{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33833937", "kind": "science-record", "revision": 7, "content_hash": "sha256:b0773a53183b12c56b2aa883364d25f013ac003a80f401478ad42e5e83f8e149", "created_at": "2026-11-01T15:41:31Z", "updated_at": "2026-11-01T22:03:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a 5-Gene-Based Scoring System by WGCNA and LASSO to Predict Prognosis for Rectal Cancer Patients.", "doi": "10.1155/2021/6697407", "pmid": "33833937", "authors": ["He Huang", "Shilei Xu", "Aidong Chen", "Fen Li", "Jiezhong Wu", "Xusheng Tu", "Kunpeng Hu"], "journal": "Analytical cellular pathology (Amsterdam)", "year": 2021, "abstract": "BACKGROUND: Although accumulating evidence suggested that a molecular signature panel may be more effective for the prognosis prediction than routine clinical characteristics, current studies mainly focused on colorectal or colon cancers. No reports specifically focused on the signature panel for rectal cancers (RC). Our present study was aimed at developing a novel prognostic signature panel for RC.\nMETHODS: Sequencing (or microarray) data and clinicopathological details of patients with RC were retrieved from The Cancer Genome Atlas (TCGA-READ) or the Gene Expression Omnibus (GSE123390, GSE56699) database. A weighted gene coexpression network was used to identify RC-related modules. The least absolute shrinkage and selection operator analysis was performed to screen the prognostic signature panel. The prognostic performance of the risk score was evaluated by survival curve analyses. Functions of prognostic genes were predicted based on the interaction proteins and the correlation with tumor-infiltrating immune cells. The Human Protein Atlas (HPA) tool was utilized to validate the protein expression levels.\nRESULTS: A total of 247 differentially expressed genes (DEGs) were commonly identified using TCGA and GSE123390 datasets. Brown and yellow modules (including 77 DEGs) were identified to be preserved for RC. Five DEGs (ASB2, GPR15, PRPH, RNASE7, and TCL1A) in these two modules constituted the optimal prognosis signature panel. Kaplan-Meier curve analysis showed that patients in the high-risk group had a poorer prognosis than those in the low-risk group. Receiver operating characteristic (ROC) curve analysis demonstrated that this risk score had high predictive accuracy for unfavorable prognosis, with the area under the ROC curve of 0.915 and 0.827 for TCGA and GSE56699 datasets, respectively. This five-mRNA classifier was an independent prognostic factor. Its predictive accuracy was also higher than all clinical factor models. A prognostic nomogram was developed by integrating the risk score and clinical factors, which showed the highest prognostic power. ASB2, PRPH, and GPR15/TCL1A were predicted to function by interacting with CASQ2/PDK4/EPHA67, PTN, and CXCL12, respectively. TCL1A and GPR15 influenced the infiltration levels of B cells and dendritic cells, while the expression of PRPH was positively associated with the abundance of macrophages. HPA analysis supported the downregulation of PRPH, RNASE7, CASQ2, EPHA6, and PDK4 in RC compared with normal controls.\nCONCLUSION: Our immune-related signature panel may be a promising prognostic indicator for RC.", "claims": [{"id": "claim-method", "statement": "The associations between the expression of selected prognostic genes and the abundance of six tumor-infiltrating immune cells in TCGA-PRAD (B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells) were estimated from the Tumor Immune Estimation Resource (TIMER; https://cistrome.shinyapps.io/timer/) based on Spearman's correlation test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33833937", "locator": "sections[8] \"2.6. Analysis of Immune Cell Infiltration\" paragraph 2", "quote": "The associations between the expression of selected prognostic genes and the abundance of six tumor-infiltrating immune cells in TCGA-PRAD (B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells) were estimated from the Tumor Immune Estimation Resource (TIMER; https://cistrome.shinyapps.io/timer/) based on Spearman's correlation test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated for this study can be found in GEO (http://www.ncbi.nlm.nih.gov/geo/; GSE123390, GSE56699) and TCGA (https://gdc-portal.nci.nih.gov/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33833937", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "The datasets generated for this study can be found in GEO (http://www.ncbi.nlm.nih.gov/geo/; GSE123390, GSE56699) and TCGA (https://gdc-portal.nci.nih.gov/)."}], "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:33833937"], "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:GSE123390"], "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:GSE123390"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33833937", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/6697407", "sha256": "sha256:d51ba826dbc64805fce1f2b1b5d4568ad236925b719609d4920c2f8ef469a6c1", "bytes": 49723, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/6697407", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8012151", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE123390", "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=GSE123390", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE123390", "version": null, "note": "The datasets generated for this study can be found in GEO (http://www.ncbi.nlm.nih.gov/geo/; GSE123390, GSE56699) and TCGA (https://gdc-portal.nci.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated for this study can be found in GEO (http://www.ncbi.nlm.nih.gov/geo/; GSE123390, GSE56699) and TCGA (https://gdc-portal.nci.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3502511", "GSM3502512", "GSM3502513", "GSM3502514", "GSM3502515", "GSM3502516", "GSM3502517", "GSM3502518", "GSM3502519", "GSM3502520", "GSM3502521", "GSM3502522", "GSM3502523", "GSM3502524", "GSM3502525", "GSM3502526", "GSM3502527", "GSM3502528", "GSM3502529", "GSM3502530", "GSM3502531", "GSM3502532", "GSM3502533", "GSM3502534", "GSM3502535", "GSM3502536", "GSM3502537", "GSM3502538", "GSM3502539", "GSM3502540", "GSM3502541", "GSM3502542", "GSM3502543"], "sample_count": 33, "group_sizes": null, "group_sizes_basis": null, "platform": "17586", "taxon": "Homo sapiens", "title": "Locally advanced rectal cancer transcriptomic-based secretome analysis according to neoadjuvant chemoradiotherapy response", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE56699", "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=GSE56699", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE56699", "version": null, "note": "The datasets generated for this study can be found in GEO (http://www.ncbi.nlm.nih.gov/geo/; GSE123390, GSE56699) and TCGA (https://gdc-portal.nci.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated for this study can be found in GEO (http://www.ncbi.nlm.nih.gov/geo/; GSE123390, GSE56699) and TCGA (https://gdc-portal.nci.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1366951", "GSM1366952", "GSM1366953", "GSM1366954", "GSM1366955", "GSM1366956", "GSM1366957", "GSM1366958", "GSM1366959", "GSM1366960", "GSM1366961", "GSM1366962", "GSM1366963", "GSM1366964", "GSM1366965", "GSM1366966", "GSM1366967", "GSM1366968", "GSM1366969", "GSM1366970", "GSM1366971", "GSM1366972", "GSM1366973", "GSM1366974", "GSM1366975", "GSM1366976", "GSM1366977", "GSM1366978", "GSM1366979", "GSM1366980", "GSM1366981", "GSM1366982", "GSM1366983", "GSM1366984", "GSM1366985", "GSM1366986", "GSM1366987", "GSM1366988", "GSM1366989", "GSM1366990", "GSM1366991", "GSM1366992", "GSM1366993", "GSM1366994", "GSM1366995", "GSM1366996", "GSM1366997", "GSM1366998", "GSM1366999", "GSM1367000", "GSM1367001", "GSM1367002", "GSM1367003", "GSM1367004", "GSM1367005", "GSM1367006", "GSM1367007", "GSM1367008", "GSM1367009", "GSM1367010", "GSM1367011", "GSM1367012", "GSM1367013", "GSM1367014", "GSM1367015", "GSM1367016", "GSM1367017", "GSM1367018", "GSM1367019", "GSM1367020", "GSM1367021", "GSM1367022"], "sample_count": 72, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "Stromal contribution to expression signatures of colorectal cancer (rectal samples)", "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:33833937:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:689b2b1ab546b895b856a2e359fb527eb8ee961d67e985a6b73ec0840f2868b9", "bytes": 1159, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tab1", "version": null, "note": "Preserved modules identified based on weighted gene coexpression network analysis.", "structure": {"pmcid": "PMC8012151", "section_index": 12, "section_title": "3.2. Identification of RC-Related Modules by WGCNA", "row_count": 11, "column_count": 8}, "table": {"label": "Table 1", "caption": "Preserved modules identified based on weighted gene coexpression network analysis.", "rows": [["ID", "Color", "Module size", "Preservation infor", "#DEGs", "Enrichment infor"], ["Z-score", "p value", "Enrichment fold (95% CI)", "p hyper"], ["Module 1", "Black", "99", "13.9321", "5.30e − 11", "—", "—", "—"], ["Module 2", "Blue", "683", "13.2267", "1.40e − 30", "—", "—", "—"], ["Module 3", "Brown", "244", "8.3117", "4.50e − 19", "34", "2.838 (1.879-4.181)", "1.38e − 06"], ["Module 4", "Green", "226", "0.9366", "4.90e − 04", "5", "0.383 (0.122-0.918)", "2.42e − 02"], ["Module 5", "Grey", "2545", "8.1319", "6.60e − 32", "146", "1.169 (0.940-1.448)", "1.55e − 01"], ["Module 6", "Pink", "86", "1.0653", "1.60e − 02", "5", "1.184 (0.371-2.911)", "6.17e − 01"], ["Module 7", "Red", "123", "10.5572", "8.80e − 09", "3", "0.497 (0.100-1.504)", "2.86e − 01"], ["Module 8", "Turquoise", "796", "8.3751", "9.20e − 14", "11", "0.291 (0.143-0.533)", "3.75e − 06"], ["Module 9", "Yellow", "230", "12.5199", "7.10e − 07", "43", "3.807 (2.617-5.440)", "2.63e − 11"]], "row_count": 11, "column_count": 8, "numeric_cells": 58, "header_rows": 2, "locator": "section[12]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:33833937:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8044b92d0bcf81b12c0349c9a731487452259876bb31d56aa2d69e9876f5a65d", "bytes": 975, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tab2", "version": null, "note": "The optimal signature for prognosis prediction.", "structure": {"pmcid": "PMC8012151", "section_index": 14, "section_title": "3.4. Development of a Prognostic Risk Score", "row_count": 7, "column_count": 11}, "table": {"label": "Table 2", "caption": "The optimal signature for prognosis prediction.", "rows": [["Symbol", "TCGA", "GSE123390", "Univariate Cox", "Multivariate Cox", "LASSO coef"], ["Log2FC", "FDR", "Log2FC", "FDR", "HR", "p value", "HR", "95% CI", "p value"], ["ASB2", "-0.53", "1.11e − 08", "-0.76", "1.13e − 04", "1.43", "1.35e − 02", "12.505", "2.639-59.260", "1.46e − 03", "0.3082"], ["GPR15", "-0.77", "6.48e − 21", "-1.17", "1.56e − 03", "0.898", "1.75e − 03", "0.688", "0.540-0.877", "2.56e − 03", "-0.0651"], ["PRPH", "-0.81", "1.11e − 08", "-0.58", "3.94e − 02", "1.21", "4.35e − 02", "2.048", "1.030-4.069", "4.09e − 02", "0.0701"], ["RNASE7", "-0.51", "1.43e − 04", "-0.65", "2.89e − 03", "0.926", "3.70e − 02", "0.686", "0.501-0.939", "1.86e − 02", "-0.1112"], ["TCL1A", "-0.98", "3.73e − 05", "-0.56", "3.44e − 02", "0.898", "4.90e − 03", "0.530", "0.372-0.754", "4.20e − 04", "-0.1428"]], "row_count": 7, "column_count": 11, "numeric_cells": 53, "header_rows": 2, "locator": "section[14]/table-wrap[1]#tab2"}}, {"id": "asset:table:pmid:33833937:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:16fa8db94cf05a9da828c665bad8409afe5a8849ef86ad0f0e3253deb9d46f68", "bytes": 1666, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#tab3", "version": null, "note": "Univariate and multivariate Cox regression of the clinical features and risk score.", "structure": {"pmcid": "PMC8012151", "section_index": 14, "section_title": "3.4. Development of a Prognostic Risk Score", "row_count": 14, "column_count": 8}, "table": {"label": "Table 3", "caption": "Univariate and multivariate Cox regression of the clinical features and risk score.", "rows": [["Clinical characteristics", "TCGA (N = 152)", "Univariate Cox", "Multivariate Cox"], ["HR", "95% CI", "p value", "HR", "95% CI", "p value"], ["Age (years, mean ± SD)", "64.16 ± 11.96", "1.100", "1.049-1.154", "3.40e − 05", "1.112", "1.056-1.170", "6.08e − 05"], ["Gender (female/male)", "72/80", "0.762", "0.321-1.807", "5.36e − 01", "—", "—", "—"], ["Pathologic M (M0/M1/-)", "119/21/12", "3.081", "1.158-8.196", "1.77e − 02", "8.911", "1.065-14.591", "4.36e − 02"], ["Pathologic N (N0/N1/N2/-)", "80/41/30/1", "1.920", "1.166-3.160", "7.48e − 03", "6.169", "1.956-19.457", "1.91e − 03"], ["Pathologic T (T1/T2/T3/T4)", "9/26/104/13", "2.147", "0.932-4.947", "7.63e − 02", "1.460", "0.563-3.789", "4.37e − 01"], ["Pathologic stage (I/II/III/IV/-)", "28/49/47/22/6", "1.976", "1.206-3.238", "5.36e − 03", "1.197", "1.041-1.946", "4.24e − 02"], ["Colon polyps present (yes/no/-)", "10/57/85", "1.006", "0.205-4.931", "9.95e − 01", "—", "—", "—"], ["History of colon polyps (yes/no/-)", "30/104/18", "1.125", "0.364-3.48", "8.38e − 01", "—", "—", "—"], ["Recurrence (yes/no/-)", "6/36/110", "2.828", "0.145-55.14", "4.80e − 01", "—", "—", "—"], ["Lymphatic invasion (yes/no/-)", "61/75/16", "0.885", "0.327-2.399", "8.10e − 01", "—", "—", "—"], ["Radiotherapy (yes/no/-)", "18/99/35", "0.345", "0.260-1.094", "7.52e − 02", "—", "—", "—"], ["Risk score model status (high/low)", "76/76", "5.001", "1.681-14.88", "9.73e − 04", "5.462", "1.371-21.754", "1.61e − 02"]], "row_count": 14, "column_count": 8, "numeric_cells": 69, "header_rows": 2, "locator": "section[14]/table-wrap[2]#tab3"}}], "gaps": ["asset:data:geo:GSE123390 not downloaded", "asset:data:geo:GSE123390 licence not read", "asset:data:geo:GSE56699 not downloaded", "asset:data:geo:GSE56699 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The associations between the expression of selected prognostic genes and the abundance of six tumor-infiltrating immune cells in TCGA-PRAD (B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells) were estimated from the Tumor Immune Estimation Resource (TIMER; https://cistrome.shinyapps.io/timer/) based on Spearman's correlation test."}}, {"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": 0.7, "band": "medium", "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": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "protein-protein interaction"}}, {"id": "method-5", "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": 0.7, "band": "medium", "quote": "ROC curve"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["spearman_rho"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: spearman."}, "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": ["GSE123390", "GSE56699"], "resolved_accessions": ["GSE123390", "GSE56699"], "statements": ["The datasets generated for this study can be found in GEO (http://www.ncbi.nlm.nih.gov/geo/; GSE123390, GSE56699) and TCGA (https://gdc-portal.nci.nih.gov/)."], "basis": "The paper names GSE123390, GSE56699 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": ["spearman_rho"], "assets": ["source:pmid:33833937", "data:geo:GSE123390", "asset:table:pmid:33833937:1", "asset:table:pmid:33833937:2", "asset:table:pmid:33833937:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE123390"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:17Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 40568, "completion_tokens": 3215, "cached_tokens": 520}}, "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:33833937", "type": "paper", "label": "pmid:33833937"}, {"id": "source:pmid:33833937", "type": "manuscript", "label": "PMID 33833937 full text"}, {"id": "data:geo:GSE123390", "type": "dataset", "label": "GEO GSE123390"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33833937", "type": "paper", "label": "pmid:33833937"}, {"id": "source:pmid:33833937", "type": "manuscript", "label": "PMID 33833937 full text"}, {"id": "data:geo:GSE123390", "type": "dataset", "label": "GEO GSE123390"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33833937", "type": "extraction", "used": ["source:pmid:33833937"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE123390", "type": "accession_resolution", "used": ["data:geo:GSE123390"], "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:33833937", "parent_hash": "sha256:65dc4432da7729db62016a0ebf9aa57ce9cd8aac402ad3104d755a119afd7984", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE123390 licence not read", "asset:data:geo:GSE123390 not downloaded", "asset:data:geo:GSE56699 licence not read", "asset:data:geo:GSE56699 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["nature panel for RC. METHODS: Sequencing (or microarray) data and clinicopathological details of pat"], "order_basis": "paper_text_order:499", "id": "assay:1"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["spearman_rho"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The associations between the expression of selected prognostic genes and the abundance of six tumor-infiltrating immune cells in TCGA-PRAD (B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells) were estimated from the Tumor Immune Estimation Resource (TIMER; https://cistrome.shinyapps.io/timer/) based on Spearman's correlation test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T04:13:53+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}}}