HLA-C", "green yellow", "0.406", "7.68E-08"], ["HLA-DMA", "blue", "0.405", "8.43E-08"], ["HLA-DQA1", "blue", "0.403", "9.76E-08"]], "row_count": 33, "column_count": 4, "numeric_cells": 66, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33330025:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f616fbe99384c66f7bc677391545e440b255ada601770d8434cc8afe49ce6f85", "bytes": 1631, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#T2", "version": null, "note": "Univariate Cox proportional hazard analysis of CD8+ T cells related genes.", "structure": {"pmcid": "PMC7713665", "section_index": 13, "section_title": "CD8+ T Cell Related Modules", "row_count": 33, "column_count": 5}, "table": {"label": "Table 2", "caption": "Univariate Cox proportional hazard analysis of CD8+ T cells related genes.", "rows": [["ID", "HR", "HR.95L", "HR.95H", "P-value"], ["PSMB10", "0.980", "0.968", "0.991", "0.0005"], ["FBXO6", "0.958", "0.934", "0.982", "0.0007"], ["PSMB8", "0.994", "0.990", "0.998", "0.002"], ["ETV7", "0.959", "0.934", "0.985", "0.0024"], ["IRF1", "0.978", "0.963", "0.993", "0.0041"], ["TAP1", "0.995", "0.991", "0.998", "0.0052"], ["PSME2", "0.993", "0.988", "0.998", "0.0087"], ["PSMB9", "0.992", "0.986", "0.998", "0.0098"], ["CD7", "0.953", "0.917", "0.989", "0.0120"], ["B2M", "0.999", "0.999", "0.999", "0.0128"], ["HLA-C", "0.999", "0.999", "0.999", "0.0148"], ["CD74", "0.999", "0.999", "0.999", "0.0161"], ["OR2I1P", "0.983", "0.969", "0.997", "0.0165"], ["CD3D", "0.977", "0.959", "0.996", "0.0188"], ["LAG3", "0.956", "0.920", "0.993", "0.0223"], ["PSMA4", "0.977", "0.958", "0.997", "0.0232"], ["HLA-DRA", "0.999", "0.999", "0.999", "0.0234"], ["PSME1", "0.996", "0.994", "0.999", "0.0234"], ["CD2", "0.976", "0.956", "0.997", "0.0242"], ["HLA-DMA", "0.994", "0.988", "0.999", "0.0244"], ["NKG7", "0.987", "0.975", "0.999", "0.0318"], ["LAP3", "0.992", "0.984", "0.999", "0.0423"], ["CCL4", "0.968", "0.938", "0.999", "0.0445"], ["CD3E", "0.974", "0.948", "0.999", "0.0445"], ["GBP5", "0.983", "0.966", "0.999", "0.0470"], ["CD8A", "0.964", "0.927", "1.002", "0.0634"], ["HLA-DQA1", "0.993", "0.985", "1.000", "0.0743"], ["GZMA", "1.001", "0.999", "1.003", "0.0753"], ["HLA-DRB1", "0.999", "0.999", "1.000", "0.0774"], ["GZMH", "0.978", "0.953", "1.005", "0.1040"], ["CTSW", "0.985", "0.965", "1.005", "0.1313"], ["CXCL9", "0.997", "0.993", "1.0012", "0.1780"]], "row_count": 33, "column_count": 5, "numeric_cells": 132, "header_rows": 1, "locator": "section[13]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:33330025:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d30b28749733e29f7e94db5fd492e6cb7212573ae9fa7f9f37d5a4da3988cf2f", "bytes": 1224, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T3", "version": null, "note": "The list of angiogenic factors and inhibitors.", "structure": {"pmcid": "PMC7713665", "section_index": 15, "section_title": "Immune Microenvironment Analysis", "row_count": 11, "column_count": 3}, "table": {"label": "Table 3", "caption": "The list of angiogenic factors and inhibitors.", "rows": [["ID", "Function", "Name"], ["VEGFD", "Lymphangiogenic growth factor", "Vascular endothelial growth factor D"], ["PDGFD", "A specific, protease-activated ligand for the PDGF beta-receptor.", "Platelet-derived growth factor D"], ["PDGFRA", "Recruit smooth muscle cells", "Platelet-derived growth factor receptor alpha"], ["FGFR1, FGFR2", "Stimulate angio/arteriogenesis", "Fibroblast growth factor receptor1/2"], ["FGF7, FGF12", "Stimulate angio/arteriogenesis", "Fibroblast growth factor 7/12"], ["TGFBR2, TGFBR3", "Stimulate extracellular matrix production", "Type II/III TGF-beta receptor"], ["IL12A, IL12B", "Inhibit endothelial migration. Downregulate bFGF. Induce interferon-g and IP-10", "Interleukin-12 subunit alpha/beta"], ["IL12RB1, IL12RB2", "Inhibit endothelial migration. Downregulate bFGF. Induce interferon-g and IP-10", "Interleukin-12 receptor beta1/2"], ["IL10RA", "Inhibit endothelial migration", "Interleukin 10 receptor subunit alpha"], ["IFNL1, IFNL2, IFNL3", "Inhibit endothelial migration; Downregulate bFGF", "Interferon lambda 1/2/3"]], "row_count": 11, "column_count": 3, "numeric_cells": 12, "header_rows": 1, "locator": "section[15]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:33330025:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d073fe124e46f0fe1c3278b16716426f40bbd2becec98e7609166e9c22da3dc9", "bytes": 1087, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T4", "version": null, "note": "The results of GSEA analysis.", "structure": {"pmcid": "PMC7713665", "section_index": 16, "section_title": "GSEA Analysis and Survival Analysis", "row_count": 10, "column_count": 9}, "table": {"label": "Table 4", "caption": "The results of GSEA analysis.", "rows": [["ID", "Antigen processing and presentation", "Chemokine signaling pathway", "Nature killer cell mediated cytotoxicity", "T cell receptor signaling pathway"], ["NOM-p", "FDR-q", "NOM-p", "FDR-q", "NOM-p", "FDR-q", "NOM-p", "FDR-q"], ["PSMB8", "<0.0001", "<0.0001", "<0.0001", "0.0037", "<0.0001", "<0.0001", "0.0020", "0.0082"], ["PSMB9", "<0.0001", "0.0002", "<0.0001", "0.0002", "<0.0001", "<0.0001", "0.0020", "0.0020"], ["PSMB10", "<0.0001", "<0.0001", "0.0080", "0.0080", "<0.0001", "<0.0001", "0.0158", "0.0150"], ["PSME2", "<0.0001", "<0.0001", "0.0368", "0.1149", "<0.0001", "<0.0001", "0.06", "0.1486"], ["TAP1", "<0.0001", "<0.0001", "<0.0001", "<0.0001", "<0.0001", "<0.0001", "<0.0001", "0.0008"], ["IRF1", "<0.0001", "<0.0001", "0.0110", "0.0272", "<0.0001", "<0.0001", "0.0056", "0.0133"], ["ETV7", "<0.0001", "<0.0001", "0.0019", "0.0143", "<0.0001", "<0.0001", "0.0320", "0.0729"], ["FBXO6", "<0.0001", "<0.0001", "<0.0001", "0.0015", "<0.0001", "<0.0001", "0.0060", "0.0066"]], "row_count": 10, "column_count": 9, "numeric_cells": 65, "header_rows": 2, "locator": "section[16]/table-wrap[1]#T4"}}, {"id": "asset:table:pmid:33330025:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8e2428f352472d77a27f14ad86c83e4072156b086108771733422bb6b5e43a04", "bytes": 716, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#T5", "version": null, "note": "Correlation Analysis of Candidate Factors and CD8+ T cells.", "structure": {"pmcid": "PMC7713665", "section_index": 17, "section_title": "Pan-Cancer Analysis", "row_count": 9, "column_count": 3}, "table": {"label": "Table 5", "caption": "Correlation Analysis of Candidate Factors and CD8+ T cells.", "rows": [["Gene", "Count", "Cancer type (CD8+ T cells cor > 0.4)"], ["IRF1", "13", "ACC, BRCA, CESC, HNSC, KIRC, KIRP, LIHC, LUAD, LUSC, PAAD, PRAD, STAD, SKCM"], ["PSMB9", "10", "THCA, BRCA-Her2, HNSC - HPVpos, KIRC, LIHC, LUAD, LUSC, OV, STAD, SKCM"], ["TAP1", "9", "THCA, BRCA-Her2, CESC, KIRC, LIHC, LUAD, LUSC, UCS, SKCM"], ["ETV7", "7", "THCA, BRCA-Her2, CHOL, HNSC, KIRC, LIHC, SKCM,"], ["PSMB10", "6", "THCA, DLBC, HNSC, LIHC, LUSC, OV,"], ["PSMB8", "4", "THCA, KIRC, LUSC, SKCM,"], ["PSEM2", "2", "THCA, SKCM"], ["FBOX6", "1", "THCA"]], "row_count": 9, "column_count": 3, "numeric_cells": 10, "header_rows": 1, "locator": "section[17]/table-wrap[1]#T5"}}], "gaps": ["asset:data:geo:GSE32894 not downloaded", "asset:data:geo:GSE32894 licence not read", "asset:data:geo:GSE48075 not downloaded", "asset:data:geo:GSE48075 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": "Kaplan–Meier survival analysis was applied to generate overall survival curves and the log-rank test was used to calculate the significance."}}, {"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": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-4", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}], "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": ["GSE32894", "GSE48075"], "resolved_accessions": ["GSE32894", "GSE48075"], "statements": ["Publicly available datasets were analyzed in this study. This data can be found here: The datasets TCGA-BLCA for this study can be found in the [The Cancer Genome Atlas] [http://cancergenome.nih.gov/)].The datasets GSE32894 and GSE48075 for this study can be found in the [GEO] [http://www.ncbi.nlm.nih.gov/geo/]."], "basis": "The paper names GSE32894, GSE48075 in 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:33330025", "data:geo:GSE32894", "asset:table:pmid:33330025:1", "asset:table:pmid:33330025:2", "asset:table:pmid:33330025:3", "asset:table:pmid:33330025:4", "asset:table:pmid:33330025:5", "asset:table:pmid:33330025:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE32894"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:25Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 24773, "completion_tokens": 1717, "cached_tokens": 512}}, "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:33330025", "type": "paper", "label": "pmid:33330025"}, {"id": "source:pmid:33330025", "type": "manuscript", "label": "PMID 33330025 full text"}, {"id": "data:geo:GSE32894", "type": "dataset", "label": "GEO GSE32894"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33330025", "type": "paper", "label": "pmid:33330025"}, {"id": "source:pmid:33330025", "type": "manuscript", "label": "PMID 33330025 full text"}, {"id": "data:geo:GSE32894", "type": "dataset", "label": "GEO GSE32894"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33330025", "type": "extraction", "used": ["source:pmid:33330025"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE32894", "type": "accession_resolution", "used": ["data:geo:GSE32894"], "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:33330025", "parent_hash": "sha256:e369b24df0cda85ca01ce04c45f87a7084d9143295feee27bf73f5276c6d1a56", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE32894 licence not read", "asset:data:geo:GSE32894 not downloaded", "asset:data:geo:GSE48075 licence not read", "asset:data:geo:GSE48075 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": ["Kaplan–Meier survival analysis was applied to generate overall survival curves and the log-rank test was used to calculate the significance."], "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":"2026-11-04T02:12:27+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}}}