{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30365077", "kind": "science-record", "revision": 6, "content_hash": "sha256:3401664c5213d16b54f01aa1419d59ae3fa58ad63e48df02e350d0aab3aca7d2", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T21:21:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "LASSO‑based Cox‑PH model identifies an 11‑lncRNA signature for prognosis prediction in gastric cancer.", "doi": "10.3892/mmr.2018.9567", "pmid": "30365077", "authors": ["Yonghong Zhang", "Huamin Li", "Wenyong Zhang", "Ya Che", "Weibing Bai", "Guanglin Huang"], "journal": "Molecular medicine reports", "year": 2018, "abstract": "The present study aimed to identify a long non‑coding (lnc) RNAs‑based signature for prognosis assessment in gastric cancer (GC) patients. By integrating gene expression data of GC and normal samples from the National Center for Biotechnology Information Gene Expression Omnibus, the EBI ArrayExpress and The Cancer Genome Atlas (TCGA) repositories, the common RNAs in Genomic Spatial Event (GSE) 65801, GSE29998, E‑MTAB‑1338, and TCGA set were screened and used to construct a weighted correlation network analysis (WGCNA) network for mining GC‑related modules. Consensus differentially expressed RNAs (DERs) between GC and normal samples in the four datasets were screened using the MetaDE method. From the overlapped lncRNAs shared by preserved WGCNA modules and the consensus DERs, an lncRNAs signature was obtained using L1‑penalized (lasso) Cox‑proportional hazard (PH) model. LncRNA‑mRNA networks were constructed for these signature lncRNAs, followed by functional annotation. A total of 14,824 common mRNAs and 2,869 common lncRNAs were identified in the 4 sets and 5 GC‑associated WGCNA modules were preserved across all sets. MetaDE method identified 1,121 consensus DERs. A total of 50 lncRNAs were shared by preserved WGCNA modules and the consensus DERs. Subsequently, an 11‑lncRNA signature was identified by LASSO‑based Cox‑PH model. The lncRNAs signature‑based risk score could divide patients into 2 risk groups with significantly different overall survival and recurrence‑free survival times. The predictive capability of this signature was verified in an independent set. These signature lncRNAs were implicated in several biological processes and pathways associated with the immune response, the inflammatory response and cell cycle control. The present study identified an 11‑lncRNA signature that could predict the survival rate for GC.", "claims": [{"id": "claim-method", "statement": "Consensus differentially expressed RNAs (DERs) between GC specimens and normal control specimens across the 4 datasets (GSE6580, GSE29998, E-MTAB-1338 and TCGA) were identified with metaDE package (22,23) (https://cran.r-project.org/web/packages/MetaDE/) in R language version 3.4.1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30365077", "locator": "sections[6] \"Identification of consensus differentially expressed RNAs\" paragraph 2", "quote": "Consensus differentially expressed RNAs (DERs) between GC specimens and normal control specimens across the 4 datasets (GSE6580, GSE29998, E-MTAB-1338 and TCGA) were identified with metaDE package (22,23) (https://cran.r-project.org/web/packages/MetaDE/) in R language version 3.4.1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the present study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30365077", "locator": "sections[19] \"Availability of data and materials\" paragraph 2", "quote": "The datasets analyzed during the present study are available from the corresponding author on reasonable request."}], "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:30365077"], "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:E-MTAB-1338"], "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:E-MTAB-1338"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30365077", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/mmr.2018.9567", "sha256": 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datasets.", "structure": {"pmcid": "PMC6236314", "section_index": 11, "section_title": "RNA expression data", "row_count": 6, "column_count": 4}, "table": {"label": "Table III.", "caption": "Numbers of mRNAs and lncRNAs in the datasets.", "rows": [["Accession ID", "Total count", "mRNA", "lncRNA"], ["GSE65801", "23,081", "17,056", "6,025"], ["E-MTAB-1338", "18,730", "15,376", "3,354"], ["GSE29998", "20,586", "15,376", "5,210"], ["TCGA", "24,840", "17,579", "7,261"], ["Common", "17,693", "14,824", "2,869"]], "row_count": 6, "column_count": 4, "numeric_cells": 18, "header_rows": 1, "locator": "section[11]/table-wrap[1]#tIII-mmr-18-06-5579"}}, {"id": "asset:table:pmid:30365077:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:73ac2c4e9cd3aae3ecefeb2702ffc52f526068f48c8ef7c822096159568cb0c7", "bytes": 1039, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tIV-mmr-18-06-5579", "version": null, "note": "Characteristics of WGCNA network modules.", "structure": {"pmcid": "PMC6236314", "section_index": 12, "section_title": "WGCNA network and modules", "row_count": 12, "column_count": 8}, "table": {"label": "Table IV.", "caption": "Characteristics of WGCNA network modules.", "rows": [["TCGA", "GSE29998", "GSE65801", "E-MTAB-133", "Color", "Module size", "Module preservation (Z-score)", "Module characterization"], ["D1M1", "D2M1", "D3M1", "D4M1", "Black", "59", "28.06", "Digestion"], ["D1M2", "D2M2", "D3M2", "D4M2", "Blue", "417", "31.59", "Immune response"], ["D1M3", "D2M3", "D3M3", "D4M3", "Brown", "411", "25.26", "Cell cycle"], ["D1M4", "D2M4", "D3M4", "D4M4", "Green", "111", "6.41", "–"], ["D1M5", "D2M5", "D3M5", "D4M5", "Grey", "1,097", "4.90", "–"], ["D1M6", "D2M6", "D3M6", "D4M6", "Nagenta", "38", "10.21", "–"], ["D1M7", "D2M7", "D3M7", "D4M7", "Pink", "56", "22.08", "–"], ["D1M8", "D2M8", "D3M8", "D4M8", "Red", "78", "17.64", "–"], ["D1M9", "D2M9", "D3M9", "D4M9", "Turquoise", "564", "29.46", "Cell adhesion"], ["D1M10", "D2M10", "D3M10", "D4M10", "Yellow", "215", "14.37", "Protein amino acid glycosylation"], ["D1M11", "D2M11", "D3M11", "D4M11", "Purple", "35", "8.30", "–"]], "row_count": 12, "column_count": 8, "numeric_cells": 33, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tIV-mmr-18-06-5579"}}, {"id": "asset:table:pmid:30365077:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f76879925aeebc4554457fc6e1ac5c09f9d60bf9d4d45d8b5c751bb378ccbf65", "bytes": 830, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tV-mmr-18-06-5579", "version": null, "note": "The 11 prognostic lncRNAs identified by LASSO-based Cox-proportion hazard model.", "structure": {"pmcid": "PMC6236314", "section_index": 14, "section_title": "Development and validation of an lncRNAs-based risk scoring system", "row_count": 12, "column_count": 4}, "table": {"label": "Table V.", "caption": "The 11 prognostic lncRNAs identified by LASSO-based Cox-proportion hazard model.", "rows": [["lncRNA", "Coefficient", "HR", "95% CI"], ["ARHGAP5-AS1", "0.0124", "1.1907", "0.8259–1.7166"], ["FLVCR1-AS1", "−0.1191", "0.6610", "0.4916–0.8886"], ["H19", "0.9171", "1.0497", "0.9390–1.1735"], ["HOTAIR", "−0.4973", "0.8970", "0.6584–1.2222"], ["LINC00221", "1.1799", "1.9190", "1.2021–3.0633"], ["MCF2L-AS1", "−0.7009", "0.7785", "0.6053–1.0014"], ["MUC2", "−0.0902", "0.9516", "0.8631–1.0492"], ["PRSS30P", "0.2572", "1.1254", "0.8263–1.5329"], ["SCARNA9", "−0.8615", "0.7383", "0.5449–1.0004"], ["TP53TG1", "0.1493", "1.1386", "0.8808–1.4720"], ["XIST", "−0.9235", "0.5469", "0.1926–1.5527"]], "row_count": 12, "column_count": 4, "numeric_cells": 38, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tV-mmr-18-06-5579"}}, {"id": "asset:table:pmid:30365077:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4b346e8a06cb7d180d3af7bcc1e46e4a779fa2e020bed81038be8b1447b43505", "bytes": 8056, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#tVI-mmr-18-06-5579", "version": null, "note": "Significant GO terms and KEGG pathways for the genes in the constructed lncRNA-mRNA network of nine prognostic lncRNAs involved in the blue module.", "structure": {"pmcid": "PMC6236314", "section_index": 15, "section_title": "Function analysis of the 11-lncRNA signature", "row_count": 32, "column_count": 5}, "table": {"label": "Table VI.", "caption": "Significant GO terms and KEGG pathways for the genes in the constructed lncRNA-mRNA network of nine prognostic lncRNAs involved in the blue module.", "rows": [["GO category", "Term", "Count", "Genes", "FDR"], ["Biology process", "Immune response", "80", "MICB, CD8A, LY86, HLA-DMB, HLA-DMA, C1QC, PDCD1, CD96, SH2D1A, CLEC4E, MS4A1, LTF, FAS, FCGR3A, SPN, CIITA, LAIR1, POU2AF1, SIT1, NCF2, GZMA, NCF1, LY96, CMKLR1, TNFRSF17, WAS, HLA-DQA1, PDCD1LG2, TRAT1, CTSW, IGSF6, C1QB, LILRB2, IL18BP, CCR5, TNFSF13B, CCR4, LAX1, LILRB4, HLA-DPA1, MADCAM1, GBP4, LCP1, GBP1, LCP2, HLA-DQB1, PSMB10, ITGAL, CCR1, GPSM3, CXCL9, CX3CL1, IL7R, CCL5, CCL4, POU2F2, ZAP70, HLA-DRB5, IL2RG, CD4, HLA-DPB1, HLA-DOA, PTPRC, IL2RA, TNFRSF13C, CCL19, SLAMF7, CD180, AIM2, CORO1A, TNFSF10, CYBB, APOL1, CD300A, CXCL13, CD209, IRF8, CD274, CD79B, CD79A", "5.39×10−49"], ["", "Regulation of cell activation", "30", "KLRK1, IL7R, HLA-DMA, CD2, ZAP70, CD4, IL2RG, FAS, HLA-DOA, LAG3, SPN, PTPRC, SIT1, IL2RA, IKZF1, PLEK, CD3E, TNFRSF13C, CD40, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, LAX1, CD274, JAK2, IRF4, SASH3", "6.22×10−20"], ["", "Regulation of lymphocyte activation", "28", "KLRK1, IL7R, HLA-DMA, CD2, ZAP70, CD4, IL2RG, FAS, HLA-DOA, LAG3, SPN, PTPRC, SIT1, IL2RA, IKZF1, CD3E, TNFRSF13C, CD40, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, LAX1, CD274, IRF4, SASH3", "1.53×10−19"], ["", "Lymphocyte activation", "31", "ITGAL, MICB, CD8A, IL21R, KLRK1, PTPN22, IL7R, HLA-DMA, DOCK2, CXCR5, ZAP70, MS4A1, CD2, CD4, FAS, SPN, RHOH, PTPRC, CD3G, CD3D, IKZF1, CD3E, SLAMF7, ITGA4, CD40, WAS, LAX1, CD79A, IRF4, BANK1, LCP1", "1.83×10−19"], ["", "Positive regulation of immune system process", "33", "C3AR1, MICB, CD247, KLRK1, PTPN22, IL7R, C1QC, HLA-DMA, SH2D1A, CD2, ZAP70, CD4, IL2RG, LAG3, SPN, PTPRC, IL2RA, IKZF1, CD3E, TNFRSF13C, CD40, PDCD1LG2, TRAT1, CD38, PRKCQ, C1QB, CORO1A, CD37, SIRPG, TNFSF13B, LAX1, CD79A, SASH3", "2.32×10−19"], ["", "Leukocyte activation", "33", "ITGAL, MICB, CD8A, IL21R, KLRK1, PTPN22, CX3CL1, IL7R, HLA-DMA, DOCK2, CXCR5, ZAP70, MS4A1, CD2, CD4, FAS, SPN, RHOH, PTPRC, CD3G, CD3D, IKZF1, CD3E, SLAMF7, ITGA4, CD40, WAS, LAX1, CD79A, IRF4, BANK1, LCP1, LCP2", "3.92×10−19"], ["", "Regulation of T cell activation", "25", "PTPRC, SIT1, IL2RA, IKZF1, CD3E, TNFRSF13C, KLRK1, IL7R, HLA-DMA, PDCD1LG2, PRKCQ, CORO1A, SIRPG, TNFSF13B, LAX1, CD274, ZAP70, CD2, CD4, IL2RG, IRF4, HLA-DOA, SPN, LAG3, SASH3", "2.21×10−18"], ["", "Defense response", "47", "C3AR1, ITGAL, PRF1, AIF1, CCR1, LY86, CXCL9, ITGB2, CX3CL1, CCL5, PTPRCAP, CCL4, C1QC, SH2D1A, AOAH, LTF, SPN, CIITA, ITK, PTPRC, IL2RA, NCF2, NCF1, LY96, HCK, CCL19, CD40, SLAMF7, WAS, CD180, SP140, TRAT1, CD163, LSP1, CD84, APOL3, SIGLEC1, C1QB, LILRB2, CORO1A, CYBB, APOL1, CCR5, CCR4, CXCL13, MNDA, PLA2G7", "3.44×10−18"], ["", "Regulation of leukocyte activation", "28", "KLRK1, IL7R, HLA-DMA, CD2, ZAP70, CD4, IL2RG, FAS, HLA-DOA, LAG3, SPN, PTPRC, SIT1, IL2RA, IKZF1, CD3E, TNFRSF13C, CD40, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, LAX1, CD274, IRF4, SASH3", "3.64×10−18"], ["", "Cell activation", "34", "ITGAL, MICB, CD8A, IL21R, KLRK1, PTPN22, CX3CL1, IL7R, HLA-DMA, DOCK2, CXCR5, ZAP70, MS4A1, CD2, CD4, FAS, SPN, RHOH, PTPRC, CD3G, CD3D, PLEK, IKZF1, CD3E, SLAMF7, ITGA4, CD40, WAS, LAX1, CD79A, IRF4, BANK1, LCP1, LCP2", "7.10×10−18"], ["", "Positive regulation of cell activation", "23", "PTPRC, IL2RA, IKZF1, PLEK, CD3E, KLRK1, TNFRSF13C, CD40, IL7R, HLA-DMA, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, CD2, ZAP70, JAK2, CD4, IL2RG, SASH3, SPN", "2.55×10−16"], ["", "Positive regulation of leukocyte activation", "21", "PTPRC, IL2RA, IKZF1, CD3E, KLRK1, TNFRSF13C, CD40, IL7R, HLA-DMA, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, CD2, ZAP70, CD4, IL2RG, SASH3, SPN", "3.41×10−14"], ["", "Positive regulation of lymphocyte activation", "20", "PTPRC, IL2RA, IKZF1, CD3E, KLRK1, TNFRSF13C, CD40, IL7R, HLA-DMA, PDCD1LG2, CD38, PRKCQ, CORO1A, SIRPG, TNFSF13B, ZAP70, CD4, IL2RG, SASH3, SPN", "1.78×10−13"], ["", "T cell activation", "21", "ITGAL, PTPRC, MICB, CD3G, CD3D, IKZF1, CD8A, CD3E, PTPN22, IL7R, HLA-DMA, WAS, DOCK2, ZAP70, CD2, CD4, FAS, IRF4, LCP1, SPN, RHOH", "1.09×10−12"], ["", "Hemopoietic or lymphoid organ development", "24", "PTPRC, CD3D, PLEK, IKZF1, CD8A, CD3E, HCLS1, PTPN22, ITGA4, IFI16, IL7R, HLA-DMA, DOCK2, CXCR5, CXCL13, IRF8, ZAP70, JAK2, CD4, FAS, CD79A, IRF4, SPN, RHOH", "2.97×10−09"], ["", "Inflammatory response", "26", "ITGAL, C3AR1, AIF1, LY86, CCR1, CXCL9, ITGB2, CCL5, C1QC, CCL4, AOAH, CIITA, IL2RA, LY96, CCL19, CD40, CD180, CD163, C1QB, SIGLEC1, APOL3, CYBB, CCR5, CXCL13, CCR4, PLA2G7", "6.83×10−09"], ["", "Immune system development", "24", "PTPRC, CD3D, PLEK, IKZF1, CD8A, CD3E, HCLS1, PTPN22, ITGA4, IFI16, IL7R, HLA-DMA, DOCK2, CXCR5, CXCL13, IRF8, ZAP70, JAK2, CD4, FAS, CD79A, IRF4, SPN, RHOH", "1.02×10−08"], ["", "Hemopoiesis", "22", "PTPRC, CD3D, PLEK, IKZF1, CD8A, CD3E, HCLS1, PTPN22, ITGA4, IFI16, IL7R, HLA-DMA, DOCK2, IRF8, ZAP70, JAK2, CD4, FAS, CD79A, IRF4, SPN, RHOH", "2.60×10−08"], ["", "Positive regulation of response to stimulus", "22", "C3AR1, PTPRC, MICB, CD3E, CD247, KLRK1, TNFRSF13C, PTPN22, CX3CL1, CCL5, HLA-DMA, C1QC, C1QB, SH2D1A, TNFSF13B, LAX1, CCR4, ZAP70, JAK2, CD79A, SASH3, LAG3", "2.60×10−08"], ["", "Response to wounding", "30", "C3AR1, ITGAL, AIF1, LY86, CCR1, CXCL9, ITGB2, CCL5, C1QC, CCL4, AOAH, CIITA, IL2RA, PLEK, LY96, CCL19, CD40, WAS, CD180, CD163, APOL3, PRKCQ, C1QB, SIGLEC1, CYBB, CCR5, CCR4, CXCL13, PLA2G7, JAK2", "4.82×10−07"], ["", "Cell surface receptor linked signal transduction", "56", "MICB, CD8A, PTPN22, CXCR5, CXCR6, SPN, LAG3, KLRB1, PIK3CG, CD3G, CD3D, LY96, CMKLR1, CD3E, GPR171, CD40, IGSF6, LILRB2, DOK2, CCR5, CCR4, LAX1, LCP2, C3AR1, ITGAL, CCR1, CD247, KLRK1, CXCL9, FPR3, ITGB2, IL7R, CCL5, P2RY6, ITGAX, ITGB7, GPR25, ZAP70, CD2, CD4, PTPRC, IL2RA, PLEK, DTX1, CCL19, RGS19, EVL, ITGA4, BIRC3, P2RY10, CD274, CD79B, JAK2, JAK3, CD79A, ADAMDEC1", "4.54×10−05"], ["", "Cell adhesion", "29", "ITGAL, CCR1, FERMT3, ITGB2, CX3CL1, CCL5, CCL4, CD96, ITGAX, ITGB7, CD2, CD22, CD4, CD6, SELPLG, PARVG, PTPRC, PLEK, SIGLEC10, ITGA4, SLAMF7, EMILIN2, CD84, SIGLEC1, CORO1A, SIRPG, CD300A, CD209, MADCAM1", "8.34×10−04"], ["", "Biological adhesion", "29", "ITGAL, CCR1, FERMT3, ITGB2, CX3CL1, CCL5, CCL4, CD96, ITGAX, ITGB7, CD2, CD22, CD4, CD6, SELPLG, PARVG, PTPRC, PLEK, SIGLEC10, ITGA4, SLAMF7, EMILIN2, CD84, SIGLEC1, CORO1A, SIRPG, CD300A, CD209, MADCAM1", "8.58×10−04"], ["KEGG pathway", "Cell adhesion molecules (CAMs)", "26", "HLA-DQB1, ITGAL, PTPRC, CD8A, ITGB2, CD40, ITGA4, HLA-DMB, HLA-DMA, PDCD1, HLA-DQA1, PDCD1LG2, SIGLEC1, ITGB7, CD274, CD2, CD22, HLA-DRB5, CD4, HLA-DPA1, MADCAM1, HLA-DPB1, HLA-DOA, CD6, SELPLG, SPN", "6.37×10−15"], ["", "Allograft rejection", "12", "HLA-DQB1, PRF1, HLA-DRB5, GZMB, HLA-DPA1, HLA-DPB1, FAS, CD40, HLA-DMB, HLA-DOA, HLA-DMA, HLA-DQA1", "8.68×10−08"], ["", "Cytokine-cytokine receptor interaction", "24", "IL2RB, IL2RA, CCR1, IL21R, TNFRSF13C, CXCL9, TNFRSF17, CCL19, CD40, CX3CL1, IL7R, CCL5, CCL4, TNFSF10, TNFSF13B, CXCR5, CCR5, CCR4, CXCL13, IL10RA, CXCR6, CSF2RB, IL2RG, FAS", "2.80×10−06"], ["", "Graft vs.host disease", "11", "HLA-DQB1, PRF1, HLA-DRB5, GZMB, HLA-DPA1, HLA-DPB1, FAS, HLA-DMB, HLA-DOA, HLA-DMA, HLA-DQA1", "4.48×10−06"], ["", "Chemokine signaling pathway", "19", "PIK3CG, ITK, NCF1, HCK, CCR1, CXCL9, CCL19, CX3CL1, CCL5, CCL4, WAS, DOCK2, CXCR5, CCR5, CCR4, CXCL13, CXCR6, JAK2, JAK3", "4.64×10−05"], ["", "Natural killer cell mediated cytotoxicity", "15", "PIK3CG, PRF1, ITGAL, MICB, CD247, KLRK1, GZMB, ITGB2, HCST, SH2D1A, TNFSF10, ZAP70, FAS, FCGR3A, LCP2", "5.69×10−04"], ["", "T cell receptor signaling pathway", "13", "PIK3CG, ITK, PRKCQ, PTPRC, CD3G, CD8A, CD3D, CD3E, CD247, ZAP70, CD4, PDCD1, LCP2", "2.20×10−03"], ["", "Antigen processing and presentation", "11", "HLA-DQB1, CIITA, CD8A, HLA-DRB5, CD4, HLA-DPA1, HLA-DPB1, HLA-DMB, HLA-DOA, HLA-DMA, HLA-DQA1", "7.92×10−03"]], "row_count": 32, "column_count": 5, "numeric_cells": 91, "header_rows": 1, "locator": "section[15]/table-wrap[1]#tVI-mmr-18-06-5579"}}, {"id": "asset:table:pmid:30365077:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ce21f75d762a32eff6eb90a4316b1cd200e918801cbfb2c9555d68a734692f79", "bytes": 4234, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#tVII-mmr-18-06-5579", "version": null, "note": "Significant GO terms and KEGG pathways for the genes in the constructed lncRNA-mRNA network of two prognostic lncRNAs in the brown module.", "structure": {"pmcid": "PMC6236314", "section_index": 15, "section_title": "Function analysis of the 11-lncRNA signature", "row_count": 19, "column_count": 5}, "table": {"label": "Table VII.", "caption": "Significant GO terms and KEGG pathways for the genes in the constructed lncRNA-mRNA network of two prognostic lncRNAs in the brown module.", "rows": [["GO category", "Term", "Count", "Genes", "FDR"], ["Biology process", "Cell cycle phase", "40", "E2F1, KIF23, PRC1, NEK3, NEK2, DBF4, TTK, PKMYT1, ANLN, AURKA, PTTG1, CEP55, AURKB, CCNE1, CDCA2, CDCA5, TRIP13, CDCA3, CDC6, MKI67, MSH5, TPX2, SKP2, NUF2, CENPF, CDC20, BIRC5, CENPE, NDC80, ESPL1, PBK, CDKN3, UBE2C, TACC3, CDC25B, CCNB1, MAD2L1, PLK1, POLD1, DSCC1", "2.14×10−22"], ["", "Cell cycle", "50", "E2F1, KIF23, CEP72, PRC1, DBF4, E2F7, TTK, PKMYT1, AURKA, PTTG1, AURKB, CDT1, CCNE2, CCNE1, CDCA2, CDCA5, CDCA3, CDC6, SKP2, TPX2, ESPL1, MCM2, PBK, TACC3, UBE2C, UHRF1, MAD2L1, DSCC1, NEK3, NEK2, FOXM1, ANLN, CEP55, CENPA, TRIP13, CKAP2, MKI67, MSH5, PSRC1, NUF2, CENPF, BIRC5, NDC80, CENPE, CDC20, CDKN3, CDC25B, CCNB1, PLK1, POLD1", "2.83×10−21"], ["", "Mitotic cell cycle", "37", "KIF23, E2F1, PRC1, NEK3, NEK2, DBF4, TTK, PKMYT1, ANLN, AURKA, PTTG1, CEP55, AURKB, CCNE1, CENPA, CDCA2, CDCA5, CDCA3, CDC6, TPX2, SKP2, NUF2, CENPF, CDC20, BIRC5, CENPE, NDC80, ESPL1, PBK, CDKN3, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1, POLD1, DSCC1", "6.89×10−21"], ["", "Cell cycle process", "42", "E2F1, KIF23, CEP72, PRC1, NEK3, NEK2, DBF4, TTK, PKMYT1, ANLN, AURKA, PTTG1, AURKB, CEP55, CCNE1, CENPA, CDCA2, CDCA5, CDCA3, TRIP13, CDC6, MKI67, MSH5, TPX2, SKP2, NUF2, CENPF, CDC20, BIRC5, CENPE, NDC80, ESPL1, PBK, CDKN3, UBE2C, TACC3, CDC25B, CCNB1, MAD2L1, PLK1, POLD1, DSCC1", "2.26×10−19"], ["", "M phase", "34", "KIF23, PRC1, NEK3, NEK2, TTK, PKMYT1, ANLN, AURKA, PTTG1, CEP55, AURKB, CDCA2, CDCA5, TRIP13, CDCA3, CDC6, MKI67, MSH5, TPX2, NUF2, CENPF, CDC20, BIRC5, CENPE, NDC80, ESPL1, PBK, UBE2C, TACC3, CDC25B, CCNB1, MAD2L1, PLK1, DSCC1", "2.68×10−19"], ["", "Mitosis", "28", "KIF23, NEK3, NEK2, PKMYT1, AURKA, ANLN, CEP55, AURKB, PTTG1, CDCA2, CDCA5, CDCA3, CDC6, TPX2, NUF2, CENPF, BIRC5, CENPE, NDC80, ESPL1, CDC20, PBK, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1, DSCC1", "1.39×10−17"], ["", "Nuclear division", "28", "KIF23, NEK3, NEK2, PKMYT1, AURKA, ANLN, CEP55, AURKB, PTTG1, CDCA2, CDCA5, CDCA3, CDC6, TPX2, NUF2, CENPF, BIRC5, CENPE, NDC80, ESPL1, CDC20, PBK, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1, DSCC1", "1.39×10−17"], ["", "M phase of mitotic cell cycle", "28", "KIF23, NEK3, NEK2, PKMYT1, AURKA, ANLN, CEP55, AURKB, PTTG1, CDCA2, CDCA5, CDCA3, CDC6, TPX2, NUF2, CENPF, BIRC5, CENPE, NDC80, ESPL1, CDC20, PBK, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1, DSCC1", "2.25×10−17"], ["", "Organelle fission", "28", "KIF23, NEK3, NEK2, PKMYT1, AURKA, ANLN, CEP55, AURKB, PTTG1, CDCA2, CDCA5, CDCA3, CDC6, TPX2, NUF2, CENPF, BIRC5, CENPE, NDC80, ESPL1, CDC20, PBK, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1, DSCC1", "4.04×10−17"], ["", "Cell division", "26", "KIF23, PRC1, NEK3, NEK2, ANLN, CEP55, PTTG1, AURKB, CCNE2, CCNE1, CDCA2, CDCA5, CDCA3, CDC6, NUF2, CENPF, BIRC5, CDC20, CENPE, NDC80, ESPL1, UBE2C, CDC25B, CCNB1, MAD2L1, PLK1", "3.42×10−12"], ["", "Regulation of cell cycle", "19", "E2F1, CDC6, HOXA13, NEK2, SKP2, CENPF, TTK, PKMYT1, ESPL1, CENPE, ANLN, BIRC5, TACC3, UBE2C, CDKN3, CDT1, CCNE2, CCNB1, MAD2L1", "4.79×10−05"], ["", "Microtubule-based process", "16", "KIFC2, KIF23, CEP72, PRC1, NEK2, PSRC1, TTK, ESPL1, AURKA, NDC80, CENPE, TACC3, UBE2C, HOOK1, CENPA, KIF20A", "2.40×10−04"], ["", "Pattern specification process", "15", "SATB2, FOXA2, FOXJ1, OTX1, HOXA11, HOXC6, FOXH1, HOXC10, HOXC9, HOXC11, HOXB7, VEGFA, HOXA10, HOXA9, HOXB9", "2.78×10−03"], ["", "DNA metabolic process", "20", "RECQL4, GINS1, CDC6, RAD51AP1, DBF4, MSH5, CENPF, MCM2, PTTG1, MCM4, CDT1, CCNE2, TYMS, UHRF1, RFC3, POLD1, DNMT3B, TOP2A, TRIP13, DSCC1", "5.77×10−03"], ["KEGG pathway", "Cell cycle", "18", "E2F1, CDC6, E2F5, DBF4, SKP2, PKMYT1, TTK, CDC20, ESPL1, MCM2, PTTG1, MCM4, CDC25B, CCNE2, CCNB1, CCNE1, MAD2L1, PLK1", "1.01×10−12"], ["", "DNA replication", "4", "RFC3, POLD1, MCM2, MCM4", "5.38×10−03"], ["", "Progesterone-mediated oocyte maturation", "5", "CCNB1, MAD2L1, PLK1, PKMYT1, CDC25B", "1.04×10−02"], ["", "Steroid biosynthesis", "3", "CYP51A1, SQLE, DHCR7", "1.22×10−02"]], "row_count": 19, "column_count": 5, "numeric_cells": 53, "header_rows": 1, "locator": "section[15]/table-wrap[2]#tVII-mmr-18-06-5579"}}], "gaps": ["asset:data:geo:E-MTAB-1338 not downloaded", "asset:data:geo:E-MTAB-1338 licence not read", "asset:data:geo:GSE29998 not downloaded", "asset:data:geo:GSE29998 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:GSE62254 licence not read", "asset:data:geo:GSE6580 not downloaded", "asset:data:geo:GSE6580 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-2", "family": null, "specific": null, "label": "MetaDE meta-analysis method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Consensus differentially expressed RNAs (DERs) between GC specimens and normal control specimens across the 4 datasets (GSE6580, GSE29998, E-MTAB-1338 and TCGA) were identified with metaDE package (22,23) (https://cran.r-project.org/web/packages/MetaDE/) in R language version 3.4.1."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE6580", "GSE29998", "E-MTAB-1338", "GSE62254"], "resolved_accessions": ["GSE6580", "GSE29998", "E-MTAB-1338", "GSE62254"], "statements": ["The datasets analyzed during the present study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE6580, GSE29998, E-MTAB-1338, GSE62254 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pathway_enrich"], "assets": ["source:pmid:30365077", "data:geo:E-MTAB-1338", "asset:table:pmid:30365077:1", "asset:table:pmid:30365077:2", "asset:table:pmid:30365077:3", "asset:table:pmid:30365077:4", "asset:table:pmid:30365077:5", "asset:table:pmid:30365077:6", "asset:table:pmid:30365077:7"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:E-MTAB-1338"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:40Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 31284, "completion_tokens": 3089, "cached_tokens": 656}}, "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:30365077", "type": "paper", "label": "pmid:30365077"}, {"id": "source:pmid:30365077", "type": "manuscript", "label": "PMID 30365077 full text"}, {"id": "data:geo:E-MTAB-1338", "type": "dataset", "label": "GEO E-MTAB-1338"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30365077", "type": "paper", "label": "pmid:30365077"}, {"id": "source:pmid:30365077", "type": "manuscript", "label": "PMID 30365077 full text"}, {"id": "data:geo:E-MTAB-1338", "type": "dataset", "label": "GEO E-MTAB-1338"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30365077", "type": "extraction", "used": ["source:pmid:30365077"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-E-MTAB-1338", "type": "accession_resolution", "used": ["data:geo:E-MTAB-1338"], "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:30365077", "parent_hash": "sha256:e4538bcbeb3055c6fd991f439b5d0410a6d876e227b12f0f1326ff0f4e5b7f78", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:E-MTAB-1338 licence not read", "asset:data:geo:E-MTAB-1338 not downloaded", "asset:data:geo:GSE29998 licence not read", "asset:data:geo:GSE29998 not downloaded", "asset:data:geo:GSE62254 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:GSE6580 licence not read", "asset:data:geo:GSE6580 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["pathway enrichment"], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T00:32:47+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}}}