{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41007695", "kind": "science-record", "revision": 4, "content_hash": "sha256:c7ea7a2933d8e0d035383eaf73b99ab0aed9fca3b99b530370809c7e73e12c8e", "created_at": "2026-11-01T20:31:04Z", "updated_at": "2026-11-01T22:57:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Biomarkers Related to Lipid Metabolism in Acute Pancreatitis and Their Regulatory Mechanisms Based on Bioinformatics and Machine Learning.", "doi": "10.3390/biomedicines13092132", "pmid": "41007695", "authors": ["Liang Zhang", "Yujie Jiang", "Taojun Jin", "Mingxian Zheng", "Yixuan Yap", "Xuanyang Min", "Jiayue Chen", "Lin Yuan", "Feng He", "Bingduo Zhou"], "journal": "Biomedicines", "year": 2025, "abstract": "Background: Acute pancreatitis (AP) is characterized by the abnormal activation of pancreatic enzymes due to various causes, leading to local pancreatic inflammation. This can trigger systemic inflammatory response syndrome and multi-organ dysfunction. Hyperlipidemia, mainly resulting from lipid metabolism disorders and elevated triglyceride levels, is a major etiological factor in AP. This study aims to investigate the role of lipid metabolism-related genes in the pathogenesis of AP and to propose novel strategies for its prevention and treatment. Methods: We obtained AP-related datasets GSE3644, GSE65146, and GSE121038 from the GEO database. Differentially expressed genes (DEGs) were identified using DEG analysis and gene set enrichment analysis (GSEA). To identify core lipid metabolism genes in AP, we performed least absolute shrinkage and selection operator (LASSO) regression and support vector machine recursive feature elimination (SVM-RFE) analysis. Gene and protein interactions were predicted using GeneMANIA and AlphaFold. Finally, biomarker expression levels were quantified using Real-Time quantitative Polymerase Chain Reaction (RT-qPCR) in an AP mouse model. Results: Seven lipid metabolism-related genes were identified as key biomarkers in AP: Amacr, Cyp39a1, Echs1, Gpd2, Osbpl9, Acsl4, and Mcee. The biological roles of these genes mainly involve fatty acid metabolism, cholesterol metabolism, lipid transport across cellular membranes, and mitochondrial function. Conclusions:Amacr, Cyp39a1, Echs1, Gpd2, Osbpl9, Acsl4, and Mcee are characteristic biomarkers of lipid metabolism abnormalities in AP. These findings are crucial for a deeper understanding of lipid metabolism pathways in AP and for the early implementation of preventive clinical measures, such as the control of blood lipid levels.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) were identified using the limma R package [21].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41007695", "locator": "sections[5] \"2.3. DEGs Identification and Functional Enrichment Analysis\" paragraph 2", "quote": "Differentially expressed genes (DEGs) were identified using the limma R package [21]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41007695", "locator": "sections[30] \"Data Availability Statement\" paragraph 2", "quote": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Seven lipid metabolism-related genes were identified as key biomarkers in acute pancreatitis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41007695", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Results: Seven lipid metabolism-related genes were identified as key biomarkers in AP: Amacr, Cyp39a1, Echs1, Gpd2, Osbpl9, Acsl4, and Mcee."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Seven lipid metabolism-related genes were identified as key biomarkers in acute pancreatitis.", "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:41007695"], "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:GSE121038"], "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:GSE121038"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41007695", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/biomedicines13092132", "sha256": "sha256:b5a55967ab5f614e494e9e8cde9e621a1a0f5352636ce736c793b8d3fad3435f", "bytes": 61846, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/biomedicines13092132", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12467098", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE121038", "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=GSE121038", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE121038", "version": null, "note": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3424897", "GSM3424898", "GSM3424899", "GSM3424900", "GSM3424901", "GSM3424902", "GSM3424903", "GSM3424904", "GSM3424905", "GSM3424906", "GSM3424907", "GSM3424908", "GSM3424909", "GSM3424910", "GSM3424911"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "10787", "taxon": "Mus musculus", "title": "The protective effect of betacellulin against acute pancreatitis is ERBB4-dependent", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE25724", "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=GSE25724", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25724", "version": null, "note": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM631755", "GSM631756", "GSM631757", "GSM631758", "GSM631759", "GSM631760", "GSM631761", "GSM631762", "GSM631763", "GSM631764", "GSM631765", "GSM631766", "GSM631767"], "sample_count": 13, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from type 2 diabetic and non-diabetic isolated human islets", "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:GSE3644", "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=GSE3644", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE3644", "version": null, "note": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM84549", "GSM84550", "GSM84551", "GSM84552", "GSM84553", "GSM84554", "GSM84555", "GSM84556", "GSM84557", "GSM84558", "GSM84559", "GSM84560"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "339", "taxon": "Mus musculus", "title": "Effects of caerulein on Mist1KO pancreas", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE65146", "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=GSE65146", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65146", "version": null, "note": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1588057", "GSM1588058", "GSM1588059", "GSM1588060", "GSM1588061", "GSM1588062", "GSM1588063", "GSM1588064", "GSM1588065", "GSM1588066", "GSM1588067", "GSM1588068", "GSM1588069", "GSM1588070", "GSM1588071", "GSM1588072", "GSM1588073", "GSM1588074", "GSM1588075", "GSM1588076", "GSM1588077", "GSM1588078", "GSM1588079", "GSM1588080", "GSM1588081", "GSM1588082", "GSM1588083", "GSM1588084", "GSM1588085", "GSM1588086", "GSM1588087", "GSM1588088", "GSM1588089", "GSM1588090", "GSM1588091", "GSM1588092", "GSM1588093", "GSM1588094", "GSM1588095", "GSM1588096", "GSM1588097", "GSM1588098", "GSM1588099", "GSM1588100", "GSM1588101", "GSM1588102", "GSM1588103", "GSM1588104", "GSM1588105", "GSM1588106", "GSM1588107", "GSM1588108", "GSM1588109", "GSM1588110", "GSM1588111", "GSM1588112", "GSM1588113", "GSM1588114", "GSM1588115", "GSM1588116", "GSM1588117", "GSM1588118", "GSM1588119", "GSM1588120", "GSM1588121", "GSM1588122", "GSM1588123", "GSM1588124", "GSM1588125", "GSM1588126", "GSM1588127", "GSM1588128", "GSM1588129"], "sample_count": 73, "group_sizes": null, "group_sizes_basis": null, "platform": "6246", "taxon": "Mus musculus", "title": "Expression data of caerulein-treated wild-type mice and KrasG12D-mutated mice at different stages of pancreatic regeneration after inflammatory injury", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE76896", "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=GSE76896", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76896", "version": null, "note": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2040049", "GSM2040050", "GSM2040051", "GSM2040052", "GSM2040053", "GSM2040054", "GSM2040055", "GSM2040056", "GSM2040057", "GSM2040058", "GSM2040059", "GSM2040060", "GSM2040061", "GSM2040062", "GSM2040063", "GSM2040064", "GSM2040065", "GSM2040066", "GSM2040067", "GSM2040068", "GSM2040069", "GSM2040070", "GSM2040071", "GSM2040072", "GSM2040073", "GSM2040074", "GSM2040075", "GSM2040076", "GSM2040077", "GSM2040078", "GSM2040079", "GSM2040080", "GSM2040081", "GSM2040082", "GSM2040083", "GSM2040084", "GSM2040085", "GSM2040086", "GSM2040087", "GSM2040088", "GSM2040089", "GSM2040090", "GSM2040091", "GSM2040092", "GSM2040093", "GSM2040094", "GSM2040095", "GSM2040096", "GSM2040097", "GSM2040098", "GSM2040099", "GSM2040100", "GSM2040101", "GSM2040102", "GSM2040103", "GSM2040104", "GSM2040105", "GSM2040106", "GSM2040107", "GSM2040108", "GSM2040109", "GSM2040110", "GSM2040111", "GSM2040112", "GSM2040113", "GSM2040114", "GSM2040115", 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"GSM2040187", "GSM2040188", "GSM2040189", "GSM2040190", "GSM2040191", "GSM2040192", "GSM2040193", "GSM2040194", "GSM2040195", "GSM2040196", "GSM2040197", "GSM2040198", "GSM2040199", "GSM2040200", "GSM2040201", "GSM2040202", "GSM2040203", "GSM2040204", "GSM2040205", "GSM2040206", "GSM2040207", "GSM2040208", "GSM2040209", "GSM2040210", "GSM2040211", "GSM2040212", "GSM2040213", "GSM2040214", "GSM2040215", "GSM2040216", "GSM2040217", "GSM2040218", "GSM2040219", "GSM2040220", "GSM2040221", "GSM2040222", "GSM2040223", "GSM2040224", "GSM2040225", "GSM2040226", "GSM2040227", "GSM2040228", "GSM2040229", "GSM2040230", "GSM2040231", "GSM2040232", "GSM2040233", "GSM2040234", "GSM2040235", "GSM2040236", "GSM2040237", "GSM2040238", "GSM2040239", "GSM2040240", "GSM2040241", "GSM2040242", "GSM2040243", "GSM2040244", "GSM2040245", "GSM2040246", "GSM2040247", "GSM2040248", "GSM2040249", "GSM2040250", "GSM2040251", "GSM2040252", "GSM2040253", "GSM2040254"], "sample_count": 206, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE121038 not downloaded", "asset:data:geo:GSE121038 licence not read", "asset:data:geo:GSE25724 not downloaded", "asset:data:geo:GSE25724 licence not read", "asset:data:geo:GSE3644 not downloaded", "asset:data:geo:GSE3644 licence not read", "asset:data:geo:GSE65146 not downloaded", "asset:data:geo:GSE65146 licence not read", "asset:data:geo:GSE76896 not downloaded", "asset:data:geo:GSE76896 licence not read"]}, "analysis": {"state": "partial", "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 identified using the limma R package [21]."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-4", "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": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["GSE3644", "GSE65146", "GSE121038", "GSE25724", "GSE76896"], "resolved_accessions": ["GSE3644", "GSE65146", "GSE121038", "GSE25724", "GSE76896"], "statements": ["The datasets generated and/or analyzed during this study are available at Gene Expression Omnibus datasets (GEO, https://www.ncbi.nlm.nih.gov/geo/, accessed on 9 October 2024 GSE3644, GSE65146, GSE121038) and https://www.gsea-msigdb.org/gsea/index.jsp, accessed on 16 November 2024, were obtained and analyzed in Gene Set Enrichment Analysis (GSEA, http://www.gsea-msigdb.org/, accessed on 6 December 2024), Gene Ontology (GO, https://geneontology.org/, accessed on 24 December 2024), and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/, accessed on 24 December 2024), and further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE3644, GSE65146, GSE121038, GSE25724, GSE76896 in Gene Expression Omnibus database (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:41007695", "data:geo:GSE121038"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE121038"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:02:04Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 17995, "completion_tokens": 2483, "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:41007695", "type": "paper", "label": "pmid:41007695"}, {"id": "source:pmid:41007695", "type": "manuscript", "label": "PMID 41007695 full text"}, {"id": "data:geo:GSE121038", "type": "dataset", "label": "GEO GSE121038"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41007695", "type": "paper", "label": "pmid:41007695"}, {"id": "source:pmid:41007695", "type": "manuscript", "label": "PMID 41007695 full text"}, {"id": "data:geo:GSE121038", "type": "dataset", "label": "GEO GSE121038"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41007695", "type": "extraction", "used": ["source:pmid:41007695"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE121038", "type": "accession_resolution", "used": ["data:geo:GSE121038"], "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:41007695", "parent_hash": "sha256:b0820a58d559c814af0b314ee95cf1a7655599fd20b0ce51021f97e6f2b2a5d4", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE121038 licence not read", "asset:data:geo:GSE121038 not downloaded", "asset:data:geo:GSE25724 licence not read", "asset:data:geo:GSE25724 not downloaded", "asset:data:geo:GSE3644 licence not read", "asset:data:geo:GSE3644 not downloaded", "asset:data:geo:GSE65146 licence not read", "asset:data:geo:GSE65146 not downloaded", "asset:data:geo:GSE76896 licence not read", "asset:data:geo:GSE76896 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Time quantitative Polymerase Chain Reaction (RT-qPCR) in an AP mouse model. Results: Seven lipid", "e quantitative Polymerase Chain Reaction (RT-qPCR) in an AP mouse model. Results: Seven lipid", "the other 8 were used for RNA extraction and RT-qPCR analysis. In RT-qPCR experiments, Actb was u", "for RNA extraction and RT-qPCR analysis. In RT-qPCR experiments, Actb was used for the internal"], "order_basis": "paper_text_order:1271", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Polymerase Chain Reaction (RT-qPCR) in an AP mouse model. Results: Seven lipid metabolism-related gen", "Polymerase Chain Reaction (RT-qPCR) in an AP mouse model. Results: Seven lipid metabolism-relat", "ions. Protein sequences of the gene-specific mouse proteins were obtained from NCBI (https://ww", "s for Gpd2 and Mcee were unavailable for the mouse host, 3D models were generated only for the"], "order_basis": "paper_text_order:1289", "id": "assay:2"}, {"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 identified using the limma R package [21]."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"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":"2026-11-04T02:59:38+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}}}