{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29050278", "kind": "science-record", "revision": 8, "content_hash": "sha256:b98076f0dcc033313d4914e310518b2f156f64d2045250d1ea57dd497a9d68f6", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T21:59:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of core genes and outcome in gastric cancer using bioinformatics analysis.", "doi": "10.18632/oncotarget.20082", "pmid": "29050278", "authors": ["Chenhua Sun", "Qi Yuan", "Dongdong Wu", "Xiaohu Meng", "Baolin Wang"], "journal": "Oncotarget", "year": 2017, "abstract": "Gastric cancer (GC) is a common malignant neoplasm of gastrointestinal tract. We chose gene expression profile of GSE54129 from GEO database aiming to find key genes during the occurrence and development of GC. 132 samples, including 111 cancer and 21 normal gastric mucosa epitheliums, were included in this analysis. Differentially expressed genes (DEGs) between GC patients and health people were picked out using GEO2R tool, then we performed gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using The Database for Annotation, Visualization and Integrated Discovery (DAVID). Moreover, Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING) and Molecular Complex Detection (MCODE) plug-in was utilized to visualize protein-protein interaction (PPI) of these DEGs. There were 971 DEGs, including 468 up-regulated genes enriched in focal adhesion, ECM-receptor interaction and PI3K-Akt signaling pathway, while 503 down-regulated genes enriched in metabolism of xenbiotics and drug by cytochrome P450, chemical carcinogenesis, retinol metabolism and gastric acid secretion. Three important modules were detected from PPI network using MCODE software. Besides, Fifteen hub genes with high degree of connectivity were selected, including BGN, MMP2, COL1A1, and FN1. Moreover, the Kaplan-Meier analysis for overall survival and correlation analysis were applied among those genes. In conclusion, this bioinformatics analysis demonstrated that DEGs and hub genes, such as BGN, might promote the development of gastric cancer, especially in tumor metastasis. In addition, it could be used as a new biomarker for diagnosis and to guide the combination medicine of gastric cancer.", "claims": [{"id": "claim-method", "statement": "Kaplan Meier-plotter (KM plotter, http://kmplot.com/analysis/) could assess the effect of 54675 genes on survival using 10,461 cancer samples, including 5143 breast, 1816 ovarian, 2437 lung and 1,065 gastric cancer patients with a mean follow-up of 69, 40, 49 and 33 months [9].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29050278", "locator": "sections[14] \"Survival analysis of hub genes\" paragraph 2", "quote": "Kaplan Meier-plotter (KM plotter, http://kmplot.com/analysis/) could assess the effect of 54675 genes on survival using 10,461 cancer samples, including 5143 breast, 1816 ovarian, 2437 lung and 1,065 gastric cancer patients with a mean follow-up of 69, 40, 49 and 33 months [9]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We chose gene expression profile of GSE54129 from GEO database, which was a public and freely available database. GSE54129, which was based on agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). The GSE54129 dataset included 132 samples, containing 111 gastric cancer samples and 21 normal gastric mucosa epithelium. We also downloaded the Series Matrix File of GSE54129 from GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29050278", "locator": "sections[9] \"Microarray data\" paragraph 2", "quote": "We chose gene expression profile of GSE54129 from GEO database, which was a public and freely available database. GSE54129, which was based on agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). The GSE54129 dataset included 132 samples, containing 111 gastric cancer samples and 21 normal gastric mucosa epithelium. We also downloaded the Series Matrix File of GSE54129 from GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GEO2R on GSE54129 from Gene Expression Omnibus, the study identified 971 differentially expressed genes and selected 15 hub genes with high degree of connectivity.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29050278", "locator": "sections[1] \"INTRODUCTION\" paragraph 4", "quote": "In this analysis, we chose GSE54129 from Gene Expression Omnibus (GEO), and used GEO2R online tool to detect the differentially expressed genes (DEGs)."}, {"asset": "source:pmid:29050278", "locator": "sections[3] \"Identification of DEGs and hub genes\" paragraph 2", "quote": "A total of 971 differential expressed genes were detected after the analysis of GSE54129; of which, 468 were up-regulated genes and 503 were down-regulated."}, {"asset": "source:pmid:29050278", "locator": "sections[3] \"Identification of DEGs and hub genes\" paragraph 2", "quote": "Besides, 15 hub genes with high degree of connectivity were selected (Table 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GEO2R on GSE54129 from Gene Expression Omnibus, the study identified 971 differentially expressed genes and selected 15 hub genes with high degree of connectivity.", "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:29050278"], "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:GSE54129"], "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:GSE54129"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29050278", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.20082", "sha256": "sha256:cb4cee10545056021b6a065e85370d53e3e61ae188fe2472d56ab26c5e717c34", "bytes": 19764, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.20082", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5642553", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE54129", "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=GSE54129", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54129", "version": null, "note": "We chose gene expression profile of GSE54129 from GEO database, which was a public and freely available database. GSE54129, which was based on agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). The GSE54129 dataset included 132 samples, containing 111 gastric cancer samples and 21 normal gastric mucosa epithelium. We also downloaded the Series Matrix File of GSE54129 from GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We chose gene expression profile of GSE54129 from GEO database, which was a public and freely available database. GSE54129, which was based on agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). The GSE54129 dataset included 132 samples, containing 111 gastric cancer samples and 21 normal gastric mucosa epithelium. 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"GSM1308523"], "sample_count": 132, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Global gene expression analysis of gastric cancer by oligonucleotide microarrays", "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:29050278:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:354c239296dea5e02083dec7d8697febff7e18ddc43a35d2ecbf48cd27d5644b", "bytes": 627, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "Top 15 hub genes with higher degree of connectivity", "structure": {"pmcid": "PMC5642553", "section_index": 3, "section_title": "Identification of DEGs and hub genes", "row_count": 16, "column_count": 3}, "table": {"label": "Table 1", "caption": "Top 15 hub genes with higher degree of connectivity", "rows": [["Gene", "Degree of connectivity", "Adjusted P value"], ["CTNNB1", "24", "3.13E-22"], ["FN1", "16", "5.13E-21"], ["FYN", "15", "1.98E-34"], ["MMP9", "14", "2.28E-09"], ["COL1A1", "11", "1.47E-33"], ["ITCH", "11", "1.62E-30"], ["TGFB1", "10", "6.43E-42"], ["THBS1", "9", "1.03E-22"], ["MMP2", "9", "3.07E-18"], ["ACTA2", "8", "1.67E-08"], ["ITGA5", "8", "5.44E-20"], ["BMP2", "8", "5.61E-24"], ["BGN", "7", "1.50E-28"], ["HSPA4", "7", "7.44E-32"], ["PIK3R1", "7", "2.29E-37"]], "row_count": 16, "column_count": 3, "numeric_cells": 30, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:29050278:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2bde0162c7e5f76545016eb2d73da5288a278f8d422ab7a36349f944d32a0ae1", "bytes": 3334, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T2", "version": null, "note": "Gene ontology analysis of differentially expressed genes associated with gastric cancer", "structure": {"pmcid": "PMC5642553", "section_index": 4, "section_title": "GO function and KEGG pathway enrichment analysis", "row_count": 31, "column_count": 7}, "table": {"label": "Table 2", "caption": "Gene ontology analysis of differentially expressed genes associated with gastric cancer", "rows": [["Expression", "Category", "Term", "Count", "%", "P-Value", "FDR"], ["Up-regulated", "GOTERM_BP_FAT", "GO:0001944∼vasculature development", "67", "19.65", "7.50E-31", "1.43E-27"], ["GOTERM_BP_FAT", "GO:0001568∼blood vessel development", "62", "18.18", "5.72E-28", "1.09E-24"], ["GOTERM_BP_FAT", "GO:0048514∼blood vessel morphogenesis", "56", "16.42", "2.00E-26", "3.82E-23"], ["GOTERM_BP_FAT", "GO:0072358∼cardiovascular system development", "75", "21.99", "1.28E-25", "2.43E-22"], ["GOTERM_BP_FAT", "GO:0072359∼circulatory system development", "75", "21.99", "1.28E-25", "2.43E-22"], ["GOTERM_MF_FAT", "GO:0005539∼glycosaminoglycan binding", "28", "8.21", "3.99E-15", "6.14E-12"], ["GOTERM_MF_FAT", "GO:0008201∼heparin binding", "23", "6.74", "4.66E-13", "7.16E-10"], ["GOTERM_MF_FAT", "GO:1901681∼sulfur compound binding", "26", "7.62", "3.41E-12", "5.23E-09"], ["GOTERM_MF_FAT", "GO:0005102∼receptor binding", "64", "18.77", "6.71E-10", "1.03E-06"], ["GOTERM_MF_FAT", "GO:0032403∼protein complex binding", "42", "12.32", "2.71E-09", "4.17E-06"], ["GOTERM_CC_FAT", "GO:0031012∼extracellular matrix", "66", "19.35", "8.53E-32", "1.23E-28"], ["GOTERM_CC_FAT", "GO:0005578∼proteinaceous extracellular matrix", "52", "15.25", "7.99E-28", "1.16E-24"], ["GOTERM_CC_FAT", "GO:0044421∼extracellular region part", "159", "46.63", "7.12E-21", "1.03E-17"], ["GOTERM_CC_FAT", "GO:0005615∼extracellular space", "87", "25.51", "9.70E-20", "1.40E-16"], ["GOTERM_CC_FAT", "GO:0005576∼extracellular region", "171", "50.15", "4.15E-18", "6.00E-15"], ["Down-regulated", "GOTERM_BP_FAT", "GO:0030855∼epithelial cell differentiation", "42", "10.85", "2.99E-13", "5.61E-10"], ["GOTERM_BP_FAT", "GO:0007586∼digestion", "21", "5.43", "5.83E-11", "1.10E-07"], ["GOTERM_BP_FAT", "GO:0060429∼epithelium development", "49", "12.66", "3.66E-08", "6.88E-05"], ["GOTERM_BP_FAT", "GO:0006805∼xenobiotic metabolic process", "14", "3.62", "5.49E-08", "1.03E-04"], ["GOTERM_BP_FAT", "GO:0006629∼lipid metabolic process", "56", "14.47", "7.06E-08", "1.33E-04"], ["GOTERM_MF_FAT", "GO:0016614∼oxidoreductase activity, acting on CH-OH group of donors", "22", "5.68", "2.20E-13", "3.43E-10"], ["GOTERM_MF_FAT", "GO:0016616∼oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor", "17", "4.39", "9.66E-10", "1.51E-06"], ["GOTERM_MF_FAT", "GO:0004745∼retinol dehydrogenase activity", "8", "2.07", "2.60E-08", "4.05E-05"], ["GOTERM_MF_FAT", "GO:0004033∼aldo-keto reductase (NADP) activity", "7", "1.81", "1.08E-05", "0.016818"], ["GOTERM_MF_FAT", "GO:0016709∼oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen", "7", "1.81", "1.71E-04", "0.266413"], ["GOTERM_CC_FAT", "GO:0044421∼extracellular region part", "124", "32.04", "5.03E-08", "7.04E-05"], ["GOTERM_CC_FAT", "GO:0005576∼extracellular region", "140", "36.18", "1.05E-07", "1.47E-04"], ["GOTERM_CC_FAT", "GO:0045177∼apical part of cell", "26", "6.72", "1.38E-07", "1.93E-04"], ["GOTERM_CC_FAT", "GO:0070062∼extracellular exosome", "92", "23.77", "3.26E-06", "0.004567"], ["GOTERM_CC_FAT", "GO:1903561∼extracellular vesicle", "92", "23.77", "4.04E-06", "0.005651"]], "row_count": 31, "column_count": 7, "numeric_cells": 150, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:29050278:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5952b42f74343482a7548af7123d5b4f7e14ba1a33d6f5960ed221844fd5a63e", "bytes": 2162, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[2]#T3", "version": null, "note": "KEGG pathway analysis of differentially expressed genes associated with gastric cancer", "structure": {"pmcid": "PMC5642553", "section_index": 4, "section_title": "GO function and KEGG pathway enrichment analysis", "row_count": 11, "column_count": 7}, "table": {"label": "Table 3", "caption": "KEGG pathway analysis of differentially expressed genes associated with gastric cancer", "rows": [["Category", "Term", "Count", "%", "P-Value", "Genes", "FDR"], ["Up-regulated DEGs", "hsa04510:Focal adhesion", "25", "7.3", "5.06E-11", "TLN1, TNC, MYL9, COL6A3, COL6A2, COL6A1, ZYX, THBS1, COL11A1, THBS2, PIK3R1, SPP1, THBS4, FN1, COL4A2, COL4A1, IGF1, FLNA, VEGFC, FYN, ITGA5, ITGA7, COL1A2, COL1A1, MYLK", "6.32E-08"], ["hsa04512:ECM-receptor interaction", "16", "4.7", "1.13E-09", "COL4A2, COL4A1, TNC, ITGA5, ITGA7, COL6A3, COL6A2, COL1A2, COL6A1, COL1A1, THBS1, THBS2, COL11A1, SPP1, THBS4, FN1", "1.42E-06"], ["hsa04151:PI3K-Akt signaling pathway", "25", "7.3", "1.34E-06", "MCL1, OSMR, TNC, BCL2L1, IL7R, COL6A3, COL6A2, COL6A1, IL2RG, THBS1, COL11A1, THBS2, PIK3R1, SPP1, THBS4, FN1, COL4A2, COL4A1, IGF1, YWHAE, VEGFC, ITGA5, ITGA7, COL1A2, COL1A1", "0.001667"], ["hsa04974:Protein digestion and absorption", "12", "3.5", "5.64E-06", "COL4A2, COL14A1, COL4A1, COL6A3, ELN, COL1A2, COL6A2, COL12A1, COL6A1, COL1A1, COL11A1, COL10A1", "0.007038"], ["hsa04270:Vascular smooth muscle contraction", "12", "3.5", "9.93E-05", "EDNRA, GNA13, ACTG2, ACTA2, CALD1, PLA2G2A, GUCY1A3, GUCY1B3, CALCRL, MYLK, KCNMB1, MYL9", "0.123856"], ["Down-regulated DEGs", "hsa00980:Metabolism of xenobiotics by cytochrome P450", "12", "3.1", "2.08E-07", "GSTA1, CYP3A4, CYP3A5, CBR1, CYP2C9, ADH1C, AKR7A3, ADH1A, ADH7, UGT2B15, AKR1C1, ALDH3A1", "2.56E-04"], ["hsa05204:Chemical carcinogenesis", "12", "3.1", "4.70E-07", "GSTA1, CYP3A4, CYP3A5, CBR1, CYP2C19, CYP2C9, CYP2C18, ADH1C, ADH1A, ADH7, UGT2B15, ALDH3A1", "5.78E-04"], ["hsa00830:Retinol metabolism", "11", "2.8", "5.47E-07", "CYP3A4, RDH12, CYP3A5, CYP2C9, CYP2C18, ADH1C, DHRS9, SDR16C5, ADH1A, ADH7, UGT2B15", "6.72E-04"], ["hsa00982:Drug metabolism - cytochrome P450", "11", "2.8", "8.44E-07", "GSTA1, CYP3A4, FMO5, CYP3A5, CYP2C19, CYP2C9, ADH1C, ADH1A, ADH7, UGT2B15, ALDH3A1", "0.001037"], ["hsa04971:Gastric acid secretion", "11", "2.8", "1.66E-06", "KCNJ16, KCNJ15, ATP4A, GNAQ, ATP4B, SLC26A7, KCNE2, GAST, CA2, SST, KCNK10", "0.002035"]], "row_count": 11, "column_count": 7, "numeric_cells": 60, "header_rows": 1, "locator": "section[4]/table-wrap[2]#T3"}}], "gaps": ["asset:data:geo:GSE54129 not downloaded", "asset:data:geo:GSE54129 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "The hazard ratio (HR) with 95% confidenc", "p_value": "intervals and log rank P value were calculated and dis"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log rank"}}, {"id": "method-3", "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-4", "family": null, "specific": null, "label": "Kaplan–Meier survival analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Kaplan Meier-plotter (KM plotter, http://kmplot.com/analysis/) could assess the effect of 54675 genes on survival using 10,461 cancer samples, including 5143 breast, 1816 ovarian, 2437 lung and 1,065 gastric cancer patients with a mean follow-up of 69, 40, 49 and 33 months [9]."}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE54129"], "resolved_accessions": ["GSE54129"], "statements": ["We chose gene expression profile of GSE54129 from GEO database, which was a public and freely available database. GSE54129, which was based on agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). The GSE54129 dataset included 132 samples, containing 111 gastric cancer samples and 21 normal gastric mucosa epithelium. We also downloaded the Series Matrix File of GSE54129 from GEO database."], "basis": "The paper names GSE54129 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": ["survival_km"], "assets": ["source:pmid:29050278", "data:geo:GSE54129", "asset:table:pmid:29050278:1", "asset:table:pmid:29050278:2", "asset:table:pmid:29050278:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE54129"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:28Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 40669, "completion_tokens": 5202, "cached_tokens": 10624}}, "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:29050278", "type": "paper", "label": "pmid:29050278"}, {"id": "source:pmid:29050278", "type": "manuscript", "label": "PMID 29050278 full text"}, {"id": "data:geo:GSE54129", "type": "dataset", "label": "GEO GSE54129"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29050278", "type": "paper", "label": "pmid:29050278"}, {"id": "source:pmid:29050278", "type": "manuscript", "label": "PMID 29050278 full text"}, {"id": "data:geo:GSE54129", "type": "dataset", "label": "GEO GSE54129"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29050278", "type": "extraction", "used": ["source:pmid:29050278"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE54129", "type": "accession_resolution", "used": ["data:geo:GSE54129"], "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:29050278", "parent_hash": "sha256:2dc6e667ea94da0495383238553a4a4648997d44ea47535909df723f33ba79dc", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE54129 licence not read", "asset:data:geo:GSE54129 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.77, "evidence": ["rall survival information were based on GEO (Affymetrix microarrays only), EGA and TCGA database. Th"], "order_basis": "paper_text_order:3764", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "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":"2026-11-04T02:43:43+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}}}