{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33315853", "kind": "science-record", "revision": 9, "content_hash": "sha256:66a1cc807285a411e49bbe40044b77a62a1574593bbbe8c4fe3d351a5329f639", "created_at": "2026-11-01T15:41:19Z", "updated_at": "2026-11-01T22:45:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics Analysis Reveals Key Candidate Genes and Cytokine Pathways Involved in COVID-19 After Rhinovirus Infection in Asthma Patients.", "doi": "10.12659/MSM.928861", "pmid": "33315853", "authors": ["Wenjuan Dai", "Dawei Cao", "Wei Zhang", "Yangyang Wei", "Daqing Ding", "Bei Li", "Yan Gao", "Lixuan Zhao", "Yi Jiang", "Xiaomei Kong"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2020, "abstract": "BACKGROUND Rhinovirus (RV) is the most common pathogen involved in asthma, and COVID-19, caused by SARS-COV-2, may be more severe in asthma patients. Here, we applied integrated bioinformatics to identify potential key genes and cytokine pathways after RV infection in asthma, and analyzed changes in angiotensin-converting enzyme 2 (ACE2), the cellular receptor of SARS-COV-2. MATERIAL AND METHODS The gene expression profile dataset GSE149273 was downloaded from NCBI-GEO, which included 90 samples of non-infected, RVA, and RVC. Differentially expressed genes (DEGs) were identified using t tests in the limma R package, and subsequently investigated by GO, KEGG, and DO analysis. Moreover, the expression of ACE2 and the proportion of immune cells were further analyzed to determine the effects of RV on cytokines. RESULTS A total of 555 DEGs of RVA and 421 of RVC were identified. There were 415 DEGs in RVA and RVC, of which 406 were upregulated and 9 were downregulated. The functional enrichment analysis showed that most DEGs were obviously enriched in cytokines, and were mainly enriched in \"influenza\" and \"hepatitis C, chronic\". In addition, the expression of ACE2 increased significantly and the proportion of immune cytokines significantly changed after RV infection. Our results suggest that RV can activate the cytokine pathway associated with COVID-19 by increasing ACE2. CONCLUSIONS The DEGs and related cytokine pathways after asthma RV infection identified using integrated bioinformatics in this study elucidate the potential link between RV and COVID-19.", "claims": [{"id": "claim-method", "statement": "The t test method in the limma R package was subsequently used to identify DEGs between RVA and RVC infected samples and non-infected samples, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33315853", "locator": "sections[4] \"Expression analysis of DEGs\" paragraph 2", "quote": "The t test method in the limma R package was subsequently used to identify DEGs between RVA and RVC infected samples and non-infected samples, respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE149273 profile dataset was downloaded from the NCBI-GEO database (https://www.ncbi.nlm.nih.gov/geo/). The platform for GSE149273 is GPL21290 Illumina HiSeq 3000 (Homo sapiens), which includes 90 samples from 30 asthma patients with non-infection, RVA, and RVC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33315853", "locator": "sections[3] \"Dataset sources\" paragraph 2", "quote": "The GSE149273 profile dataset was downloaded from the NCBI-GEO database (https://www.ncbi.nlm.nih.gov/geo/). The platform for GSE149273 is GPL21290 Illumina HiSeq 3000 (Homo sapiens), which includes 90 samples from 30 asthma patients with non-infection, RVA, and RVC."}], "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:33315853"], "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:GSE149273"], "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:GSE149273"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33315853", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.928861", "sha256": "sha256:4d8184b6c29d993758f8cf30f250c3ba74d3a2df558224c97949b79b3efffb6f", "bytes": 29375, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.928861", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7747473", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE149273", "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=GSE149273", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE149273", "version": null, "note": "The GSE149273 profile dataset was downloaded from the NCBI-GEO database (https://www.ncbi.nlm.nih.gov/geo/). 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"GSM4495331", "GSM4495332", "GSM4495333", "GSM4495334", "GSM4495335", "GSM4495336", "GSM4495337", "GSM4495338", "GSM4495339", "GSM4495340", "GSM4495341", "GSM4495342", "GSM4495343", "GSM4495344", "GSM4495345", "GSM4495346", "GSM4495347", "GSM4495348", "GSM4495349", "GSM4495350", "GSM4495351", "GSM4495352", "GSM4495353", "GSM4495354", "GSM4495355", "GSM4495356", "GSM4495357", "GSM4495358", "GSM4495359", "GSM4495360", "GSM4495361", "GSM4495362", "GSM4495363", "GSM4495364", "GSM4495365", "GSM4495366"], "sample_count": 90, "group_sizes": null, "group_sizes_basis": null, "platform": "21290", "taxon": "Homo sapiens", "title": "RV infections in asthmatics increase ACE2 expression and stimulate cytokine pathways implicated in COVID19", "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:33315853:1", "role": "table", "format": "jats-table", 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IFIH1, ZC3HAV1, PARP10, TRIM21, DDX60, PARP14, IFITM1, NMI, SLC25A28, ISG20, ETV7, STAT2, NLRC5, TRIM5, MYD88, TDRD7, SMCHD1, XRN1, TRIM22, PHF11, SAMD9, GTPBP2, RNF213, NT5C3A, LAP3, ZCCHC2, FAM46A, IFI44L, TREX1, SCO2, GTPBP1, PML, FBXO6, TOR1B, PLEKHA4, UBA7, AIM2, TNFSF10, TAP1, NUB1, GBP4, LMO2, MOV10, APOL6, TAPSAR1, GBP1, SCAMP1-AS1, STARD5, EIF2AK2, N4BP1, BST2, TYMP, IFITM3, IRF9, HELZ2, RNF19B, HLA-E, MOB3C, LGALS9, CNP, SPATS2L, ZNFX1, GMPR, OPTN, CXCL10, C5orf56, RBCK1, APOBEC3G, HDX, CSRNP1, SECTM1, PRKD2, PSMB8, FBXO39, TTC39B, PSMB9, WARS, IRF1, BATF2, TRIM38, LGALS17A, LY6E, IFI6, JAK2, CLEC7A, SAMHD1, SP140L, EXOC3L1, PI4K2B, NUPR1, SIDT1, PCGF5, IFNL3, CASP1, ACSL1, EHD4, CD68, TAP2, SLFN5, TLR3, LOC101927027, TRIB2, LIFR, GRIP2, ACE2, MASTL, BCL2L14, TRAFD1, PRICKLE4, APOL2, BCL3, GBP5, BTC, PIK3AP1, SLC15A3, NFE2L3, ZBP1, ZFYVE26, RASGRP3, TMEM140, ZC3H12A, KIAA1551, CTRL, MLKL, NFKBIA, LYSMD2, MAB21L2, GNB4, C17orf67, GBP1P1, DUOX2, PMAIP1, USP30-AS1, SOD2, CIITA, OGFR, LYPD5, APOBEC3A, IFNL1, AKAP7, ACKR4, TNFAIP3, RBMS2, HESX1, HTR2B, MXD1, IL4I1, BLZF1, DUOXA2, NCOA7, RBM11, HRASLS2, SUSD3, FGD2, CCL5, IFI27, TICAM1, CCDC109B, APOBEC3F, GCH1, IL22RA1, TNFSF13B, C19orf38, IKBKE, IFNL2, CASP10, LRRN2, PPM1K, CD7, APOL3, IRAK2, NFKBIZ, UBQLNL, C21orf91, IL7, HLA-F, CD38, RELB, GCNT4, RHBDF2, CX3CL1, CD83, TNFRSF6B, PPM1J, TAGAP, BTN3A3, TMEM229B, FFAR2, CARD16, SOCS1, STX11, OVOL1, IL19, BIRC3, GLRX, CPNE5, MAFF, CXorf49, CXorf49B, CEACAM1, SEC16B, PRDM1, ADCY4, ATF3, LINC00623, TLR2, IFITM2, NRG2, BBC3, SOCS3, KIAA0226, CXCL11, CXCL9, IL15RA, LAG3, STARD4, IDO1, SOCS2, ICOSLG, C1GALT1, FANCA, KCNQ4, NCF1, C10orf105, AP5B1, TMEM171, GBP2, HK2, BRIP1, RAB43, MUC13, IFI30, NCF1C, SP140, HAPLN3, ARID5A, SLC16A1, CD274, KLHDC7B, CACNA1A, CSF3, MAP2, CCL20, TMEM106A, SERPING1, TNFAIP2, CLCA3P, TNIP3, DLG2, CXCL8, MAPK8IP2, IL17C, PLAUR, NEURL3, PROX1, APOBEC3B, TNF, MB21D1, THEMIS2, FRMD3, HBEGF, BRCA2, DUXAP10, TMEM92, DUSP5, EXOC3L4, APOL4, C11orf82, RIMS2, C15orf48, C2CD4B, NOV, ADAM8, SLFN12, MICB, GBP3, GRIN3A, C1R, LOC102724163, SEMA3D, IL2RG, LOC645638, FGF2, FAM169B, LOC100294362, MT2A, ABCD1, ZNF618, LRRC3, SAA4, CYP21A1P, SLC26A4-AS1, SERPINB9, SERPINB9P1, BATF, LOC388692, TLDC2, IL36G, PRRX2, TGM1, ELOVL7, CXCL3, TNFRSF10A, RTKN2, CCL22, HDAC9, ATP10A, IL6, SBK1, BCL2A1, DOC2B, C2CD4A, C1S, ADM, HCG4B, PTPRH, HCAR3, PDCD1LG2, C8orf4, CXCL2, STS, RET, NOS2, SLC26A4, SLCO4A1, SELL, NTNG2, HLA-J, RND1, CFB, XDH, MMP13, TRIM31, SAA2, SPRR2A, PTGS2, MTNR1A, AKAP2, ACHE, DEFB4A, ICAM1, EREG, SPRR2F, CH25H, IL1RN, NEXN, CSF1, HSPA6, LOC554223, APOL1, SLAMF7, LIF, MEF2C, SSC5D, TGM2, ZDHHC14, CXCL13, ERAP2, ANGPTL4, SH2D1B, THSD1, PLA2G4E"], ["Downregulated", "C20orf195, FAM13C, HPX, INHBB, GPATCH11, PTGFR, PRR18, SLC16A14, SLC47A2"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[8]/table-wrap[1]#t1-medscimonit-26-e928861"}}, {"id": "asset:table:pmid:33315853:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:08cc4c06ea5d4eed0f58bfce0058233eed081ed3837bccebe807f8a351ef1212", "bytes": 1637, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#t2-medscimonit-26-e928861", "version": null, "note": "GO functional annotation for the most significantly related targets of 415 DEGs.", "structure": {"pmcid": "PMC7747473", "section_index": 9, "section_title": "Functional enrichment analysis", "row_count": 23, "column_count": 4}, "table": {"label": "Table 2", "caption": "GO functional annotation for the most significantly related targets of 415 DEGs.", "rows": [["GO ID", "GO Term", "Count", "P-value"], ["BP"], ["GO: 0009615", "Response to virus", "75", "9.27E-60"], ["GO: 0051607", "Defense response to virus", "67", "1.20E-59"], ["GO: 0034341", "Response to interferon-gamma", "51", "5.09E-43"], ["GO: 0060337", "Type I interferon signaling pathway", "38", "1.25E-40"], ["GO: 0071357", "Cellular response to type i interferon", "38", "1.25E-40"], ["GO: 0034340", "Response to type i interferon", "38", "8.46E-40"], ["GO: 0071346", "Cellular response to interferon-gamma", "45", "1.81E-37"], ["GO: 0048525", "Negative regulation of viral process", "33", "2.80E-32"], ["GO: 0060333", "Interferon-gamma-mediated signaling pathway", "32", "3.39E-32"], ["GO: 1903901", "Negative regulation of viral life cycle", "31", "8.43E-32"], ["MF"], ["GO: 0005125", "Cytokine activity", "29", "1.03E-15"], ["GO: 0048018", "Receptor ligand activity", "39", "1.62E-13"], ["GO: 0005126", "Cytokine receptor binding", "29", "9.81E-13"], ["GO: 0042379", "Chemokine receptor binding", "13", "5.95E-10"], ["GO: 0008009", "Chemokine activity", "11", "2.92E-09"], ["GO: 0045236", "CXCR chemokine receptor binding", "6", "2.79E-08"], ["GO: 0003725", "Double-stranded RNA binding", "12", "3.25E-08"], ["GO: 0016814", "Hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines", "7", "4.39E-06"], ["GO: 0042056", "Chemoattractant activity", "7", "9.61E-06"], ["GO: 0048020", "CCR chemokine receptor binding", "7", "2.25E-05"]], "row_count": 23, "column_count": 4, "numeric_cells": 60, "header_rows": 1, "locator": "section[9]/table-wrap[1]#t2-medscimonit-26-e928861"}}, {"id": "asset:table:pmid:33315853:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1ab9fe2c14fc59367c9c193f87f770f3faae42816742f246a401aae46d3242d7", "bytes": 2121, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#t3-medscimonit-26-e928861", "version": null, "note": "KEGG functional annotation for 415 DEGs.", "structure": {"pmcid": "PMC7747473", "section_index": 9, "section_title": "Functional enrichment analysis", "row_count": 33, "column_count": 4}, "table": {"label": "Table 3", "caption": "KEGG functional annotation for 415 DEGs.", "rows": [["KEGG ID", "KEGG Term", "Count", "P-value"], ["hsa05164", "Influenza A", "33", "4.44E-20"], ["hsa04621", "NOD-like receptor signaling pathway", "30", "2.20E-16"], ["hsa04060", "Cytokine-cytokine receptor interaction", "34", "1.28E-13"], ["hsa04061", "Viral protein interaction with cytokine and cytokine receptor", "20", "7.62E-13"], ["hsa04668", "TNF signaling pathway", "20", "7.04E-12"], ["hsa05162", "Measles", "22", "7.43E-12"], ["hsa05169", "Epstein-Barr virus infection", "24", "3.95E-10"], ["hsa05160", "Hepatitis C", "20", "3.30E-09"], ["hsa04064", "NF-kappa B signaling pathway", "16", "9.32E-09"], ["hsa04657", "IL-17 signaling pathway", "15", "1.65E-08"], ["hsa05167", "Kaposi sarcoma-associated herpesvirus infection", "21", "1.77E-08"], ["hsa04630", "JAK-STAT signaling pathway", "19", "3.65E-08"], ["hsa04623", "Cytosolic DNA-sensing pathway", "12", "6.12E-08"], ["hsa04620", "Toll-like receptor signaling pathway", "15", "6.73E-08"], ["hsa04622", "RIG-I-like receptor signaling pathway", "12", "2.08E-07"], ["hsa04625", "C-type lectin receptor signaling pathway", "14", "4.49E-07"], ["hsa04217", "Necroptosis", "17", "7.52E-07"], ["hsa05134", "Legionellosis", "10", "1.77E-06"], ["hsa04062", "Chemokine signaling pathway", "18", "1.94E-06"], ["hsa05133", "Pertussis", "11", "3.86E-06"], ["hsa05161", "Hepatitis B", "16", "4.60E-06"], ["hsa05168", "Herpes simplex virus 1 infection", "29", "2.77E-05"], ["hsa05323", "Rheumatoid arthritis", "11", "2.78E-05"], ["hsa05170", "Human immunodeficiency virus 1 infection", "16", "0.000129"], ["hsa05145", "Toxoplasmosis", "11", "0.000155"], ["hsa05140", "Leishmaniasis", "9", "0.000166"], ["hsa05144", "Malaria", "7", "0.000289"], ["hsa05143", "African trypanosomiasis", "6", "0.00035"], ["hsa05235", "PD-L1 expression and PD-1 checkpoint pathway in cancer", "9", "0.000498"], ["hsa04612", "Antigen processing and presentation", "8", "0.000928"], ["hsa04930", "Type II diabetes mellitus", "6", "0.00116"], ["hsa05142", "Chagas disease (American trypanosomiasis)", "9", "0.001339"]], "row_count": 33, "column_count": 4, "numeric_cells": 100, "header_rows": 1, "locator": "section[9]/table-wrap[2]#t3-medscimonit-26-e928861"}}], "gaps": ["asset:data:geo:GSE149273 not downloaded", "asset:data:geo:GSE149273 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": "The t test method in the limma R package was subsequently used to identify DEGs between RVA and RVC infected samples and non-infected samples, respectively."}}], "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": ["GSE149273"], "resolved_accessions": ["GSE149273"], "statements": ["The GSE149273 profile dataset was downloaded from the NCBI-GEO database (https://www.ncbi.nlm.nih.gov/geo/). The platform for GSE149273 is GPL21290 Illumina HiSeq 3000 (Homo sapiens), which includes 90 samples from 30 asthma patients with non-infection, RVA, and RVC."], "basis": "The paper names GSE149273 in NCBI-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:33315853", "data:geo:GSE149273", "asset:table:pmid:33315853:1", "asset:table:pmid:33315853:2", "asset:table:pmid:33315853:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE149273"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:02Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 23250, "completion_tokens": 847, "cached_tokens": 520}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33315853", "type": "paper", "label": "pmid:33315853"}, {"id": "source:pmid:33315853", "type": "manuscript", "label": "PMID 33315853 full text"}, {"id": "data:geo:GSE149273", "type": "dataset", "label": "GEO GSE149273"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33315853", "type": "paper", "label": "pmid:33315853"}, {"id": "source:pmid:33315853", "type": "manuscript", "label": "PMID 33315853 full text"}, {"id": "data:geo:GSE149273", "type": "dataset", "label": "GEO GSE149273"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33315853", "type": "extraction", "used": ["source:pmid:33315853"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE149273", "type": "accession_resolution", "used": ["data:geo:GSE149273"], "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:33315853", "parent_hash": "sha256:1df1c969fb3fe526f7f341755d354d990904ccde3b33fab7178d30fefd095f97", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE149273 licence not read", "asset:data:geo:GSE149273 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": ["The t test method in the limma R package was subsequently used to identify DEGs between RVA and RVC infected samples and non-infected samples, respectively."], "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":"2026-11-04T02:16:43+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}}}