Machine learning and bioinformatics analysis to identify autophagy-related biomarkers in peripheral blood for rheumatoid arthritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37779906", "kind": "science-record", "revision": 5, "content_hash": "sha256:85291049cffb67188b5404e872b7a4abe03597155ca7ef4180e788841419f0a5", "created_at": "2026-11-01T19:02:37Z", "updated_at": "2026-11-01T22:52:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Machine learning and bioinformatics analysis to identify autophagy-related biomarkers in peripheral blood for rheumatoid arthritis.", "doi": "10.3389/fgene.2023.1238407", "pmid": "37779906", "authors": ["Guoqi Dong", "Hui Gao", "Yingqi Chen", "Huayuan Yang"], "journal": "Frontiers in genetics", "year": 2023, "abstract": "Background: Although rheumatoid arthritis (RA) is a common autoimmune disease, the precise pathogenesis of the disease remains unclear. Recent research has unraveled the role of autophagy in the development of RA. This research aims to explore autophagy-related diagnostic biomarkers in the peripheral blood of RA patients. Methods: The gene expression profiles of GSE17755 were retrieved from the gene expression ontology (GEO) database. Differentially expressed autophagy-related genes (DE-ARGs) were identified for the subsequent research by inserting autophagy-related genes and differentially expressed genes (DEGs). Three machine learning algorithms, including random forest, support vector machine recursive feature elimination (SVM-RFE), and least absolute shrinkage and selection operator (LASSO), were employed to identify diagnostic biomarkers. A nomogram model was constructed to assess the diagnostic value of the biomarkers. The CIBERSORT algorithm was performed to investigate the correlation of the diagnostic biomarkers with immune cells and immune factors. Finally, the diagnostic efficacy and differential expression trend of diagnostic biomarkers were validated in multiple cohorts containing different tissues and diseases. Results: In this study, 25 DE-ARGs were identified between RA and healthy individuals. In addition to \"macroautophagy\" and \"autophagy-animal,\" DE-ARGs were also associated with several types of programmed cell death and immune-related pathways according to GO and KEGG analysis. Three diagnostic biomarkers, EEF2, HSP90AB1 and TNFSF10, were identified by the random forest, SVM-RFE, and LASSO. The nomogram model demonstrated excellent diagnostic value in GSE17755 (AUC = 0.995, 95% CI: 0.988-0.999). Furthermore, immune infiltration analysis showed a remarkable association between EEF2, HSP90AB1, and TNFSF10 expression with various immune cells and immune factors. The three diagnostic biomarkers also exhibited good diagnostic efficacy and demonstrated the same trend of differential expression in multiple validation cohorts. Conclusion: This study identified autophagy-related diagnostic biomarkers based on three machine learning algorithms, providing promising targets for the diagnosis and treatment of RA.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed by the “limma” package (version 3.56.1) with the following threshold: p_adj < 0.05 and abs (logFC) > 0.45.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37779906", "locator": "sections[4] \"2.2 Identification of differentially expressed autophagy-related genes (DE-ARGs)\" paragraph 2", "quote": "Differential expression analysis was performed by the “limma” package (version 3.56.1) with the following threshold: p_adj < 0.05 and abs (logFC) > 0.45."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37779906", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The nomogram model demonstrated excellent diagnostic value in GSE17755 (AUC = 0.995, 95% CI: 0.988–0.999).", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "The nomogram model demonstrated excellent diagnostic value in GSE17755 (AUC = 0.995, 95% CI: 0.988–0.999)."}, "evidence": [{"asset": "source:pmid:37779906", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The nomogram model demonstrated excellent diagnostic value in GSE17755 (AUC = 0.995, 95% CI: 0.988–0.999)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The nomogram model demonstrated excellent diagnostic value in GSE17755 (AUC = 0.995, 95% CI: 0.988–0.999).", "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:37779906"], "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:GSE100191"], "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:GSE100191"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37779906", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2023.1238407", "sha256": "sha256:bd0de59a2a178e9afa3dbaad3455148524f327b2405a6fcf1c3ecff55e1b9fa3", "bytes": 45496, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2023.1238407", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10533932", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100191", "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=GSE100191", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100191", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2674341", "GSM2674342", "GSM2674343", "GSM2674344", "GSM2674345", "GSM2674346", "GSM2674347", "GSM2674348", "GSM2674349", "GSM2674350", "GSM2674351", "GSM2674352", "GSM2674353", "GSM2674354", "GSM2674355", "GSM2674356", "GSM2674357", "GSM2674358", "GSM2674359"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "13497", "taxon": "Homo sapiens", "title": "Transcriptional Signature Associated with Early Rheumatoid Arthritis and Healthy Individuals at high risk to develop the disease.", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE12021", "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=GSE12021", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12021", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM302859", "GSM302864", "GSM302866", "GSM302870", "GSM302872", "GSM302874", "GSM302876", "GSM302878", "GSM302880", "GSM302881", "GSM302882", "GSM302895", "GSM302896", "GSM302897", "GSM302900", "GSM302905", "GSM302924", "GSM302926", "GSM302927", "GSM302929", "GSM302930", "GSM302932", "GSM302933", "GSM302934", "GSM302943", "GSM302944", "GSM303326", "GSM303339", "GSM303341", "GSM303355", "GSM303356", "GSM303357", "GSM303358", "GSM303359", "GSM303360", "GSM303361", "GSM303362", "GSM303363", "GSM303364", "GSM303365", "GSM303366", "GSM303367", "GSM303368", "GSM303369", "GSM303370", "GSM303377", "GSM303520", "GSM303521", "GSM303522", "GSM303523", "GSM303524", "GSM303525", "GSM303530", "GSM303531", "GSM303532", "GSM303533", "GSM303534"], "sample_count": 57, "group_sizes": null, "group_sizes_basis": null, "platform": "96;97", "taxon": "Homo sapiens", "title": "Identification of inter-individual and gene-specific variances in mRNA expression profiles in the RA SM", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE17755", "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=GSE17755", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17755", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM443237", "GSM443238", "GSM443239", "GSM443240", "GSM443241", "GSM443242", "GSM443243", "GSM443244", "GSM443245", "GSM443246", "GSM443247", "GSM443248", "GSM443249", "GSM443250", "GSM443251", "GSM443252", "GSM443253", "GSM443254", "GSM443255", "GSM443256", "GSM443257", "GSM443258", "GSM443259", "GSM443260", "GSM443261", "GSM443262", "GSM443263", "GSM443264", "GSM443265", "GSM443266", "GSM443267", "GSM443268", "GSM443269", "GSM443270", "GSM443271", "GSM443272", "GSM443273", "GSM443274", "GSM443275", "GSM443276", "GSM443277", "GSM443278", "GSM443279", "GSM443280", "GSM443281", "GSM443282", "GSM443283", "GSM443284", "GSM443285", "GSM443286", "GSM443287", "GSM443288", "GSM443289", "GSM443290", "GSM443291", "GSM443292", "GSM443293", "GSM443294", "GSM443295", "GSM443296", "GSM443297", "GSM443298", "GSM443299", "GSM443300", "GSM443301", "GSM443302", "GSM443303", "GSM443304", "GSM443305", "GSM443306", "GSM443307", "GSM443308", "GSM443309", "GSM443310", "GSM443311", "GSM443312", "GSM443313", "GSM443314", "GSM443315", "GSM443316", "GSM443317", "GSM443318", "GSM443319", "GSM443320", "GSM443321", "GSM443322", "GSM443324", "GSM443325", "GSM443326", "GSM443327", "GSM443328", "GSM443329", "GSM443330", "GSM443331", "GSM443332", "GSM443333", "GSM443334", "GSM443335", "GSM443336", "GSM443337", "GSM443338", "GSM443339", "GSM443340", "GSM443341", "GSM443342", "GSM443343", "GSM443344", "GSM443345", "GSM443346", "GSM443347", "GSM443348", "GSM443349", "GSM443350", "GSM443351", "GSM443352", "GSM443353", "GSM443354", "GSM443355", "GSM443356", "GSM443357", "GSM443358", "GSM443359", "GSM443360", "GSM443361", "GSM443362", "GSM443363", "GSM443364", "GSM443365", "GSM443366", "GSM443367", "GSM443368", "GSM443369", "GSM443370", "GSM443371", "GSM443372", "GSM443373", "GSM443374", "GSM443375", "GSM443376", "GSM443377", "GSM443378", "GSM443379", "GSM443380", "GSM443381", "GSM443382", "GSM443383", "GSM443384", "GSM443385", "GSM443386", "GSM443387", "GSM443388", "GSM443389", "GSM443390", "GSM443391", "GSM443392", "GSM443393", "GSM443394", "GSM443395", "GSM443396", "GSM443397", "GSM443398", "GSM443399", "GSM443400", "GSM443401", "GSM443402", "GSM443403", "GSM443404", "GSM443405", "GSM443406", "GSM443407", "GSM443408", "GSM443409", "GSM443410", "GSM443411", "GSM443412", "GSM443413", "GSM443414", "GSM443415", "GSM443416", "GSM443417", "GSM443418", "GSM443419", "GSM443420", "GSM443421", "GSM443422", "GSM443423", "GSM443424", "GSM443425", "GSM443426", "GSM443427", "GSM443428", "GSM443429", "GSM443430", "GSM443431", "GSM443432", "GSM443433", "GSM443434", "GSM443435", "GSM443436", "GSM443437", "GSM443438", "GSM443439", "GSM443440", "GSM443441", "GSM443442", "GSM443443", "GSM443444", "GSM443445", "GSM443446", "GSM443447", "GSM443448", "GSM443449", "GSM443450", "GSM443451", "GSM443452", "GSM443453", "GSM443454", "GSM443455", "GSM443456", "GSM443457", "GSM443458", "GSM443459", "GSM443460", "GSM443461", "GSM443462", "GSM443463", "GSM443464", "GSM443465", "GSM443466", "GSM443467", "GSM443468", "GSM443469", "GSM443470", "GSM443471", "GSM521769", "GSM521770", "GSM521771", "GSM521772", "GSM521773", "GSM521774", "GSM521775", "GSM521776", "GSM521777", "GSM521778"], "sample_count": 244, "group_sizes": null, "group_sizes_basis": null, "platform": "1291", "taxon": "Homo sapiens", "title": "Human peripheral blood cells: autoimmune diseases vs. healthy individuals", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE205962", "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=GSE205962", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE205962", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM6236060", "GSM6236061", "GSM6236062", "GSM6236063", "GSM6236064", "GSM6236065", "GSM6236066", "GSM6236067", "GSM6236068", "GSM6236069", "GSM6236070", "GSM6236071", "GSM6236072", "GSM6236073", "GSM6236074", "GSM6236075", "GSM6236076", "GSM6236077", "GSM6236078", "GSM6236079"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "16043", "taxon": "Homo sapiens", "title": "Expression data from whole blood sample of eight kinds of TCM syndromes of rheumatoid arthritis patients.", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE39340", "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=GSE39340", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39340", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM966252", "GSM966253", "GSM966254", "GSM966255", "GSM966256", "GSM966257", "GSM966258", "GSM966259", "GSM966260", "GSM966261", "GSM966262", "GSM966263", "GSM966264", "GSM966265", "GSM966266", "GSM966267", "GSM966268", "GSM966269", "GSM966270", "GSM966271", "GSM966272", "GSM966273"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Indentification of special gene expressions in synovial tissues of rheumatoid arthritis", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE55235", "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=GSE55235", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE55235", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1332201", "GSM1332202", "GSM1332203", "GSM1332204", "GSM1332205", "GSM1332206", "GSM1332207", "GSM1332208", "GSM1332209", "GSM1332210", "GSM1332211", "GSM1332212", "GSM1332213", "GSM1332214", "GSM1332215", "GSM1332216", "GSM1332217", "GSM1332218", "GSM1332219", "GSM1332220", "GSM1332221", "GSM1332222", "GSM1332223", "GSM1332224", "GSM1332225", "GSM1332226", "GSM1332227", "GSM1332228", "GSM1332229", "GSM1332230"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE89408", "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=GSE89408", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE89408", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2370970", "GSM2370971", "GSM2370972", "GSM2370973", "GSM2370974", "GSM2370975", "GSM2370976", "GSM2370977", "GSM2370978", "GSM2370979", "GSM2370980", "GSM2370981", "GSM2370982", "GSM2370983", "GSM2370984", "GSM2370985", "GSM2370986", "GSM2370987", "GSM2370988", "GSM2370989", "GSM2370990", "GSM2370991", "GSM2370992", "GSM2370993", "GSM2370994", "GSM2370995", "GSM2370996", "GSM2370997", "GSM2370998", "GSM2370999", "GSM2371000", "GSM2371001", "GSM2371002", "GSM2371003", "GSM2371004", "GSM2371005", "GSM2371006", "GSM2371007", "GSM2371008", "GSM2371009", "GSM2371010", "GSM2371011", "GSM2371012", "GSM2371013", "GSM2371014", "GSM2371015", "GSM2371016", "GSM2371017", "GSM2371018", "GSM2371019", "GSM2371020", "GSM2371021", "GSM2371022", "GSM2371023", "GSM2371024", "GSM2371025", "GSM2371026", "GSM2371027", "GSM2371028", "GSM2371029", "GSM2371030", "GSM2371031", "GSM2371032", "GSM2371033", "GSM2371034", "GSM2371035", "GSM2371036", "GSM2371037", "GSM2371038", "GSM2371039", "GSM2371040", "GSM2371041", "GSM2371042", "GSM2371043", "GSM2371044", "GSM2371045", "GSM2371046", "GSM2371047", "GSM2371048", "GSM2371049", "GSM2371050", "GSM2371051", "GSM2371052", "GSM2371053", "GSM2371054", "GSM2371055", "GSM2371056", "GSM2371057", "GSM2371058", "GSM2371059", "GSM2371060", "GSM2371061", "GSM2371062", "GSM2371063", "GSM2371064", "GSM2371065", "GSM2371066", "GSM2371067", "GSM2371068", "GSM2371069", "GSM2371070", "GSM2371071", "GSM2371072", "GSM2371073", "GSM2371074", "GSM2371075", "GSM2371076", "GSM2371077", "GSM2371078", "GSM2371079", "GSM2371080", "GSM2371081", "GSM2371082", "GSM2371083", "GSM2371084", "GSM2371085", "GSM2371086", "GSM2371087", "GSM2371088", "GSM2371089", "GSM2371090", "GSM2371091", "GSM2371092", "GSM2371093", "GSM2371094", "GSM2371095", "GSM2371096", "GSM2371097", "GSM2371098", "GSM2371099", "GSM2371100", "GSM2371101", "GSM2371102", "GSM2371103", "GSM2371104", "GSM2371105", "GSM2371106", "GSM2371107", "GSM2371108", "GSM2371109", "GSM2371110", "GSM2371111", "GSM2371112", "GSM2371113", "GSM2371114", "GSM2371115", "GSM2371116", "GSM2371117", "GSM2371118", "GSM2371119", "GSM2371120", "GSM2371121", "GSM2371122", "GSM2371123", "GSM2371124", "GSM2371125", "GSM2371126", "GSM2371127", "GSM2371128", "GSM2371129", "GSM2371130", "GSM2371131", "GSM2371132", "GSM2371133", "GSM2371134", "GSM2371135", "GSM2371136", "GSM2371137", "GSM2371138", "GSM2371139", "GSM2371140", "GSM2371141", "GSM2371142", "GSM2371143", "GSM2371144", "GSM2371145", "GSM2371146", "GSM2371147", "GSM2371148", "GSM2371149", "GSM2371150", "GSM2371151", "GSM2371152", "GSM2371153", "GSM2371154", "GSM2371155", "GSM2371156", "GSM2371157", "GSM2371158", "GSM2371159", "GSM2371160", "GSM2371161", "GSM2371162", "GSM2371163", "GSM2371164", "GSM2371165", "GSM2371166", "GSM2371167", "GSM2371168", "GSM2371169", "GSM2371170", "GSM2371171", "GSM2371172", "GSM2371173", "GSM2371174", "GSM2371175", "GSM2371176", "GSM2371177", "GSM2371178", "GSM2371179", "GSM2371180", "GSM2371181", "GSM2371182", "GSM2371183", "GSM2371184", "GSM2371185", "GSM2371186", "GSM2371187"], "sample_count": 218, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "RNAseq study of synovial biopsies", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE93272", "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=GSE93272", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE93272", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2449608", "GSM2449609", "GSM2449610", "GSM2449611", "GSM2449612", "GSM2449613", "GSM2449614", "GSM2449615", "GSM2449616", "GSM2449617", "GSM2449618", "GSM2449619", "GSM2449620", "GSM2449621", "GSM2449622", "GSM2449623", "GSM2449624", "GSM2449625", "GSM2449626", "GSM2449627", "GSM2449628", "GSM2449629", "GSM2449630", "GSM2449631", "GSM2449632", "GSM2449633", "GSM2449634", "GSM2449635", "GSM2449636", "GSM2449637", "GSM2449638", "GSM2449639", "GSM2449640", "GSM2449641", "GSM2449642", "GSM2449643", "GSM2449644", "GSM2449645", "GSM2449646", "GSM2449647", "GSM2449648", "GSM2449649", "GSM2449650", "GSM2449651", "GSM2449652", "GSM2449653", "GSM2449654", "GSM2449655", "GSM2449656", "GSM2449657", "GSM2449658", "GSM2449659", "GSM2449660", "GSM2449661", "GSM2449662", "GSM2449663", "GSM2449664", "GSM2449665", "GSM2449666", "GSM2449667", "GSM2449668", "GSM2449669", "GSM2449670", "GSM2449671", "GSM2449672", "GSM2449673", "GSM2449674", "GSM2449675", "GSM2449676", "GSM2449677", "GSM2449678", "GSM2449679", "GSM2449680", "GSM2449682", "GSM2449683", "GSM2449684", "GSM2449685", "GSM2449686", "GSM2449687", "GSM2449688", "GSM2449689", "GSM2449690", "GSM2449691", "GSM2449692", "GSM2449693", "GSM2449694", "GSM2449695", "GSM2449696", "GSM2449697", "GSM2449698", "GSM2449699", "GSM2449700", "GSM2449701", "GSM2449702", "GSM2449703", "GSM2449704", "GSM2449705", "GSM2449706", "GSM2449707", "GSM2449708", "GSM2449709", "GSM2449710", "GSM2449711", "GSM2449712", "GSM2449713", "GSM2449714", "GSM2449715", "GSM2449716", "GSM2449717", "GSM2449718", "GSM2449719", "GSM2449720", "GSM2449721", "GSM2449722", "GSM2449723", "GSM2449724", "GSM2449725", "GSM2449726", "GSM2449727", "GSM2449728", "GSM2449729", "GSM2449730", "GSM2449731", "GSM2449732", "GSM2449733", "GSM2449734", "GSM2449735", "GSM2449736", "GSM2449737", "GSM2449738", "GSM2449739", "GSM2449740", "GSM2449741", "GSM2449742", "GSM2449743", "GSM2449744", "GSM2449745", "GSM2449746", "GSM2449747", "GSM2449748", "GSM2449749", "GSM2449750", "GSM2449751", "GSM2449752", "GSM2449753", "GSM2449754", "GSM2449755", "GSM2449756", "GSM2449757", "GSM2449758", "GSM2449759", "GSM2449760", "GSM2449761", "GSM2449762", "GSM2449763", "GSM2449764", "GSM2449765", "GSM2449766", "GSM2449767", "GSM2449768", "GSM2449769", "GSM2449770", "GSM2449771", "GSM2449772", "GSM2449773", "GSM2449774", "GSM2449775", "GSM2449776", "GSM2449777", "GSM2449778", "GSM2449779", "GSM2449780", "GSM2449781", "GSM2449782", "GSM2449783", "GSM2449784", "GSM2449785", "GSM2449786", "GSM2449789", "GSM2449790", "GSM2449791", "GSM2449792", "GSM2449793", "GSM2449794", "GSM2449795", "GSM2449796", "GSM2449797", "GSM2449798", "GSM2449799", "GSM2449800", "GSM2449801", "GSM2449802", "GSM2449803", "GSM2449804", "GSM2449805", "GSM2449806", "GSM2449807", "GSM2449808", "GSM2449809", "GSM2449810", "GSM2449811", "GSM2449812", "GSM2449813", "GSM2449814", "GSM2449815", "GSM2449816", "GSM2449817", "GSM2449818", "GSM2449819", "GSM2449820", "GSM2449821", "GSM2449822", "GSM2449823", "GSM2449824", "GSM2449825", "GSM2449826", "GSM2449827", "GSM2449828", "GSM2449829", "GSM2449830", "GSM2449831", "GSM2449832", "GSM2449833", "GSM2449834", "GSM2449835", "GSM2449836", "GSM2449837", "GSM2449839", "GSM2449840", "GSM2449841", "GSM2449842", "GSM2449843", "GSM2449844", "GSM2449845", "GSM2449846", "GSM2449847", "GSM2449848", "GSM2449849", "GSM2449850", "GSM2449851", "GSM2449852", "GSM2449853", "GSM2449854", "GSM2449855", "GSM2449856", "GSM2449857", "GSM2449858", "GSM2449859", "GSM2449860", "GSM2449861", "GSM2449863", "GSM2449864", "GSM2449865", "GSM2449866", "GSM2449867", "GSM2449868", "GSM2449869", "GSM2449870", "GSM2449871", "GSM2449872", "GSM2449873", "GSM2449874", "GSM2449875", "GSM2449876", "GSM2449877", "GSM2449878", "GSM2449879", "GSM2449880", "GSM2449881", "GSM2449882", "GSM2449883", "GSM2449884", "GSM2449885", "GSM2449886", "GSM2449887"], "sample_count": 275, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Whole blood gene expression of rheumatoid arthritis", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE100191 not downloaded", "asset:data:geo:GSE100191 licence not read", "asset:data:geo:GSE12021 not downloaded", "asset:data:geo:GSE12021 licence not read", "asset:data:geo:GSE17755 not downloaded", "asset:data:geo:GSE17755 licence not read", "asset:data:geo:GSE205962 not downloaded", "asset:data:geo:GSE205962 licence not read", "asset:data:geo:GSE39340 not downloaded", "asset:data:geo:GSE39340 licence not read", "asset:data:geo:GSE55235 not downloaded", "asset:data:geo:GSE55235 licence not read", "asset:data:geo:GSE89408 not downloaded", "asset:data:geo:GSE89408 licence not read", "asset:data:geo:GSE93272 not downloaded", "asset:data:geo:GSE93272 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": "Differential expression analysis was performed by the “limma” package (version 3.56.1) with the following threshold: p_adj < 0.05 and abs (logFC) > 0.45."}}, {"id": "method-2", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "random forest"}}, {"id": "method-3", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "support vector machine"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cross_validate", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-auc", "claim_id": "claim-target-result", "operation": "cross_validate", "expected_value": 0.995, "unit": "auc", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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": ["GSE17755", "GSE93272", "GSE100191", "GSE205962", "GSE12021", "GSE55235", "GSE89408", "GSE39340"], "resolved_accessions": ["GSE17755", "GSE93272", "GSE100191", "GSE205962", "GSE12021", "GSE55235", "GSE89408", "GSE39340"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE17755, GSE93272, GSE100191, GSE205962, GSE12021, GSE55235, GSE89408, GSE39340 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:37779906", "data:geo:GSE100191"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE100191"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:54:48Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14137, "completion_tokens": 2835, "cached_tokens": 264}}, "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:37779906", "type": "paper", "label": "pmid:37779906"}, {"id": "source:pmid:37779906", "type": "manuscript", "label": "PMID 37779906 full text"}, {"id": "data:geo:GSE100191", "type": "dataset", "label": "GEO GSE100191"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37779906", "type": "paper", "label": "pmid:37779906"}, {"id": "source:pmid:37779906", "type": "manuscript", "label": "PMID 37779906 full text"}, {"id": "data:geo:GSE100191", "type": "dataset", "label": "GEO GSE100191"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37779906", "type": "extraction", "used": ["source:pmid:37779906"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE100191", "type": "accession_resolution", "used": ["data:geo:GSE100191"], "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:37779906", "parent_hash": "sha256:fcb36dadbcb27df5652508da0e94639cd997425f3efe27fa9180d25056ceaffb", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE100191 licence not read", "asset:data:geo:GSE100191 not downloaded", "asset:data:geo:GSE12021 licence not read", "asset:data:geo:GSE12021 not downloaded", "asset:data:geo:GSE17755 licence not read", "asset:data:geo:GSE17755 not downloaded", "asset:data:geo:GSE205962 licence not read", "asset:data:geo:GSE205962 not downloaded", "asset:data:geo:GSE39340 licence not read", "asset:data:geo:GSE39340 not downloaded", "asset:data:geo:GSE55235 licence not read", "asset:data:geo:GSE55235 not downloaded", "asset:data:geo:GSE89408 licence not read", "asset:data:geo:GSE89408 not downloaded", "asset:data:geo:GSE93272 licence not read", "asset:data:geo:GSE93272 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ts of KEGG, DE-ARGs were mainly enriched in “apoptosis,” “pathogenic Escherichia coli infection” an", "nts (CC). CC mainly contained “melanosome,” “caspase complex,” and “focal adhesion” (Figure 3B)."], "order_basis": "paper_text_order:3366", "id": "assay:1"}, {"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": ["Differential expression analysis was performed by the “limma” package (version 3.56.1) with the following threshold: p_adj < 0.05 and abs (logFC) > 0.45."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}