{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32160184", "kind": "science-record", "revision": 8, "content_hash": "sha256:09c367a4ce58f005dcea46947483398f7ecf77624e6f6a8e9f9fae60482b9d25", "created_at": "2026-11-01T15:40:57Z", "updated_at": "2026-11-01T22:44:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Crucial Gene Identification in Carotid Atherosclerosis Based on Peripheral Blood Mononuclear Cell (PBMC) Data by Weighted (Gene) Correlation Network Analysis (WGCNA).", "doi": "10.12659/MSM.921692", "pmid": "32160184", "authors": ["Siliang Chen", "Dan Yang", "Zhili Liu", "Fangda Li", "Bao Liu", "Yuexin Chen", "Wei Ye", "Yuehong Zheng"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2020, "abstract": "BACKGROUND Many patients are not responsive or tolerant to medical therapies for carotid atherosclerosis. Thus, elucidating the molecular mechanism for the pathogenesis and progression of carotid atherosclerosis and identifying new potential molecular targets for medical therapies that can slow progression of carotid atherosclerosis and prevent ischemic events are quite important. MATERIAL AND METHODS We downloaded the expression profiling data of PBMC in Biobank of Karolinska Endarterectomy (BiKE, GSE21545) for GEO. The WGCNA and DEG screening were conducted. The co-expression pattern between patients with ischemic events (the events group) and patients without ischemic events (the no-events group) were compared. Then, we identified hub genes of each module. Finally, the DEG co-expression network was constructed and MCODE was used to identify crucial genes based on this co-expression network. RESULTS In the study, 183 DEGs were screened and 8 and 6 modules were assessed in the events group and no-events group, respectively. Compared to the no-events group, genes associated with inflammation and immune response were clustered in the green-yellow module of the events group. The hub gene of the green-yellow module of the events group was KIR2DL5A. We obtained 1 DEG co-expression network, which has 16 nodes and 24 edges, and we detected 5 crucial genes: SIRT1, THRAP3, RBM43, PEX1, and KLHDC2. The upregulated genes (THRAP3 and RBM43) showed potential diagnostic and prognostic value for the occurrence of ischemic events. CONCLUSIONS We detected 8 modules for the events group and 6 modules for the no-events group. The hub genes for modules and crucial genes of the DEG co-expression network were also identified. These genes might serve as potential targets for medical therapies and biomarkers for diagnosis and prognosis. Further experimental and biological studies are needed to elucidate the role of these crucial genes in the progression of carotid atherosclerosis.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) were screened using the “limma” R package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32160184", "locator": "sections[4] \"DEG analysis\" paragraph 2", "quote": "Differentially expressed genes (DEGs) were screened using the “limma” R package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Supplementary/raw data available from the corresponding author on request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32160184", "locator": "sections[18] \"Footnotes\" paragraph 2", "quote": "Supplementary/raw data available from the corresponding author on 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:32160184"], "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:GSE21545"], "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:GSE21545"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32160184", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.921692", "sha256": 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MCODE.", "structure": {"pmcid": "PMC7085238", "section_index": 14, "section_title": "Identification of crucial genes mediating ischemic events", "row_count": 6, "column_count": 3}, "table": {"label": "Table 3", "caption": "Crucial genes detected by MCODE.", "rows": [["Entrez ID", "Gene symbol", "Official full gene name"], ["23411", "SIRT1", "Sirtuin 1"], ["9967", "THRAP3", "Thyroid Hormone Receptor Associated Protein 3"], ["375287", "RBM43", "RNA Binding Motif Protein 43"], ["23588", "KLHDC2", "Kelch Domain Containing 2"], ["5189", "PEX1", "Peroxisomal Biogenesis Factor 1"]], "row_count": 6, "column_count": 3, "numeric_cells": 11, "header_rows": 1, "locator": "section[14]/table-wrap[1]#t3-medscimonit-26-e921692"}}, {"id": "asset:table:pmid:32160184:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:21aba4eb72122578b6d8b2704bad1e15b662a14860957022d5e1b44a6d9d8f56", "bytes": 1585, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#t4-medscimonit-26-e921692", "version": null, "note": "Top10 up-regulated and down-regulated DEGs.", "structure": {"pmcid": "PMC7085238", "section_index": 17, "section_title": "Supplementary Data", "row_count": 23, "column_count": 3}, "table": {"label": "Supplementary Table 1", "caption": "Top10 up-regulated and down-regulated DEGs.", "rows": [["Gene symbol", "Official full gene name", "log2 (fold-change) (patients with events/patients without events)"], ["Up-regulated"], ["TNFAIP6", "TNF alpha induced protein 6", "9.968020902"], ["PTX3", "Pentraxin 3", "8.826641354"], ["RNASE2", "Ribonuclease A family member 2", "7.978917622"], ["KCNJ2", "Potassium inwardly rectifying channel subfamily J member 2", "7.481378497"], ["SERPINB2", "Serpin family B member 2", "7.18837765"], ["PLA2G7", "Phospholipase A2 group VII", "6.901998631"], ["BCL2A1", "BCL2 related protein A1", "6.719719825"], 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"Platelet activation", "11", "5.10"], ["", "hsa05322", "Systemic lupus erythematosus", "13", "5.13", "", "hsa05322", "Systemic lupus erythematosus", "11", "4.98"], ["", "hsa04611", "Platelet activation", "11", "3.80", "", "hsa05034", "Alcoholism", "11", "3.94"], ["", "hsa05203", "Viral carcinogenesis", "10", "1.82", "", "hsa04512", "ECM-receptor interaction", "8", "3.83"], ["", "hsa05202", "Transcriptional misregulation in cancer", "9", "1.87", "", "hsa05203", "Viral carcinogenesis", "8", "1.71"], ["", "hsa04062", "Chemokine signaling pathway", "9", "1.62", "", "hsa04510", "Focal adhesion", "8", "1.70"], ["", "hsa04512", "ECM-receptor interaction", "6", "1.62", "", "hsa04810", "Regulation of actin cytoskeleton", "8", "1.66"], ["", "hsa04540", "Gap junction", "6", "1.60", "", "hsa04540", "Gap junction", "6", "2.20"], ["", "hsa05219", "Bladder cancer", "4", "1.38", "", "hsa04670", "Leukocyte transendothelial migration", "6", "1.73"], ["", "Blue", "", "", "", "", "hsa05410", "Hypertrophic cardiomyopathy (HCM)", "5", "1.70"], ["", "hsa01100", "Metabolic pathways", "218", "3.72", "", "hsa05414", "Dilated cardiomyopathy", "5", "1.59"], ["", "hsa05166", "HTLV-I infection", "49", "1.56", "", "hsa04640", "Hematopoietic cell lineage", "5", "1.54"], ["", "hsa04144", "Endocytosis", "48", "1.76", "", "hsa04530", "Tight junction", "5", "1.54"], ["", "hsa04141", "Protein processing in endoplasmic reticulum", "45", "4.34", "", "hsa05130", "Pathogenic Escherichia coli infection", "4", "1.52"], ["", "hsa01130", "Biosynthesis of antibiotics", "45", "2.15", "", "hsa00590", "Arachidonic acid metabolism", "4", "1.32"], ["", "hsa05016", "Huntington’s disease", "38", "1.42", "", "Green", "", "", ""], ["", "hsa04932", "Non-alcoholic fatty liver disease (NAFLD)", "36", "2.60", "", "hsa04151", "PI3K-Akt signaling pathway", "16", "1.30"], ["", "hsa05168", "Herpes simplex infection", "36", "1.33", "", "hsa04144", "Endocytosis", "15", "2.22"], ["", "hsa00190", "Oxidative phosphorylation", "31", 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reticulum", "30", "2.64"], ["", "Pink", "", "", "", "", "hsa03040", "Spliceosome", "25", "2.57"], ["", "hsa05168", "Herpes simplex infection", "8", "1.91", "", "hsa04110", "Cell cycle", "22", "1.99"], ["", "hsa04931", "Insulin resistance", "6", "1,80", "", "hsa03018", "RNA degradation", "21", "4,38"], ["", "hsa04145", "Phagosome", "7", "1,78", "", "hsa05161", "Hepatitis B", "21", "1,09"], ["", "hsa00190", "Oxidative phosphorylation", "6", "1,46", "", "hsa04114", "Oocyte meiosis", "18", "1,33"], ["", "Red", "", "", "", "", "hsa03015", "mRNA surveillance pathway", "17", "1,78"], ["", "hsa01100", "Metabolic pathways", "37", "2.07", "", "hsa04070", "Phosphatidylinositol signaling system", "17", "1.50"], ["", "hsa04114", "Oocyte meiosis", "8", "2.17", "", "hsa04668", "TNF signaling pathway", "17", "1.20"], ["", "hsa04120", "Ubiquitin mediated proteolysis", "8", "1.70", "", "hsa04066", "HIF-1 signaling pathway", "15", "1.04"], ["", "hsa04668", "TNF signaling pathway", "7", "1.69", "", "hsa04720", "Long-term potentiation", "14", "1.93"], ["", "hsa01200", "Carbon metabolism", "7", "1.59", "", "hsa04115", "p53 signaling pathway", "13", "1.51"], ["", "hsa04722", "Neurotrophin signaling pathway", "7", "1.48", "", "hsa05120", "Epithelial cell signaling in Helicobacter pylori infection", "13", "1.51"], ["", "hsa04666", "Fc gamma R-mediated phagocytosis", "6", "1.58", "", "hsa04210", "Apoptosis", "12", "1.40"], ["", "hsa05230", "Central carbon metabolism in cancer", "5", "1.41", "", "hsa00562", "Inositol phosphate metabolism", "12", "1.04"], ["", "hsa05211", "Renal cell carcinoma", "5", "1.37", "", "hsa00520", "Amino sugar and nucleotide sugar metabolism", "11", "1.75"], ["", "hsa00010", "Glycolysis / Gluconeogenesis", "5", "1.35", "", "hsa05130", "Pathogenic Escherichia coli infection", "11", "1.58"], ["", "hsa04662", "B cell receptor signaling pathway", "5", "1.31", "", "hsa05110", "Vibrio cholerae infection", "11", "1.52"], ["", "hsa00512", "Mucin type O-Glycan biosynthesis", "4", "1.63", "", "hsa00510", "N-Glycan biosynthesis", "10", "1.30"], ["", "hsa00620", "Pyruvate metabolism", "4", "1.34", "", "hsa00280", "Valine, leucine and isoleucine degradation", "9", "1.05"], ["", "Yellow", "", "", "", "", "hsa03420", "Nucleotide excision repair", "9", "1.05"], ["", "hsa05152", "Tuberculosis", "21", "4.97", "", "hsa03060", "Protein export", "8", "2.26"], ["", "hsa04142", "Lysosome", "19", "6.25", "", "hsa03430", "Mismatch repair", "6", "1.15"], ["", "hsa04145", "Phagosome", "19", "4.88", "", "Yellow", "", "", ""], ["", "hsa05164", "Influenza A", "17", "3.05", "", "hsa05166", "HTLV-I infection", "16", "2.96"], ["", "hsa05166", "HTLV-I infection", "17", "1.50", "", "hsa05152", "Tuberculosis", "11", "2.00"], ["", "hsa04380", "Osteoclast differentiation", "16", "3.92", "", "hsa04010", "MAPK signaling pathway", "11", "1.08"], ["", "hsa05162", "Measles", "15", "3.31", "", "hsa04145", "Phagosome", "10", "2.01"], ["", "hsa01130", "Biosynthesis of antibiotics", "15", "1.52", "", "hsa05168", "Herpes simplex infection", "10", "1.50"], ["", "hsa04640", "Hematopoietic cell lineage", "14", "4.68", "", "hsa05203", "Viral carcinogenesis", "10", "1.24"], ["", "hsa05140", "Leishmaniasis", "13", "4.92", "", "hsa05161", "Hepatitis B", "9", "1.64"], ["", "hsa05323", "Rheumatoid arthritis", "13", "3.96", "", "hsa05164", "Influenza A", "9", "1.24"], ["", "hsa05145", "Toxoplasmosis", "12", "2.54", "", "hsa05140", "Leishmaniasis", "8", "2.83"], ["", "hsa04064", "NF-kappa B signaling pathway", "11", "2.80", "", "hsa04660", "T cell receptor signaling pathway", "8", "2.00"], ["", "hsa05150", "Staphylococcus aureus infection", "10", "3.77", "", "hsa05169", "Epstein-Barr virus infection", "8", "1.57"], ["", "hsa04066", "HIF-1 signaling pathway", "10", "1.99", "", "hsa05162", "Measles", "8", "1.39"], ["", "hsa04620", "Toll-like receptor signaling pathway", "10", "1.72", "", "hsa04612", "Antigen processing and presentation", "7", "2.02"], ["", "hsa04612", "Antigen processing and presentation", "9", "2.11", "", "hsa05145", "Toxoplasmosis", "7", "1.32"], ["", "hsa04666", "Fc gamma R-mediated phagocytosis", "9", "1.86", "", "hsa03040", "Spliceosome", "7", "1.00"], ["", "hsa04660", "T cell receptor signaling pathway", "9", "1.45", "", "hsa05332", "Graft-versus-host disease", "6", "2.99"], ["", "hsa04672", "Intestinal immune network for IgA production", "8", "2.75", "", "hsa05330", "Allograft rejection", "6", "2.76"], ["", "hsa05134", "Legionellosis", "8", "2.40", "", "hsa04940", "Type I diabetes mellitus", "6", "2.51"], ["", "hsa05321", "Inflammatory bowel disease (IBD)", "8", "1.99", "", "hsa03050", "Proteasome", "6", "2.42"], ["", "hsa01230", "Biosynthesis of amino acids", "8", "1.73", "", "hsa05320", "Autoimmune thyroid disease", "6", "2.11"], ["", "hsa05133", "Pertussis", "8", "1.64", "", "hsa05416", "Viral myocarditis", "6", "1.94"], ["", "hsa05204", "Chemical carcinogenesis", "8", "1.50", "", "hsa05323", "Rheumatoid arthritis", "6", "1.22"], ["", "hsa00480", "Glutathione metabolism", "7", "1.92", "", "hsa05310", "Asthma", "5", "2.27"], ["", "hsa05416", "Viral myocarditis", "7", "1.69", "", "hsa04672", "Intestinal immune network for IgA production", "5", "1.59"], ["", "hsa05310", "Asthma", "6", "2.31", "", "hsa05223", "Non-small cell lung cancer", "5", "1.35"], ["", "hsa05332", "Graft-versus-host disease", "5", "1.46", "", "hsa05321", "Inflammatory bowel disease (IBD)", "5", "1.17"], ["", "hsa00920", "Sulfur metabolism", "4", "2.42", "", "hsa04662", "B cell receptor signaling pathway", "5", "1.08"], ["", "hsa00511", "Other glycan degradation", "4", "1.54", "", "hsa01230", "Biosynthesis of amino acids", "5", "1.03"], ["", "", "", "", "", "", "hsa03022", "Basal transcription factors", "4", "1.03"]], "row_count": 116, "column_count": 10, "numeric_cells": 649, "header_rows": 1, "locator": "section[22]/table-wrap[2]#db_ds_table-wrap2_reqid_"}}], "gaps": ["asset:data:geo:GSE21545 not downloaded", "asset:data:geo:GSE21545 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed genes (DEGs) were screened using the “limma” R package."}}, {"id": "method-2", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "dendrogram"}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE21545"], "resolved_accessions": ["GSE21545"], "statements": ["Supplementary/raw data available from the corresponding author on request."], "basis": "The paper names GSE21545 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32160184", "data:geo:GSE21545", "asset:table:pmid:32160184:1", "asset:table:pmid:32160184:2", "asset:table:pmid:32160184:3", "asset:table:pmid:32160184:4", "asset:table:pmid:32160184:5", "asset:table:pmid:32160184:6", "asset:table:pmid:32160184:7"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21545"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:18:38Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 44886, "completion_tokens": 877, "cached_tokens": 785}}, "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:32160184", "type": "paper", "label": "pmid:32160184"}, {"id": "source:pmid:32160184", "type": "manuscript", "label": "PMID 32160184 full text"}, {"id": "data:geo:GSE21545", "type": "dataset", "label": "GEO GSE21545"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32160184", "type": "paper", "label": "pmid:32160184"}, {"id": "source:pmid:32160184", "type": "manuscript", "label": "PMID 32160184 full text"}, {"id": "data:geo:GSE21545", "type": "dataset", "label": "GEO GSE21545"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32160184", "type": "extraction", "used": ["source:pmid:32160184"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21545", "type": "accession_resolution", "used": ["data:geo:GSE21545"], "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:32160184", "parent_hash": "sha256:6d22ef57fe02db3a54abbd83034d32b59b30569ea7332621c115ce16275ac9a0", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE21545 licence not read", "asset:data:geo:GSE21545 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes (DEGs) were screened using the “limma” R package."], "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":"2026-11-04T01:33:14+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}}}