{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33574831", "kind": "science-record", "revision": 7, "content_hash": "sha256:be3eb917b3248b92c4d76d4254a7fbce035b223d45f6e11130830b4b91f8cc37", "created_at": "2026-11-01T15:41:25Z", "updated_at": "2026-11-01T22:03:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Weighted Gene Co-expression Network Analysis Identified That TLR2 and CD40 Are Related to Coronary Artery Disease.", "doi": "10.3389/fgene.2020.613744", "pmid": "33574831", "authors": ["Bin Qi", "Jian-Hong Chen", "Lin Tao", "Chuan-Meng Zhu", "Yong Wang", "Guo-Xiong Deng", "Liu Miao"], "journal": "Frontiers in genetics", "year": 2020, "abstract": "The current research attempted to identify possible hub genes and pathways of coronary artery disease (CAD) and to detect the possible mechanisms. Array data from GSE90074 were downloaded from the Gene Expression Omnibus (GEO) database. Integrated weighted gene co-expression network analysis (WGCNA) was performed to analyze the gene module and clinical characteristics. Gene Ontology annotation (GO), Disease Ontology (DO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by clusterProfiler and the DOSE package in R. A protein-protein interaction (PPI) network was established using Cytoscape software, and significant modules were analyzed using Molecular Complex Detection (MCODE) to identify hub genes. Then, further functional validation of hub genes in other microarrays and population samples was performed, and survival analysis was performed to investigate the prognosis. A total of 660 genes were located in three modules and associated with CAD. GO functions identified 484 biological processes, 39 cellular components, and 22 molecular functions with an adjusted P < 0.05. In total, 38 pathways were enriched in KEGG pathway analysis, and 147 DO items were identified with an adjusted P < 0.05 (false discovery rate, FDR set at < 0.05). There was a total of four modules with a score > 10 after PPI network analysis using the MCODE app, and two hub genes (TLR2 and CD14) were identified. Then, we validated the information from the GSE60993 dataset using the GSE59867 dataset and population samples, and we found that these two genes were associated with plaque vulnerability. These two genes varied at different time points after myocardial infarction, and both of them had the lowest prognosis of heart failure when they were expressed at low levels. We performed an integrated WGCNA and validated that TLR2 and CD14 were closely associated with the severity of coronary artery disease, plaque instability and the prognosis of heart failure after myocardial infarction.", "claims": [{"id": "claim-method", "statement": "We performed Pearson's correlation tests to assess the correlation between clinical characteristics and modules and to identify the meaningful modules.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33574831", "locator": "sections[5] \"Finding Module of Interest\" paragraph 2", "quote": "We performed Pearson's correlation tests to assess the correlation between clinical characteristics and modules and to identify the meaningful modules."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33574831", "locator": "sections[16] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33574831"], "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:GSE59867"], "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:GSE59867"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33574831", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2020.613744", "sha256": 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"asset:table:pmid:33574831:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:959579675901863625e4bb2f06dd611bf98fc24a839a196f8c2fa5bf794e964c", "bytes": 6885, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "GO analysis for genes (top 10 significantly enriched terms).", "structure": {"pmcid": "PMC7870792", "section_index": 12, "section_title": "Functional Annotation", "row_count": 31, "column_count": 5}, "table": {"label": "Table 1", "caption": "GO analysis for genes (top 10 significantly enriched terms).", "rows": [["Item", "ID", "Description", "P. adjust", "geneID"], ["BP", "GO:0042119", "Neutrophil activation", "2.94E-34", "ALOX5/ARHGAP9/BIN2/BST1/CCL5/CD14/CD53/CFP/CXCR1/CXCR2/FCER1G/FCGR3B/FCN1/FGL2/FGR/FPR1/FPR2/HBB/HSPA6/HVCN1/IL18RAP/ITGAM/ITGAX/ITGB2/LILRA2/LILRA3/LILRB2/LILRB3/MCEMP1/MGAM/MMP25/MNDA/OSCAR/PECAM1/PPBP/PRAM1/PTAFR/PTPN6/RAB37/S100A12/S100A8/S100A9/SIGLEC5/SIRPB1/SLC11A1/STK10/TLR2/TNFRSF1B/TYROBP/ADAM8/ADGRE3/C5AR1/CD300A/CLEC4D/CTSS/FCGR2A/HSP90AB1/ITGAL/KMT2E/LRMP/MMP9/PGLYRP1/PLEKHO2/PRKCD/RAB24/SELL/SPTAN1/SYK/TBC1D10C"], ["BP", "GO:0002283", "Neutrophil activation involved in immune response", "3.13E-32", "ALOX5/ARHGAP9/BIN2/BST1/CD14/CD53/CFP/CXCR1/CXCR2/FCER1G/FCGR3B/FCN1/FGL2/FGR/FPR1/FPR2/HBB/HSPA6/HVCN1/ITGAM/ITGAX/ITGB2/LILRA2/LILRA3/LILRB2/LILRB3/MCEMP1/MGAM/MMP25/MNDA/OSCAR/PECAM1/PPBP/PRAM1/PTAFR/PTPN6/RAB37/S100A12/S100A8/S100A9/SIGLEC5/SIRPB1/SLC11A1/STK10/TLR2/TNFRSF1B/TYROBP/ADAM8/ADGRE3/C5AR1/CD300A/CLEC4D/CTSS/FCGR2A/HSP90AB1/ITGAL/LRMP/MMP9/PGLYRP1/PLEKHO2/PRKCD/RAB24/SELL/SPTAN1/SYK/TBC1D10C"], ["BP", "GO:0002446", "Neutrophil mediated immunity", "8.39E-32", "ALOX5/ARHGAP9/BIN2/BST1/CD14/CD53/CFP/CXCR1/CXCR2/FCER1G/FCGR3B/FCN1/FGL2/FGR/FPR1/FPR2/HBB/HSPA6/HVCN1/ITGAM/ITGAX/ITGB2/LILRA3/LILRB2/LILRB3/MCEMP1/MGAM/MMP25/MNDA/OSCAR/PECAM1/PPBP/PRAM1/PTAFR/PTPN6/RAB37/S100A12/S100A8/S100A9/SIGLEC5/SIRPB1/SLC11A1/STK10/TLR2/TNFRSF1B/TYROBP/ADAM8/ADGRE3/C5AR1/CD300A/CLEC4D/CTSS/FCGR2A/HSP90AB1/ITGAL/KMT2E/LRMP/MMP9/PGLYRP1/PLEKHO2/PRKCD/RAB24/SELL/SPTAN1/SYK/TBC1D10C"], ["BP", "GO:0043312", "Neutrophil degranulation", "9.61E-32", "ALOX5/ARHGAP9/BIN2/BST1/CD14/CD53/CFP/CXCR1/CXCR2/FCER1G/FCGR3B/FCN1/FGL2/FGR/FPR1/FPR2/HBB/HSPA6/HVCN1/ITGAM/ITGAX/ITGB2/LILRA3/LILRB2/LILRB3/MCEMP1/MGAM/MMP25/MNDA/OSCAR/PECAM1/PPBP/PRAM1/PTAFR/PTPN6/RAB37/S100A12/S100A8/S100A9/SIGLEC5/SIRPB1/SLC11A1/STK10/TLR2/TNFRSF1B/TYROBP/ADAM8/ADGRE3/C5AR1/CD300A/CLEC4D/CTSS/FCGR2A/HSP90AB1/ITGAL/LRMP/MMP9/PGLYRP1/PLEKHO2/PRKCD/RAB24/SELL/SPTAN1/SYK/TBC1D10C"], ["BP", "GO:0050900", "Leukocyte migration", "9.49E-20", "BST1/CCL4/CCL5/CCR7/CORO1A/CSF3R/CXCR1/CXCR2/DOK2/DYSF/FCER1G/FFAR2/FPR2/HCK/IL16/ITGAM/ITGAX/ITGB2/JAML/PECAM1/PF4/PPBP/PTAFR/PTPN6/S100A12/S100A8/S100A9/SELPLG/SIRPG/SLC7A7/STK10/TBX21/TNFSF14/TREM1/ADAM8/C5AR1/CD2/CD244/CD300A/CXCR3/DAPK2/GPSM3/IL17RA/IL1B/IL6R/ITGAL/LYN/MMP9/SELL/SYK/VAV1"], ["BP", "GO:0030595", "Leukocyte chemotaxis", "7.16E-16", "BST1/CCL4/CCL5/CCR7/CORO1A/CSF3R/CXCR1/CXCR2/DYSF/FCER1G/FFAR2/FPR2/IL16/ITGB2/JAML/PF4/PPBP/S100A12/S100A8/S100A9/TNFSF14/ADAM8/C5AR1/CXCR3/DAPK2/GPSM3/IL17RA/IL1B/IL6R/LYN/SYK/VAV1"], ["BP", "GO:0097530", "Granulocyte migration", "1.31E-14", "BST1/CCL4/CCL5/CCR7/CSF3R/CXCR1/CXCR2/DYSF/FCER1G/ITGB2/JAML/PECAM1/PF4/PPBP/S100A12/S100A8/S100A9/ADAM8/C5AR1/CD300A/DAPK2/IL17RA/IL1B/SYK/VAV1"], ["BP", "GO:0060326", "Cell chemotaxis", "1.45E-14", "BIN2/BST1/CCL4/CCL5/CCR7/CORO1A/CSF3R/CXCR1/CXCR2/DYSF/FCER1G/FFAR2/FPR2/IL16/ITGB2/JAML/PF4/PPBP/S100A12/S100A8/S100A9/TNFSF14/ADAM8/ARRB2/C5AR1/CXCR3/DAPK2/GPSM3/IL17RA/IL1B/IL6R/LYN/PRKCD/SYK/VAV1"], ["BP", "GO:1990266", "Neutrophil migration", "2.12E-14", "BST1/CCL4/CCL5/CCR7/CSF3R/CXCR1/CXCR2/DYSF/FCER1G/ITGB2/JAML/PECAM1/PF4/PPBP/S100A12/S100A8/S100A9/ADAM8/C5AR1/DAPK2/IL1B/SYK/VAV1"], ["BP", "GO:0006909", "Phagocytosis", "1.90E-13", "ARHGAP25/BIN2/CD14/CD300LF/CORO1A/DYSF/FCER1G/FCGR3A/FCN1/FGR/HCK/ITGAM/ITGB2/MARCO/NCF2/NCF4/PECAM1/SIRPB1/SIRPG/SLC11A1/TLR2/TMEM175/WAS/CD300A/CEACAM4/FCGR2A/HSP90AB1/IL1B/ITGAL/LYN/NCK1/PLCG2/PRKCD/SYK/VAV1/WIPF1"], ["CC", "GO:0030667", "Secretory granule membrane", "5.17E-19", "BST1/CD14/CD53/CXCR1/CXCR2/FCER1G/FCGR3B/FPR1/FPR2/HVCN1/ITGAM/ITGAX/ITGB2/LILRA3/LILRB2/LILRB3/MCEMP1/MGAM/MMP25/PECAM1/PTAFR/RAB37/SIGLEC5/SIRPB1/SLC11A1/STK10/TLR2/TNFRSF1B/TYROBP/ADAM8/ADGRE3/C5AR1/CD300A/CLEC4D/FCGR2A/ITGAL/LRMP/RAB24/SELL/TBC1D10C"], ["CC", "GO:0070820", "Tertiary granule", "7.56E-16", "CD53/CFP/FCER1G/FPR1/FPR2/HBB/ITGAM/ITGAX/ITGB2/LILRA3/LILRB2/MCEMP1/MGAM/OSCAR/PPBP/PTAFR/PTPN6/SIGLEC5/SLC11A1/ADAM8/ADGRE3/CD300A/CLEC4D/CTSS/MMP9/PGLYRP1/SPTAN1/TBC1D10C"], ["CC", "GO:0101002", "Ficolin-1-rich granule", "1.07E-12", "ALOX5/BIN2/FCER1G/FCN1/FGL2/FPR1/FPR2/HBB/HSPA6/ITGAX/ITGB2/LILRA3/LILRB2/MGAM/MNDA/SIGLEC5/SLC11A1/ADAM8/ADGRE3/CD300A/CLEC4D/CTSS/HSP90AB1/MMP9/PLEKHO2/TBC1D10C"], ["CC", "GO:0101003", "Ficolin-1-rich granule membrane", "9.10E-11", "FCER1G/FPR1/FPR2/ITGAX/ITGB2/LILRA3/LILRB2/MGAM/SIGLEC5/SLC11A1/ADAM8/ADGRE3/CD300A/CLEC4D/TBC1D10C"], ["CC", "GO:0070821", "Tertiary granule membrane", "9.10E-11", "CD53/FCER1G/FPR2/ITGAM/ITGAX/ITGB2/LILRA3/LILRB2/MCEMP1/MGAM/PTAFR/SIGLEC5/SLC11A1/ADAM8/CD300A/CLEC4D"], ["CC", "GO:0030139", "Endocytic vesicle", "4.36E-09", "CORO1A/DYSF/FCGR1B/GNLY/HBB/HLA-DRA/HLA-DRB4/HLA-DRB5/MARCO/NCF1/NCF2/NCF4/SLC11A1/TLR2/WAS/ADAM8/ARRB2/CD163/DVL2/HLA-DRB1/HLA-DRB3/LPAR2/PGLYRP1/RAB11FIP1/RAB24/SYK/TLR1"], ["CC", "GO:0042581", "Specific granule", "5.40E-09", "BST1/CD53/CFP/FPR2/HVCN1/ITGAM/ITGB2/LILRA3/MCEMP1/MMP25/OSCAR/PTPN6/RAB37/STK10/TNFRSF1B/ADAM8/CLEC4D/ITGAL/PGLYRP1/SPTAN1"], ["CC", "GO:0035579", "Specific granule membrane", "2.13E-08", "BST1/CD53/FPR2/HVCN1/ITGAM/ITGB2/LILRA3/MCEMP1/MMP25/RAB37/STK10/TNFRSF1B/ADAM8/CLEC4D/ITGAL"], ["CC", "GO:0060205", "Cytoplasmic vesicle lumen", "1.28E-06", "ALOX5/ARHGAP9/BIN2/CFP/DEFA3/F13A1/FCN1/FGR/GNLY/HBB/HSPA6/MNDA/OSCAR/PF4/PPBP/PTPN6/S100A12/S100A8/S100A9/SRGN/GHRL/HSP90AB1/PGLYRP1/PRKCD/SPTAN1"], ["CC", "GO:0031983", "Vesicle lumen", "1.28E-06", "ALOX5/ARHGAP9/BIN2/CFP/DEFA3/F13A1/FCN1/FGR/GNLY/HBB/HSPA6/MNDA/OSCAR/PF4/PPBP/PTPN6/S100A12/S100A8/S100A9/SRGN/GHRL/HSP90AB1/PGLYRP1/PRKCD/SPTAN1"], ["MF", "GO:0008329", "Signaling pattern recognition receptor activity", "1.07E-06", "CD14/FCN1/MARCO/PTAFR/TLR2/TLR8/PGLYRP1/TLR4"], ["MF", "GO:0038187", "Pattern recognition receptor activity", "1.07E-06", "CD14/FCN1/MARCO/PTAFR/TLR2/TLR8/PGLYRP1/TLR4"], ["MF", "GO:0004896", "Cytokine receptor activity", "9.91E-05", "CCR7/CSF3R/CXCR1/CXCR2/IL18RAP/IL1R2/IL2RB/CSF2RA/CXCR3/IL10RA/IL17RA/IL6R"], ["MF", "GO:0019864", "IgG binding", "0.00020022", "FCER1G/FCGR1B/FCGR3A/FCGR3B/FCGR2A"], ["MF", "GO:0035325", "Toll-like receptor binding", "0.00020022", "S100A8/S100A9/TLR2/SYK/TLR1"], ["MF", "GO:0019865", "Immunoglobulin binding", "0.00061902", "FCER1G/FCGR1B/FCGR3A/FCGR3B/LILRA2/FCGR2A"], ["MF", "GO:0019955", "Cytokine binding", "0.00110874", "CCR7/CSF1R/CSF3R/CXCR1/CXCR2/IL1R2/IL2RB/TNFRSF1B/CSF2RA/CXCR3/IL10RA/IL6R"], ["MF", "GO:0050786", "RAGE receptor binding", "0.00380145", "FPR1/S100A12/S100A8/S100A9"], ["MF", "GO:0008528", "G protein-coupled peptide receptor activity", "0.00380145", "CCR7/CXCR1/CXCR2/FPR1/FPR2/GALR3/KISS1R/OGFR/UTS2R/CXCR3/INPP5K/SIGMAR1"], ["MF", "GO:0001653", "Peptide receptor activity", "0.00507011", "CCR7/CXCR1/CXCR2/FPR1/FPR2/GALR3/KISS1R/OGFR/UTS2R/CXCR3/INPP5K/SIGMAR1"]], "row_count": 31, "column_count": 5, "numeric_cells": 88, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33574831:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c6d92fb3df3c1d02f2d1d075dd811853b7590bf7f403a834872a4439905aa511", "bytes": 5885, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#T2", "version": null, "note": "KEGG and DO analysis for genes (top 15 significantly enriched terms).", "structure": {"pmcid": "PMC7870792", "section_index": 12, "section_title": "Functional Annotation", "row_count": 31, "column_count": 5}, "table": {"label": "Table 2", "caption": "KEGG and DO analysis for genes (top 15 significantly enriched terms).", "rows": [["Item", "ID", "Description", "P. adjust", "geneID"], ["KEGG", "hsa05150", "Staphylococcus aureus infection", "1.72E-10", "DEFA3/FCGR3A/FCGR3B/FPR1/FPR2/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGAM/ITGB2/PTAFR/SELPLG/C5AR1/FCGR2A/HLA-DRB1/HLA-DRB3/ITGAL"], ["KEGG", "hsa04380", "Osteoclast differentiation", "1.72E-10", "CSF1R/FCGR3A/FCGR3B/LCP2/LILRA2/LILRA3/LILRA4/LILRB2/LILRB3/NCF1/NCF2/NCF4/OSCAR/SIRPB1/SIRPG/TYROBP/FCGR2A/IL1B/LILRA5/PLCG2/SPI1/SYK"], ["KEGG", "hsa05140", "Leishmaniasis", "3.34E-10", "FCGR3A/FCGR3B/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGAM/ITGB2/NCF1/NCF2/NCF4/PTPN6/TLR2/FCGR2A/HLA-DRB1/HLA-DRB3/IL1B/TLR4"], ["KEGG", "hsa05152", "Tuberculosis", "1.98E-09", "BCL2/CD14/CLEC4E/CORO1A/FCER1G/FCGR3A/FCGR3B/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGAM/ITGAX/ITGB2/TLR2/CTSS/FCGR2A/HLA-DRB1/HLA-DRB3/IL10RA/IL1B/LSP1/SYK/TLR1/TLR4"], ["KEGG", "hsa04060", "Cytokine-cytokine receptor interaction", "5.06E-07", "BMP8B/CCL4/CCL5/CCR7/CSF1R/CSF3R/CXCR1/CXCR2/IL16/IL18RAP/IL1R2/IL2RB/LTB/OSM/PF4/PPBP/TNFRSF10C/TNFRSF1B/TNFSF14/CD27/CSF2RA/CXCR3/IL10RA/IL17RA/IL1B/IL6R/TNFSF10"], ["KEGG", "hsa04145", "Phagosome", "5.32E-07", "CD14/CORO1A/FCGR3A/FCGR3B/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGAM/ITGB2/MARCO/NCF1/NCF2/NCF4/TLR2/CTSS/FCGR2A/HLA-DRB1/HLA-DRB3/TLR4"], ["KEGG", "hsa04640", "Hematopoietic cell lineage", "8.96E-07", "CD14/CD37/CSF1R/CSF3R/HLA-DRA/HLA-DRB4/HLA-DRB5/IL1R2/ITGAM/CD2/CSF2RA/HLA-DRB1/HLA-DRB3/IL1B/IL6R"], ["KEGG", "hsa04650", "Natural killer cell mediated cytotoxicity", "7.99E-06", "FCER1G/FCGR3A/FCGR3B/GZMB/HCST/ITGB2/LCP2/PRF1/PTPN6/TYROBP/CD244/ITGAL/PLCG2/SYK/TNFSF10/VAV1"], ["KEGG", "hsa04062", "Chemokine signaling pathway", "5.75E-05", "CCL4/CCL5/CCR7/CXCR1/CXCR2/FGR/HCK/NCF1/PF4/PPBP/RASGRP2/WAS/ARRB2/CXCR3/LYN/PLCB2/PRKCD/VAV1"], ["KEGG", "hsa05323", "Rheumatoid arthritis", "9.05E-05", "CCL5/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGB2/LTB/TLR2/HLA-DRB1/HLA-DRB3/IL1B/ITGAL/TLR4"], ["KEGG", "hsa05321", "Inflammatory bowel disease (IBD)", "0.00013055", "HLA-DRA/HLA-DRB4/HLA-DRB5/IL18RAP/TBX21/TLR2/HLA-DRB1/HLA-DRB3/IL1B/TLR4"], ["KEGG", "hsa05332", "Graft-vs.-host disease", "0.00016688", "GZMB/HLA-DRA/HLA-DRB4/HLA-DRB5/PRF1/HLA-DRB1/HLA-DRB3/IL1B"], ["KEGG", "hsa04940", "Type I diabetes mellitus", "0.0002234", "GZMB/HLA-DRA/HLA-DRB4/HLA-DRB5/PRF1/HLA-DRB1/HLA-DRB3/IL1B"], ["KEGG", "hsa04514", "Cell adhesion molecules (CAMs)", "0.00037834", "CADM3/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGAM/ITGB2/PECAM1/SELPLG/CD2/HLA-DRB1/HLA-DRB3/ITGAL/NTNG2/SELL"], ["KEGG", "hsa05330", "Allograft rejection", "0.00072889", "GZMB/HLA-DRA/HLA-DRB4/HLA-DRB5/PRF1/HLA-DRB1/HLA-DRB3"], ["DO", "DOID:104", "Bacterial infectious disease", "7.86E-12", "ALOX5/BCL2/CCL4/CCL5/CCR7/CD14/CXCR2/DEFA3/FPR2/GZMA/HLA-DRB4/ITGAM/ITGAX/ITGB2/NLRP3/OSM/PECAM1/PRF1/PTAFR/SLC11A1/TLR2/TNFRSF1B/TREM1/C5AR1/CD27/FCGR2A/GHRL/HLA-DRB1/IL1B/ITGAL/MCL1/MMP9/SELL/TLR1/TLR4/TP53"], ["DO", "DOID:0050338", "Primary bacterial infectious disease", "5.63E-10", "ALOX5/BCL2/CCL4/CCL5/CCR7/CD14/CXCR2/DEFA3/GZMA/HLA-DRB4/ITGAX/NLRP3/PECAM1/PRF1/SLC11A1/TLR2/TNFRSF1B/TREM1/C5AR1/CD27/FCGR2A/GHRL/HLA-DRB1/IL1B/ITGAL/MCL1/MMP9/SELL/TLR1/TLR4/TP53"], ["DO", "DOID:399", "Tuberculosis", "4.17E-09", "ALOX5/BCL2/CCL4/CCL5/CD14/CXCR2/DEFA3/GZMA/ITGAX/NLRP3/PECAM1/PRF1/SLC11A1/TLR2/TNFRSF1B/CD27/HLA-DRB1/IL1B/ITGAL/MCL1/MMP9/TLR1/TLR4/TP53"], ["DO", "DOID:74", "Hematopoietic system disease", "1.49E-07", "BCAM/BCL2/CCL5/CSF3R/CXCR1/F13A1/FCGR3A/FCGR3B/HBB/HLA-DRA/ITGAM/ITGB2/PF4/PRF1/PTPN6/RASGRP4/SLC11A1/TBX21/TLR2/TLR8/TNFRSF1B/WAS/ZFPM1/CSF2RA/CXCR3/DCK/ETV6/FCGR2A/HLA-DRB1/HLA-DRB3/IL1B/MMP9/SELL/SPTAN1/TINF2/TLR4/TNFSF10/TP53/VAV1/WIPF1"], ["DO", "DOID:75", "Lymphatic system disease", "5.22E-07", "CCR7/FOXC2/GZMB/ITGAX/PECAM1/PRF1/S100A12/S100A8/S100A9/SLC11A1/CD163/HLA-DRB1/IL1B/ITGAL/MMP9/TLR4/TP53"], ["DO", "DOID:1936", "Atherosclerosis", "5.22E-07", "ALOX5/ALOX5AP/APOBR/CCL5/CD14/CXCR2/FCGR3A/FPR1/MNDA/NLRP3/PECAM1/PF4/S100A12/S100A8/S100A9/SOX18/TLR2/UTS2R/ADAM8/ADRB2/CD163/CTSS/CXCR3/FCGR2A/GHRL/IL1B/KLF2/MMP9/PGLYRP1/TLR4/TNFSF10/TP53"], ["DO", "DOID:2348", "Arteriosclerotic cardiovascular disease", "5.22E-07", "ALOX5/ALOX5AP/APOBR/CCL5/CD14/CXCR2/FCGR3A/FPR1/MNDA/NLRP3/PECAM1/PF4/S100A12/S100A8/S100A9/SOX18/TLR2/UTS2R/ADAM8/ADRB2/CD163/CTSS/CXCR3/FCGR2A/GHRL/IL1B/KLF2/MMP9/PGLYRP1/TLR4/TNFSF10/TP53"], ["DO", "DOID:2349", "Arteriosclerosis", "9.86E-07", "ALOX5/ALOX5AP/APOBR/CCL5/CD14/CXCR2/FCGR3A/FPR1/MNDA/NLRP3/PECAM1/PF4/S100A12/S100A8/S100A9/SOX18/TLR2/UTS2R/ADAM8/ADRB2/CD163/CTSS/CXCR3/FCGR2A/GHRL/IL1B/KLF2/MMP9/PGLYRP1/TLR4/TNFSF10/TP53"], ["DO", "DOID:850", "Lung disease", "3.13E-06", "BCL2/CCL5/CD14/CSTA/CXCR1/FCGR3B/FGL2/GZMA/HBB/HCK/IL16/IL18RAP/ITGAM/ITGB2/NCF1/NCF2/S100A9/SELPLG/SLC11A1/TBX21/TLR2/TREM1/ADAM8/ADRB2/C5AR1/CSF2RA/CTSS/CXCR3/FCGR2A/HLA-DRB1/IL10RA/IL1B/ITGAL/MMP9/NLRP1/PRKCD/TLR4/TP53"], ["DO", "DOID:3083", "Chronic obstructive pulmonary disease", "6.69E-06", "BCL2/CCL5/CD14/CSTA/FGL2/GZMA/HBB/HCK/IL16/ITGAM/ITGB2/SLC11A1/TLR2/TREM1/ADRB2/C5AR1/CTSS/CXCR3/IL10RA/IL1B/ITGAL/MMP9/TLR4"], ["DO", "DOID:3388", "Periodontal disease", "6.69E-06", "CCL5/CD14/CXCR2/DEFA3/FCGR3A/FCGR3B/FPR1/IL16/IL1R2/OSM/PECAM1/S100A8/TLR2/FCGR2A/IL1B/MMP9/TLR4/TNFSF10"], ["DO", "DOID:1247", "Blood coagulation disease", "1.55E-05", "CCL5/F13A1/FCGR3B/HLA-DRA/ITGAM/ITGB2/PF4/PRF1/TLR2/WAS/ZFPM1/FCGR2A/HLA-DRB1/HLA-DRB3/IL1B/MMP9/SELL/TLR4/TNFSF10/WIPF1"], ["DO", "DOID:2320", "Obstructive lung disease", "1.56E-05", "BCL2/CCL5/CD14/CSTA/FGL2/GZMA/HBB/HCK/IL16/IL18RAP/ITGAM/ITGB2/SELPLG/SLC11A1/TBX21/TLR2/TREM1/ADAM8/ADRB2/C5AR1/CTSS/CXCR3/IL10RA/IL1B/ITGAL/MMP9/TLR4"], ["DO", "DOID:824", "Periodontitis", "1.81E-05", "CCL5/CD14/CXCR2/DEFA3/FCGR3A/FCGR3B/FPR1/IL16/IL1R2/OSM/S100A8/TLR2/FCGR2A/IL1B/MMP9/TLR4"], ["DO", "DOID:1555", "Urticaria", "1.81E-05", "ALOX5/ALOX5AP/FPR2/NLRP3/PF4/PPBP/ADRB2/HLA-DRB1/MMP9/SYK"]], "row_count": 31, "column_count": 5, "numeric_cells": 80, "header_rows": 1, "locator": "section[12]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:33574831:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cb150017d2b2c27de6c3f1c7a6336dcb7a8851dad182f08f52629f6426ab962e", "bytes": 2818, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T3", "version": null, "note": "Comparison of demographic, lifestyle characteristics and serum lipid levels among different groups.", "structure": {"pmcid": "PMC7870792", "section_index": 14, "section_title": "Hub Gene Validation", "row_count": 27, "column_count": 6}, "table": {"label": "Table 3", "caption": "Comparison of demographic, lifestyle characteristics and serum lipid levels among different groups.", "rows": [["Parameter", "Control", "CAD", "UA", "NSTEMI", "STEMI"], ["Number", "212", "220", "204", "191", "202"], ["Male/female", "44/174", "39/181", "44/160", "34/157", "48/154"], ["Age (years)1", "55.27 ± 8.24", "54.29 ± 8.43", "55.57 ± 7.92", "56.11 ± 8.91", "56.02 ± 7.78"], ["Height (cm)", "166.13 ± 6.74", "167.63 ± 7.10", "167.49 ± 7.26", "166.52 ± 6.88", "167.09 ± 8.74"], ["Weight (kg)", "52.46 ± 6.88", "54.72 ± 9.93", "58.61 ± 8.21a", "57.89 ± 9.13a", "58.12 ± 9.32a"], ["Body mass index (kg/m2)", "29.21 ± 5.23", "30.24 ± 6.57a", "30.87 ± 7.32a", "30.89 ± 7.14a", "30.96 ± 6.19a"], ["Waist circumference (cm)", "74.29 ± 6.71", "73.54 ± 9.28", "74.63 ± 7.65", "75.28 ± 7.22", "76.25 ± 6.31"], ["Smoking status [n (%)]", "56 (26.0)", "79 (35.7)a", "93 (45.8)a", "92 (48.4)a", "99 (48.9)a"], ["Alcohol consumption [n (%)]", "51 (24.2)", "57 (25.7)", "48 (23.3)", "56 (29.2)a", "58 (28.8)a"], ["SBP (mmHg)", "123.15 ± 16.22", "129.32 ± 22.16a", "148.01 ± 23.77c", "141.45 ± 23.14b", "106.45 ± 10.16c"], ["DBP (mmHg)", "81.54 ± 11.23", "81.34 ± 12.01", "89.04 ± 15.21a", "83.23 ± 8.20", "62.51 ± 18.74c"], ["PP (mmHg)", "49.64 ± 14.13", "51.42 ± 13.59", "51.66 ± 15.24", "50.84 ± 15.22", "50.22 ± 14.21"], ["Glucose (mmol/L)", "5.93 ± 1.81", "6.22 ± 2.23", "7.74 ± 2.21b", "8.55 ± 2.31c", "8.44 ± 2.69c"], ["TC (mmol/L)", "4.95 ± 1.32", "5.26 ± 1.28a", "5.69 ± 1.02a", "5.99 ± 1.24a", "5.84 ± 1.46a"], ["TG (mmol/L)2", "1.48 (0.51)", "1.52 (1.21)", "1.53 (1.22)", "1.46 (1.41)", "1.46 (1.38)"], ["HDL-C (mmol/L)", "1.51 ± 0.43", "1.29 ± 0.34a", "1.31 ± 0.31a", "1.40 ± 0.31a", "1.43 ± 0.35"], ["LDL-C (mmol/L)", "2.87 ± 0.83", "3.24 ± 0.75a", "3.99 ± 0.81a", "3.89 ± 0.98a", "3.96 ± 0.81a"], ["ApoA1 (g/L)", "1.23 ± 0.24", "1.16 ± 0.22", "1.18 ± 0.26", "1.14 ± 0.26", "1.15 ± 0.28"], ["ApoB (g/L)", "0.84 ± 0.19", "0.82 ± 0.32", "0.81 ± 0.31", "0.94 ± 0.31", "0.88 ± 0.28"], ["ApoA1/ApoB", "1.68 ± 0.49", "1.67 ± 0.56", "1.65 ± 0.52", "1.66 ± 0.63", "1.68 ± 0.55"], ["Heart rate (beats/minutes)", "72.43 ± 10.22", "72.36 ± 10.34", "77.21 ± 10.54a", "76.45 ± 9.32a", "79.78 ± 10.25a"], ["Creatinine, (μmol/L)", "72.55 ± 12.21", "71.38 ± 11.44", "74.43 ± 11.42", "77.55 ± 10.21", "76.68 ± 12.84"], ["Uric acid, (μmol/L)", "280.96 ± 74.23", "283.89 ± 72.32", "278.88 ± 84.32", "286.91 ± 82.32", "284.76 ± 76.38"], ["Troponin T, (μg/L)", "0.01 ± 0.02", "0.02 ± 0.02", "0.02 ± 0.01", "2.74 ± 3.93c", "2.86 ± 6.28c"], ["CK, (U/L)", "87.82 ± 43.21", "88.84 ± 47.31", "92.81 ± 51.32", "1,211.93 ± 688.32c", "1,224.89 ± 793.18c"], ["CKMB, (U/L)", "11.41 ± 3.53", "12.11 ± 2.88", "11.22 ± 3.42", "131.87 ± 63.45c", "138.74 ± 57.16c"]], "row_count": 27, "column_count": 6, "numeric_cells": 132, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:GSE59867 not downloaded", "asset:data:geo:GSE59867 licence not read", "asset:data:geo:GSE60993 not downloaded", "asset:data:geo:GSE60993 licence not read", "asset:data:geo:GSE90074 not downloaded", "asset:data:geo:GSE90074 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We performed Pearson's correlation tests to assess the correlation between clinical characteristics and modules and to identify the meaningful modules."}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "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": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "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": ["GSE90074", "GSE60993", "GSE59867"], "resolved_accessions": ["GSE90074", "GSE60993", "GSE59867"], "statements": ["The original contributions presented in the study are included in the Supplementary Material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE90074, GSE60993, GSE59867 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": ["pearson_r"], "assets": ["source:pmid:33574831", "data:geo:GSE59867", "asset:table:pmid:33574831:1", "asset:table:pmid:33574831:2", "asset:table:pmid:33574831:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE59867"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22201, "completion_tokens": 1501, "cached_tokens": 792}}, "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:33574831", "type": "paper", "label": "pmid:33574831"}, {"id": "source:pmid:33574831", "type": "manuscript", "label": "PMID 33574831 full text"}, {"id": "data:geo:GSE59867", "type": "dataset", "label": "GEO GSE59867"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33574831", "type": "paper", "label": "pmid:33574831"}, {"id": "source:pmid:33574831", "type": "manuscript", "label": "PMID 33574831 full text"}, {"id": "data:geo:GSE59867", "type": "dataset", "label": "GEO GSE59867"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33574831", "type": "extraction", "used": ["source:pmid:33574831"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE59867", "type": "accession_resolution", "used": ["data:geo:GSE59867"], "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:33574831", "parent_hash": "sha256:2470cf5ce4fe88ba6ae3c8e2444902adabed0a661eafd7a74dcae722167ed42a", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE59867 licence not read", "asset:data:geo:GSE59867 not downloaded", "asset:data:geo:GSE60993 licence not read", "asset:data:geo:GSE60993 not downloaded", "asset:data:geo:GSE90074 licence not read", "asset:data:geo:GSE90074 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We performed Pearson's correlation tests to assess the correlation between clinical characteristics and modules and to identify the meaningful modules."], "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":"2026-11-04T03:38:12+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}}}