{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34122426", "kind": "science-record", "revision": 7, "content_hash": "sha256:629dd2f5ac024a1fca1fa0342f1b24eded499062c1b90a919237985ac3ccfd16", "created_at": "2026-11-01T15:41:38Z", "updated_at": "2026-11-01T22:03:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis.", "doi": "10.3389/fimmu.2021.667690", "pmid": "34122426", "authors": ["Wenxing Su", "Ying Zhao", "Yuqian Wei", "Xiaoyan Zhang", "Jiang Ji", "Shun Yang"], "journal": "Frontiers in immunology", "year": 2021, "abstract": "Background: Although more and more evidence has supported psoriasis is prone to atherosclerosis, the common mechanism of its occurrence is still not fully elucidated. The purpose of this study is to further explore the molecular mechanism of the occurrence of this complication.\nMethods: The gene expression profiles of psoriasis (GSE30999) and atherosclerosis (GSE28829) were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the common differentially expressed genes (DEGs) of psoriasis and atherosclerosis, three kinds of analyses were performed, namely functional annotation, protein-protein interaction (PPI) network and module construction, and hub gene identification and co-expression analysis.\nResults: A total of 94 common DEGs (24 downregulated genes and 70 upregulated genes) was selected for subsequent analyses. Functional analysis emphasizes the important role of chemokines and cytokines in these two diseases. In addition, lipopolysaccharide-mediated signaling pathway is closely related to both. Finally, 16 important hub genes were identified using cytoHubba, including LYN, CSF2RB, IL1RN, RAC2, CCL5, IRF8, C1QB, MMP9, PLEK, PTPRC, FYB, BCL2A1, LCP2, CD53, NCF2 and TLR2.\nConclusions: Our study reveals the common pathogenesis of psoriasis and atherosclerosis. These common pathways and hub genes may provide new ideas for further mechanism research.", "claims": [{"id": "claim-method", "statement": "The comparison between the two sets of data was performed with the T-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34122426", "locator": "sections[8] \"Validation of Hub Genes Expression in Other Data Sets\" paragraph 2", "quote": "The comparison between the two sets of data was performed with the T-test."}], "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 authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34122426", "locator": "sections[19] \"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 authors."}], "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:34122426"], "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:GSE100927"], "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:GSE100927"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34122426", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2021.667690", "sha256": "sha256:8f7e71aa4465d7792b439d0720588ce73cfa28d0dbddfa7379259097514a03bb", "bytes": 30671, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2021.667690", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8190392", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100927", "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=GSE100927", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100927", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . 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"access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T1", "version": null, "note": "The top 20 hub genes rank in cytoHubba.", "structure": {"pmcid": "PMC8190392", "section_index": 7, "section_title": "Selection and Analysis of Hub Genes", "row_count": 21, "column_count": 7}, "table": {"label": "Table 1", "caption": "The top 20 hub genes rank in cytoHubba.", "rows": [["MCC", "MNC", "Degree", "Closeness", "Radiality", "Stress", "EPC"], ["PLEK", "PLEK", "IL7R", "PLAUR", "PLAUR", "SERPINA1", "PLEK"], ["CXCL2", "CXCL2", "PLEK", "PLEK", "PLEK", "PLAUR", "CXCL2"], ["C1QB", "C1QB", "CXCL2", "CXCL2", "CXCL2", "PLEK", "C1QB"], ["CD48", "CD48", "C1QB", "C1QB", "C1QB", "C1QB", "CD48"], ["CCL5", "CCL5", "CD48", "CD48", "CD48", "CCL5", "CCL5"], ["CYTIP", "CYTIP", "CCL5", "CCL5", "CCL5", "MMP12", "CYTIP"], ["CD53", "CD53", "CD53", "CD53", "CD53", "CD53", "CD53"], ["GPR183", "GPR183", "GPR183", "GPR183", "GPR183", "BCL2A1", "GPR183"], ["BCL2A1", "BCL2A1", "BCL2A1", "BCL2A1", "BCL2A1", "LCP2", "BCL2A1"], ["LCP2", "LCP2", "LCP2", "LCP2", "LCP2", "RAC2", "LCP2"], ["RAC2", "RAC2", "RAC2", "RAC2", "RAC2", "FYB", "RAC2"], ["FYB", "FYB", "FYB", "FYB", "FYB", "IL1RN", "FYB"], ["IL1RN", "IL1RN", "IL1RN", "IL1RN", "IL1RN", "JAK3", "IL1RN"], ["IRF8", "IRF8", "IRF8", "IRF8", "IRF8", "TLR2", "IRF8"], ["TLR2", "TLR2", "TLR2", "TLR2", "TLR2", "IRF8", "TLR2"], ["LYN", "LYN", "LYN", "LYN", "LYN", "LYN", "LYN"], ["MMP9", "MMP9", "MMP9", "MMP9", "MMP9", "MMP9", "MMP9"], ["NCF2", "NCF2", "NCF2", "NCF2", "NCF2", "NCF2", "NCF2"], ["PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC"], ["CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB"]], "row_count": 21, "column_count": 7, "numeric_cells": 20, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34122426:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:99290b17173e2e62ad43ba5a087daf920425cf3725d4c4e3580378b76ffad20d", "bytes": 3150, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#T2", "version": null, "note": "The details of the hub genes.", "structure": {"pmcid": "PMC8190392", "section_index": 7, "section_title": "Selection and Analysis of Hub Genes", "row_count": 17, "column_count": 4}, "table": {"label": "Table 2", "caption": "The details of the hub genes.", "rows": [["No.", "Gene symbol", "Full name", "Function"], ["1", "LYN", "v-yes-1 Yanaguchi sarcoma viral related oncogene homolog", "Belongs to the Src protein kinase family. LYN is involved in cell proliferation, differentiation, apoptosis, migration and Metabolic activity and regulation of cellular immunity."], ["2", "CSF2RB", "Colony Stimulating Factor 2 Receptor, Beta", "It is the shared subunit of receptors for interleukin 3, colony stimulating factor 2 (CSF2) and IL5, and is responsible for the initiation of signal transduction triggered by ligand binding."], ["3", "IL1RN", "interleukin-1-receptor antagonist", "IL1RN is a protein that binds to IL-1 receptors and inhibits the binding of IL-1α and IL-1β."], ["4", "RAC2", "ras-related C3 botulinum toxin substrate 2", "belongs to the Rho family of GTP-binding proteins, Rac2 is only found in cells of myeloid origin, Involves in regulating human monocyte chemotaxis and NADPH oxidase activity."], ["5", "CCL5", "chemokine (C-C motif) ligand 5", "CCL5 is highly expressed in cancer where it contributes to inflammation and malignant progression."], ["6", "IRF8", "Interferon regulatory factor 8", "Plays critical roles in interferon (IFN) signaling pathways governing the establishment of innate immune responses by myeloid and dendritic cells."], ["7", "C1QB", "complement C1q subcomponent subunit B", "Plays an important role in maintaining the stability of the body’s environment, oxidative stress, glucose and lipid metabolism and other processes"], ["8", "MMP9", "matrix metalloproteinase 9", "endoprotease with collagenase and/or gelatinase activity which exert deleterious effects on the endothelium integrity and collagen fibers."], ["9", "PLEK", "Pleckstrin homology domain containing", "Involves in the apoptosis of vascular endothelial cells."], ["10", "PTPRC", "encoding protein-tyrosine phosphatase receptor-type C", "PTPRC is one of the most abundant leukocyte cell surface glycoproteins and is expressed exclusively upon cells of the hematopoietic system."], ["11", "FYB", "Fyn-binding protein", "FYB is a hematopoietic-specific adapter, which associates with and modulates function of SH2-containing leukocyte phosphoprotein of 76 kilodaltons (SLP-76)."], ["12", "BCL2A1", "B-cell lymphoma-2 related protein A1", "BCL2A1 is important cell death regulators, whose main function is to control the release of cytochrome c from mitochondria in the intrinsic apoptotic pathway."], ["13", "LCP2", "lymphocyte cytosolic protein 2", "Participates in immune response and intracellular signal transduction."], ["14", "CD53", "CD53", "CD53 has been implicated in B cell development and function. CD53 is a transcriptional target of EBF1, a critical transcription factor for early B cell development."], ["15", "NCF2", "neutrophil cytosolic factor 2", "NCF2, the gene encoding the NADPH oxidase cytosolic component p67phox, is up-regulated by TNF-α."], ["16", "TLR2", "Toll-like receptor 2", "TLR-2 triggers receptor-mediated events, including cytokine-mediated inflammation."]], "row_count": 17, "column_count": 4, "numeric_cells": 35, "header_rows": 1, "locator": "section[14]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:34122426:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2b7b59afd0821c60e6b15c622293fd91bcb31025fa636a53f68dd7383e136535", "bytes": 1327, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T1", "version": null, "note": "The top 20 hub genes rank in cytoHubba.", "structure": {"pmcid": "PMC8190392", "section_index": 14, "section_title": "Selection and Analysis of Hub Genes", "row_count": 21, "column_count": 7}, "table": {"label": "Table 1", "caption": "The top 20 hub genes rank in cytoHubba.", "rows": [["MCC", "MNC", "Degree", "Closeness", "Radiality", "Stress", "EPC"], ["PLEK", "PLEK", "IL7R", "PLAUR", "PLAUR", "SERPINA1", "PLEK"], ["CXCL2", "CXCL2", "PLEK", "PLEK", "PLEK", "PLAUR", "CXCL2"], ["C1QB", "C1QB", "CXCL2", "CXCL2", "CXCL2", "PLEK", "C1QB"], ["CD48", "CD48", "C1QB", "C1QB", "C1QB", "C1QB", "CD48"], ["CCL5", "CCL5", "CD48", "CD48", "CD48", "CCL5", "CCL5"], ["CYTIP", "CYTIP", "CCL5", "CCL5", "CCL5", "MMP12", "CYTIP"], ["CD53", "CD53", "CD53", "CD53", "CD53", "CD53", "CD53"], ["GPR183", "GPR183", "GPR183", "GPR183", "GPR183", "BCL2A1", "GPR183"], ["BCL2A1", "BCL2A1", "BCL2A1", "BCL2A1", "BCL2A1", "LCP2", "BCL2A1"], ["LCP2", "LCP2", "LCP2", "LCP2", "LCP2", "RAC2", "LCP2"], ["RAC2", "RAC2", "RAC2", "RAC2", "RAC2", "FYB", "RAC2"], ["FYB", "FYB", "FYB", "FYB", "FYB", "IL1RN", "FYB"], ["IL1RN", "IL1RN", "IL1RN", "IL1RN", "IL1RN", "JAK3", "IL1RN"], ["IRF8", "IRF8", "IRF8", "IRF8", "IRF8", "TLR2", "IRF8"], ["TLR2", "TLR2", "TLR2", "TLR2", "TLR2", "IRF8", "TLR2"], ["LYN", "LYN", "LYN", "LYN", "LYN", "LYN", "LYN"], ["MMP9", "MMP9", "MMP9", "MMP9", "MMP9", "MMP9", "MMP9"], ["NCF2", "NCF2", "NCF2", "NCF2", "NCF2", "NCF2", "NCF2"], ["PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC"], ["CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB"]], "row_count": 21, "column_count": 7, "numeric_cells": 20, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34122426:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:99290b17173e2e62ad43ba5a087daf920425cf3725d4c4e3580378b76ffad20d", "bytes": 3150, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#T2", "version": null, "note": "The details of the hub genes.", "structure": {"pmcid": "PMC8190392", "section_index": 14, "section_title": "Selection and Analysis of Hub Genes", "row_count": 17, "column_count": 4}, "table": {"label": "Table 2", "caption": "The details of the hub genes.", "rows": [["No.", "Gene symbol", "Full name", "Function"], ["1", "LYN", "v-yes-1 Yanaguchi sarcoma viral related oncogene homolog", "Belongs to the Src protein kinase family. LYN is involved in cell proliferation, differentiation, apoptosis, migration and Metabolic activity and regulation of cellular immunity."], ["2", "CSF2RB", "Colony Stimulating Factor 2 Receptor, Beta", "It is the shared subunit of receptors for interleukin 3, colony stimulating factor 2 (CSF2) and IL5, and is responsible for the initiation of signal transduction triggered by ligand binding."], ["3", "IL1RN", "interleukin-1-receptor antagonist", "IL1RN is a protein that binds to IL-1 receptors and inhibits the binding of IL-1α and IL-1β."], ["4", "RAC2", "ras-related C3 botulinum toxin substrate 2", "belongs to the Rho family of GTP-binding proteins, Rac2 is only found in cells of myeloid origin, Involves in regulating human monocyte chemotaxis and NADPH oxidase activity."], ["5", "CCL5", "chemokine (C-C motif) ligand 5", "CCL5 is highly expressed in cancer where it contributes to inflammation and malignant progression."], ["6", "IRF8", "Interferon regulatory factor 8", "Plays critical roles in interferon (IFN) signaling pathways governing the establishment of innate immune responses by myeloid and dendritic cells."], ["7", "C1QB", "complement C1q subcomponent subunit B", "Plays an important role in maintaining the stability of the body’s environment, oxidative stress, glucose and lipid metabolism and other processes"], ["8", "MMP9", "matrix metalloproteinase 9", "endoprotease with collagenase and/or gelatinase activity which exert deleterious effects on the endothelium integrity and collagen fibers."], ["9", "PLEK", "Pleckstrin homology domain containing", "Involves in the apoptosis of vascular endothelial cells."], ["10", "PTPRC", "encoding protein-tyrosine phosphatase receptor-type C", "PTPRC is one of the most abundant leukocyte cell surface glycoproteins and is expressed exclusively upon cells of the hematopoietic system."], ["11", "FYB", "Fyn-binding protein", "FYB is a hematopoietic-specific adapter, which associates with and modulates function of SH2-containing leukocyte phosphoprotein of 76 kilodaltons (SLP-76)."], ["12", "BCL2A1", "B-cell lymphoma-2 related protein A1", "BCL2A1 is important cell death regulators, whose main function is to control the release of cytochrome c from mitochondria in the intrinsic apoptotic pathway."], ["13", "LCP2", "lymphocyte cytosolic protein 2", "Participates in immune response and intracellular signal transduction."], ["14", "CD53", "CD53", "CD53 has been implicated in B cell development and function. CD53 is a transcriptional target of EBF1, a critical transcription factor for early B cell development."], ["15", "NCF2", "neutrophil cytosolic factor 2", "NCF2, the gene encoding the NADPH oxidase cytosolic component p67phox, is up-regulated by TNF-α."], ["16", "TLR2", "Toll-like receptor 2", "TLR-2 triggers receptor-mediated events, including cytokine-mediated inflammation."]], "row_count": 17, "column_count": 4, "numeric_cells": 35, "header_rows": 1, "locator": "section[14]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:34122426:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bde423475cc0e472b6be088cdf052a76957933bb11497a88f834c6dd2c8ada0c", "bytes": 1258, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T3", "version": null, "note": "Key transcriptional factors (TFs) of hub genes.", "structure": {"pmcid": "PMC8190392", "section_index": 16, "section_title": "Prediction and Verification of TFs", "row_count": 12, "column_count": 4}, "table": {"label": "Table 3", "caption": "Key transcriptional factors (TFs) of hub genes.", "rows": [["Key TFs", "Description", "P-value", "Genes"], ["RELA", "v-rel reticuloendotheliosis viral oncogene homolog A (avian)", "2.14E-05", "BCL2A1, MMP9, IL1RN, TLR2, CCL5"], ["NFKB1", "nuclear factor of kappa light polypeptide gene enhancer in B-cells 1", "2.14E-05", "CCL5, MMP9, BCL2A1, IL1RN, TLR2"], ["IRF1", "interferon regulatory factor 1", "3.72E-05", "CCL5, NCF2, MMP9"], ["NFKBIA", "nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha", "0.000314", "MMP9, CCL5"], ["REL", "v-rel reticuloendotheliosis viral oncogene homolog (avian)", "0.000339", "BCL2A1, CCL5"], ["SPI1", "spleen focus forming virus (SFFV) proviral integration oncogene spi1", "0.00227", "NCF2, CCL5"], ["HDAC1", "histone deacetylase 1", "0.00254", "MMP9, BCL2A1"], ["STAT1", "signal transducer and activator of transcription 1, 91kDa", "0.0031", "MMP9, IRF8"], ["STAT3", "signal transducer and activator of transcription 3 (acute-phase response factor)", "0.00691", "IL1RN, MMP9"], ["SP1", "Sp1 transcription factor", "0.00691", "TLR2, MMP9, CCL5"], ["JUN", "jun proto-oncogene", "0.00691", "CCL5, MMP9"]], "row_count": 12, "column_count": 4, "numeric_cells": 16, "header_rows": 1, "locator": "section[16]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:GSE100927 not downloaded", "asset:data:geo:GSE100927 licence not read", "asset:data:geo:GSE14905 not downloaded", "asset:data:geo:GSE14905 licence not read", "asset:data:geo:GSE28829 not downloaded", "asset:data:geo:GSE28829 licence not read", "asset:data:geo:GSE30999 not downloaded", "asset:data:geo:GSE30999 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "Pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "T-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The comparison between the two sets of data was performed with the T-test."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE30999", "GSE28829", "GSE14905", "GSE100927"], "resolved_accessions": ["GSE30999", "GSE28829", "GSE14905", "GSE100927"], "statements": ["The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE30999, GSE28829, GSE14905, GSE100927 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:34122426", "data:geo:GSE100927", "asset:table:pmid:34122426:1", "asset:table:pmid:34122426:2", "asset:table:pmid:34122426:3", "asset:table:pmid:34122426:4", "asset:table:pmid:34122426:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE100927"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:30:48Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22177, "completion_tokens": 1445, "cached_tokens": 7424}}, "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:34122426", "type": "paper", "label": "pmid:34122426"}, {"id": "source:pmid:34122426", "type": "manuscript", "label": "PMID 34122426 full text"}, {"id": "data:geo:GSE100927", "type": "dataset", "label": "GEO GSE100927"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34122426", "type": "paper", "label": "pmid:34122426"}, {"id": "source:pmid:34122426", "type": "manuscript", "label": "PMID 34122426 full text"}, {"id": "data:geo:GSE100927", "type": "dataset", "label": "GEO GSE100927"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34122426", "type": "extraction", "used": ["source:pmid:34122426"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE100927", "type": "accession_resolution", "used": ["data:geo:GSE100927"], "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:34122426", "parent_hash": "sha256:3ee040297d8817c865581fdb469bd1b8865f3284d19e56f190d3ebe26991f525", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE100927 licence not read", "asset:data:geo:GSE100927 not downloaded", "asset:data:geo:GSE14905 licence not read", "asset:data:geo:GSE14905 not downloaded", "asset:data:geo:GSE28829 licence not read", "asset:data:geo:GSE28829 not downloaded", "asset:data:geo:GSE30999 licence not read", "asset:data:geo:GSE30999 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["oriasis Complicated With Atherosclerosis via Microarray Data Analysis."], "order_basis": "paper_text_order:32", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:48:52+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}}}