{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33532314", "kind": "science-record", "revision": 6, "content_hash": "sha256:ea5b5b5e750eceffd4fc188bf27ffa6c75c1b6bfbcc17153523b8e5e43153d6f", "created_at": "2026-11-01T15:41:24Z", "updated_at": "2026-11-01T22:03:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative bioinformatics approaches for identifying potential biomarkers and pathways involved in non-obstructive azoospermia.", "doi": "10.21037/tau-20-1029", "pmid": "33532314", "authors": ["Tengfei Hu", "Shaoge Luo", "Yu Xi", "Xuchong Tu", "Xiaojian Yang", "Hui Zhang", "Jiarong Feng", "Chunlin Wang", "Yan Zhang"], "journal": "Translational andrology and urology", "year": 2021, "abstract": "BACKGROUND: Non-obstructive azoospermia (NOA) is a disease related to spermatogenic disorders. Currently, the specific etiological mechanism of NOA is unclear. This study aimed to use integrated bioinformatics to screen biomarkers and pathways involved in NOA and reveal their potential molecular mechanisms.\nMETHODS: GSE145467 and GSE108886 gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between NOA tissues and matched obstructive azoospermia (OA) tissues were identified using the GEO2R tool. Common DEGs in the two datasets were screened out by the VennDiagram package. For the functional annotation of common DEGs, DAVID v.6.8 was used to perform Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. In accordance with data collected from the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, a protein-protein interaction (PPI) network was constructed by Cytoscape. Cytohubba in Cytoscape was used to screen the hub genes. Furthermore, the hub genes were validated based on a separate dataset, GSE9210. Finally, potential micro RNAs (miRNAs) of hub genes were predicted by miRWalk 3.0.\nRESULTS: A total of 816 common DEGs, including 52 common upregulated and 764 common downregulated genes in two datasets, were screened out. Some of the more important of these pathways, including focal adhesion, PI3K-Akt signaling pathway, cell cycle, oocyte meiosis, AMP-activated protein kinase (AMPK) signaling pathway, FoxO signaling pathway, and Huntington disease, were involved in spermatogenesis. We further identified the top 20 hub genes from the PPI network, including CCNB2, DYNLL2, HMMR, NEK2, KIF15, DLGAP5, NUF2, TTK, PLK4, PTTG1, PBK, CEP55, CDKN3, CDC25C, MCM4, DNAI1, TYMS, PPP2R1B, DNAI2, and DYNLRB2, which were all downregulated genes. In addition, potential miRNAs of hub genes, including hsa-miR-3666, hsa-miR-130b-3p, hsa-miR-15b-5p, hsa-miR-6838-5p, and hsa-miR-195-5p, were screened out.\nCONCLUSIONS: Taken together, the identification of the above hub genes, miRNAs and pathways will help us better understand the mechanisms associated with NOA, and provide potential biomarkers and therapeutic targets for NOA.", "claims": [{"id": "claim-method", "statement": "The Wilcox test was used to determine whether there were differences in the expression of hub genes between the two subgroups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33532314", "locator": "sections[7] \"Analysis of hub genes in the NOA subgroup\" paragraph 2", "quote": "The Wilcox test was used to determine whether there were differences in the expression of hub genes between the two subgroups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE145467 dataset, which was contributed by Hodžić et al. (11), is based on the GPL4133 platform of the Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) and includes 10 NOA samples and 10 OA testicular samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33532314", "locator": "sections[3] \"Microarray data source\" paragraph 3", "quote": "The GSE145467 dataset, which was contributed by Hodžić et al. (11), is based on the GPL4133 platform of the Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) and includes 10 NOA samples and 10 OA testicular samples."}], "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:33532314"], "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:GSE108886"], "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:GSE108886"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33532314", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tau-20-1029", "sha256": "sha256:9ef1586877c1eb8f1bd7a38f50650aa2d83d797f3e27429501b4af6e41b033cd", "bytes": 34021, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tau-20-1029", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7844508", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE108886", "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=GSE108886", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE108886", "version": null, "note": "The GSE145467 dataset, which was contributed by Hodžić et al. (11), is based on the GPL4133 platform of the Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) and includes 10 NOA samples and 10 OA testicular samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE145467 dataset, which was contributed by Hodžić et al. 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"GSM233026", "GSM233027"], "sample_count": 58, "group_sizes": null, "group_sizes_basis": null, "platform": "887", "taxon": "Homo sapiens", "title": "A testicular gene expression profile for NOA patients, and ART3 as a genetic susceptibility gene for NOA", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33532314:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8247ef6c61968cd5f37887e526e1aa5b1ef08582ab580b9341537773bd2f1316", "bytes": 2470, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t1", "version": null, "note": "Gene ontology analysis of common upregulated and downregulated DEGs", "structure": {"pmcid": "PMC7844508", "section_index": 13, "section_title": "GO enrichment analysis", "row_count": 33, "column_count": 5}, "table": {"label": "Table 1", "caption": "Gene ontology analysis of common upregulated and downregulated DEGs", "rows": [["Category", "Term", "Count", "Gene ratio", "P value"], ["Upregulated", "", "", "", ""], ["BP", "GO:0030198~extracellular matrix organization", "6", "0.0775294", "2.59E-04"], ["BP", "GO:0008285~negative regulation of cell proliferation", "6", "0.0775294", "0.005787"], ["BP", "GO:0007155~cell adhesion", "6", "0.0775294", "0.0105986"], ["BP", "GO:0044267~cellular protein metabolic process", "5", "0.0646078", "3.85E-04"], ["BP", "GO:0043066~negative regulation of apoptotic process", "5", "0.0646078", "0.04328502"], ["CC", "GO:0070062~extracellular exosome", "25", "0.3230392", "5.98E-08"], ["CC", "GO:0005615~extracellular space", "20", "0.2584313", "9.39E-10"], ["CC", "GO:0005576~extracellular region", "18", "0.2325882", "6.52E-07"], ["CC", "GO:0031012~extracellular matrix", "11", "0.1421372", "6.35E-09"], ["CC", "GO:0005578~proteinaceous extracellular matrix", "6", "0.0775294", "8.18E-04"], ["MF", "GO:0005102~receptor binding", "6", "0.0775294", "0.00290085"], ["MF", "GO:0005509~calcium ion binding", "6", "0.0775294", "0.04816598"], ["MF", "GO:0005518~collagen binding", "5", "0.0646078", "2.29E-05"], ["MF", "GO:0008201~heparin binding", "5", "0.0646078", "0.00100954"], ["MF", "GO:0017147~Wnt-protein binding", "3", "0.0387647", "0.00335112"], ["Downregulated", "", "", "", ""], ["BP", "GO:0007283~spermatogenesis", "68", "0.0747565", "1.86E-33"], ["BP", "GO:0007275~multicellular organism development", "50", "0.054968", "2.82E-13"], ["BP", "GO:0030154~cell differentiation", "44", "0.0483718", "1.24E-11"], ["BP", "GO:0007286~spermatid development", "24", "0.0263846", "1.21E-17"], ["BP", "GO:0030317~sperm motility", "21", "0.0230866", "1.32E-17"], ["CC", "GO:0005634~nucleus", "221", "0.2429586", "3.59E-05"], ["CC", "GO:0005737~cytoplasm", "197", "0.216574", "0.00769222"], ["CC", 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"state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#t2", "version": null, "note": "KEGG pathway analysis of common upregulated and downregulated DEGs", "structure": {"pmcid": "PMC7844508", "section_index": 14, "section_title": "KEGG pathway enrichment analysis", "row_count": 17, "column_count": 6}, "table": {"label": "Table 2", "caption": "KEGG pathway analysis of common upregulated and downregulated DEGs", "rows": [["Pathway", "ID", "Count", "Fold Enrichment", "P value", "Genes"], ["Upregulated", "", "", "", "", ""], ["Focal adhesion", "hsa04510", "6", "7.155686546", "1.08E-03", "LAMA2, COL6A3, PDGFRA, IGF1, COL6A1, SHC1"], ["PI3K-Akt signaling pathway", "hsa04151", "6", "4.272670807", "9.99E-03", "LAMA2, COL6A3, PDGFRA, IGF1, COL6A1, GNG11"], ["Glioma", "hsa05214", "3", "11.33901099", "2.65E-02", "PDGFRA, IGF1, SHC1"], ["ECM-receptor interaction", "hsa04512", "3", "8.471674877", "4.52E-02", "LAMA2, COL6A3, COL6A1"], ["Protein digestion and absorption", "hsa04974", "3", "8.375405844", "4.62E-02", "COL6A3, CPA3, COL6A1"], ["Downregulated", "", "", "", "", ""], ["Oocyte meiosis", "hsa04114", "9", "4.323695789", "1.02E-03", "PPP2R1B, PGR, PLCZ1, SPDYA, MAPK1, CCNB2, PPP3R2, PTTG1, CDC25C"], ["Glycolysis/gluconeogenesis", "hsa00010", "7", "5.5713294", "1.46E-03", "GAPDHS, LDHC, LDHAL6B, PFKP, PGAM2, PDHA2, PGK2"], ["Cell cycle", "hsa04110", "8", "3.44036009", "8.15E-03", "CCNB2, CDC14A, DBF4, TTK, PTTG1, CCNA1, CDC25C, MCM4"], ["Progesterone-mediated oocyte maturation", "hsa04914", "6", "3.677626303", "2.26E-02", "PGR, SPDYA, MAPK1, CCNB2, CCNA1, CDC25C"], ["AMPK signaling pathway", "hsa04152", "7", "3.034789185", "2.68E-02", "PPP2R1B, CPT1B, CAB39L, PFKP, CCNA1, PPP2R2B, PPP2R3C"], ["Glucagon signaling pathway", "hsa04922", "6", "3.231853418", "3.68E-02", "LDHC, CPT1B, LDHAL6B, PPP3R2, PGAM2, PDHA2"], ["Metabolic pathways", "hsa01100", "32", "1.399851193", "3.76E-02", "INPP1, LDHC, PLCZ1, KYNU, GCNT3, SGMS2, GK2, OLAH, COX7B2, NT5C1B, ACSBG2, PGAM2, TKTL2, CERS3, AZIN2, STT3B, ALDH1A2, TYMS, GALNTL5, PHOSPHO2, PDHA2, COX6B2, PRPS1L1, PCYT2, SPAM1, ADSSL1, LDHAL6B, SI, PFKP, GAPDHS, INPP4B, PGK2"], ["Protein processing in endoplasmic reticulum", "hsa04141", "8", "2.524287877", "3.78E-02", "HSPA1L, NGLY1, STT3B, DNAJC5B, UBQLNL, HSPA4L, UBQLN3, DNAJC5G"], ["Biosynthesis of amino acids", "hsa01230", "5", "3.703165375", "4.46E-02", "PFKP, PGAM2, TKTL2, PRPS1L1, PGK2"]], "row_count": 17, "column_count": 6, "numeric_cells": 61, "header_rows": 1, "locator": "section[14]/table-wrap[1]#t2"}}, {"id": "asset:table:pmid:33532314:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dd18fd717fdab0c77ec3e4938d887041576a261c2db088dde5f64bd63c04ca01", "bytes": 1269, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#t3", "version": null, "note": "Degree values and descriptions of the top 20 hub genes", "structure": {"pmcid": "PMC7844508", "section_index": 15, "section_title": "PPI network and hub gene analysis", "row_count": 21, "column_count": 4}, "table": {"label": "Table 3", "caption": "Degree values and descriptions of the top 20 hub genes", "rows": [["Rank", "Gene symbol", "Gene description", "Degree"], ["1", "CCNB2", "Cyclin B2", "25"], ["2", "DYNLL2", "Dynein light chain LC8-type 2", "22"], ["3", "HMMR", "Hyaluronan mediated motility receptor", "21"], ["4", "KIF15", "Kinesin family member 15", "20"], ["4", "NEK2", "NIMA related kinase 2", "20"], ["6", "DLGAP5", "DLG associated protein 5", "19"], ["7", "PTTG1", "Pituitary tumor-transforming 1", "18"], ["7", "PLK4", "Polo like kinase 4", "18"], ["7", "TTK", "TTK protein kinase", "18"], ["7", "NUF2", "NUF2, NDC80 kinetochore complex component", "18"], ["11", "PBK", "PDZ binding kinase", "17"], ["12", "CEP55", "Centrosomal protein 55", "16"], ["13", "CDKN3", "Cyclin dependent kinase inhibitor 3", "15"], ["14", "CDC25C", "Cell division cycle 25C", "14"], ["15", "DNAI1", "Dynein axonemal intermediate chain 1", "13"], ["15", "MCM4", "Minichromosome maintenance complex component 4", "13"], ["17", "DNAI2", "Dynein axonemal intermediate chain 2", "12"], ["17", "PPP2R1B", "Protein phosphatase 2 scaffold subunit Abeta", "12"], ["17", "TYMS", "Thymidylate synthetase", "12"], ["20", "DYNLRB2", "Dynein light chain roadblock-type 2", "11"]], "row_count": 21, "column_count": 4, "numeric_cells": 58, "header_rows": 1, "locator": "section[15]/table-wrap[1]#t3"}}, {"id": "asset:table:pmid:33532314:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1038435750bc179bba8c44e55b013a4bba16de7ccce35aa34c6e90604c5b7a2e", "bytes": 1028, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#t4", "version": null, "note": "Hub genes and corresponded target miRNAs", "structure": {"pmcid": "PMC7844508", "section_index": 18, "section_title": "Integrated network analysis of miRNA–mRNA interactions", "row_count": 5, "column_count": 2}, "table": {"label": "Table 4", "caption": "Hub genes and corresponded target miRNAs", "rows": [["Gene", "miRNA"], ["NEK2", "hsa-miR-216a-3p"], ["CEP55", "hsa-miR-130b-3p hsa-miR-6838-5p hsa-miR-3666 hsa-miR-15b-5p"], ["PPP2R1B", "hsa-miR-382-5p hsa-miR-497-5p hsa-miR-125a-5p hsa-miR-6838-5p hsa-miR-15b-5p hsa-miR-195-5p hsa-miR-125b-5p hsa-miR-4319"], ["DYNLL2", "hsa-miR-193a-3p hsa-miR-148a-3p hsa-miR-139-5p hsa-miR-329-3p hsa-miR-330-3p hsa-miR-296-5p hsa-miR-19b-3p hsa-miR-129-2-3p hsa-miR-204-5p hsa-miR-4644 hsa-miR-1306-5p hsa-miR-130a-3p hsa-miR-130b-3p hsa-miR-150-5p hsa-miR-6088 hsa-miR-181c-5p hsa-miR-185-5p hsa-miR-148b-3p hsa-miR-193b-3p hsa-miR-195-5p hsa-miR-200a-3p hsa-miR-211 -5p hsa-miR-454-3p hsa-miR-331-3p hsa-miR-141-3p hsa-miR-103a-3p hsa-miR-129-1-3p hsa-miR-212-3p hsa-miR-328-3p hsa-miR-301b-3p hsa-miR-3666 hsa-miR-4295 hsa-miR-532-3p hsa-miR-152-3p hsa-miR-181d-5p hsa-miR-107 hsa-miR-132-3p hsa-miR-6835-3p"]], "row_count": 5, "column_count": 2, "numeric_cells": 5, "header_rows": 1, "locator": "section[18]/table-wrap[1]#t4"}}, {"id": "asset:table:pmid:33532314:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3354b0f414bf6dab8364c3e8da04de6613fe3cd5f410a272d11e1c1521f06ad9", "bytes": 933, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#t5", "version": null, "note": "Several hub genes play a functional role in spermatogenesis", "structure": {"pmcid": "PMC7844508", "section_index": 19, "section_title": "Discussion", "row_count": 10, "column_count": 3}, "table": {"label": "Table 5", "caption": "Several hub genes play a functional role in spermatogenesis", "rows": [["Gene", "Function", "Reference"], ["CCNB2", "G2/M transition in both mitosis and meiosis", "Baker et al. (19)"], ["HMMR", "Sperm count, motility and number of sperm with normal morphology", "Abu-Halima et al. (20)"], ["Nek2", "G2/M phase transition of the cell cycle", "Matsuoka et al. (21)"], ["TTK", "Mitotic checkpoint activity", "Poss et al. (22)"], ["PLK4", "Necessary for centriole duplication", "Bettencourt-Dias et al. (23)"], ["PBK", "In the outer cell layer of spermatogenic tubules", "Zhao et al. (24)"], ["CEP55", "Maintaining stable germ cell intercellular bridges", "Chang et al. (25)"], ["CDC25C", "G2/M phase transition of the cell cycle", "Nilsson et al. (26)"], ["DNAI1", "Ciliary function and ultrastructure", "Escudier et al. (27)"]], "row_count": 10, "column_count": 3, "numeric_cells": 11, "header_rows": 1, "locator": "section[19]/table-wrap[1]#t5"}}], "gaps": ["asset:data:geo:GSE108886 not downloaded", "asset:data:geo:GSE108886 licence not read", "asset:data:geo:GSE145467 not downloaded", "asset:data:geo:GSE145467 licence not read", "asset:data:geo:GSE9210 not downloaded", "asset:data:geo:GSE9210 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": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "Wilcox test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Wilcox test was used to determine whether there were differences in the expression of hub genes between the two subgroups."}}], "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": ["GSE145467", "GSE108886", "GSE9210"], "resolved_accessions": ["GSE145467", "GSE108886", "GSE9210"], "statements": ["The GSE145467 dataset, which was contributed by Hodžić et al. (11), is based on the GPL4133 platform of the Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) and includes 10 NOA samples and 10 OA testicular samples."], "basis": "The paper names GSE145467, GSE108886, GSE9210 in Gene Expression Omnibus (GEO) database 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:33532314", "data:geo:GSE108886", "asset:table:pmid:33532314:1", "asset:table:pmid:33532314:2", "asset:table:pmid:33532314:3", "asset:table:pmid:33532314:4", "asset:table:pmid:33532314:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE108886"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:43Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 29016, "completion_tokens": 1791, "cached_tokens": 784}}, "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:33532314", "type": "paper", "label": "pmid:33532314"}, {"id": "source:pmid:33532314", "type": "manuscript", "label": "PMID 33532314 full text"}, {"id": "data:geo:GSE108886", "type": "dataset", "label": "GEO GSE108886"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33532314", "type": "paper", "label": "pmid:33532314"}, {"id": "source:pmid:33532314", "type": "manuscript", "label": "PMID 33532314 full text"}, {"id": "data:geo:GSE108886", "type": "dataset", "label": "GEO GSE108886"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33532314", "type": "extraction", "used": ["source:pmid:33532314"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE108886", "type": "accession_resolution", "used": ["data:geo:GSE108886"], "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:33532314", "parent_hash": "sha256:30a33247dbd18508bc0e0b0df5627b07ab066b7d34d96a8bea7d747bb2f63d77", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE108886 licence not read", "asset:data:geo:GSE108886 not downloaded", "asset:data:geo:GSE145467 licence not read", "asset:data:geo:GSE145467 not downloaded", "asset:data:geo:GSE9210 licence not read", "asset:data:geo:GSE9210 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T00:47:27+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}}}