{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34824764", "kind": "science-record", "revision": 4, "content_hash": "sha256:035ae751c44fdd99c51b26c1802247c9cca555320bb4d8bc9d747f98ac9b60a7", "created_at": "2026-11-01T17:36:31Z", "updated_at": "2026-11-01T22:05:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and Analysis of Key Genes in miRNA-mRNA Regulatory Network of Membranous Nephropathy.", "doi": "10.1155/2021/5331948", "pmid": "34824764", "authors": ["Yawei Hou", "Yameng Li", "Yichuan Wang", "Wenpu Li", "Zhenwei Xiao"], "journal": "Journal of healthcare engineering", "year": 2021, "abstract": "Background: MicroRNAs (miRNAs) are confirmed to participate in occurrence, development, and prevention of membranous nephropathy (MN), but their mechanism of action is unclear.\nObjective: With the GEO database and the use of bioinformatics, miRNA-mRNA regulatory network genes relevant to MN were explored and their potential mechanism of action was explained.\nMethods: The MN-related miRNA chip data set (GSE51674) and mRNA chip data set (GSE108109) were downloaded from the GEO database. Differential analysis was performed using the GEO2R online tool. TargetScan, miRTarBase, and StarBase databases were used to predict potential downstream target genes regulated by differentially expressed miRNAs, and the intersection with differential genes were taken to obtain candidate target genes. According to the regulatory relationship between miRNA and mRNA, the miRNA-mRNA relationship pair was clarified and Cytoscape was used to construct a miRNA-mRNA regulatory network. WebGestalt was used to conduct enrichment analysis of the biological process of differential mRNAs in the regulatory network; FunRich analyzes the differential mRNA pathways in the miRNA-mRNA regulatory network. And the STRING database was used to construct a PPI network for candidate target genes, and Cytoscape visually analyzes the PPI network.\nResults: Experiments were conducted to screen differentially expressed miRNAs and mRNAs. There were 30 differentially expressed miRNAs, including 22 upregulated and 8 downregulated; and 1267 differentially expressed mRNAs, including 536 upregulated and 731 downregulated. Using TargetScan, miRTarBase, and StarBase databases to predict the downstream targets of differentially expressed miRNAs, 2957 downstream target genes coexisting in the 3 databases were predicted to intersect with differentially expressed mRNAs to obtain 175 candidate target genes. Finally, 36 miRNA-mRNA relationship pairs comprising 10 differentially expressed miRNAs and 27 differentially expressed mRNAs were screened out, and the regulatory network was constructed. Further analysis revealed that the miRNA regulatory network genes may be involved in the development of membranous nephropathy by mTOR, PDGFR-β, LKB1, and VEGF/VEGFR signaling pathways.\nConclusion: The miRNA regulatory network genes may participate in the regulation of podocyte autophagy, lipid metabolism, and renal fibrosis through mTOR, PDGFR-β, LKB1, and VEGF/VEGFR signaling pathways, thereby affecting the occurrence and development of membranous nephropathy.", "claims": [{"id": "claim-method", "statement": "The online analysis tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) from NCBI's GEO online analysis tool was used to obtain differential mRNAs and miRNAs and screen the differential genes. The standard setting is adj. p value <0.01 and |log2 fold change (FC)| > 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34824764", "locator": "sections[7] \"2.4.1. Data Processing and Differential Expression Analysis\" paragraph 2", "quote": "The online analysis tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) from NCBI's GEO online analysis tool was used to obtain differential mRNAs and miRNAs and screen the differential genes. The standard setting is adj. p value <0.01 and |log2 fold change (FC)| > 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34824764", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Finally, 36 miRNA-mRNA relationship pairs comprising 10 differentially expressed miRNAs and 27 differentially expressed mRNAs were screened out, and the regulatory network was constructed.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34824764", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Finally, 36 miRNA-mRNA relationship pairs comprising 10 differentially expressed miRNAs and 27 differentially expressed mRNAs were screened out, and the regulatory network was constructed."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Finally, 36 miRNA-mRNA relationship pairs comprising 10 differentially expressed miRNAs and 27 differentially expressed mRNAs were screened out, and the regulatory network was constructed.", "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:34824764"], "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:GSE108109"], "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:GSE108109"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34824764", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/5331948", "sha256": "sha256:741a61d9ecd2eb465a9ebc0018d9fbc95478627ef06a9e6d523744331b44cb45", "bytes": 34694, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/5331948", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8610666", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE108109", "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=GSE108109", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE108109", "version": null, "note": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2889849", "GSM2889850", "GSM2889851", "GSM2889852", "GSM2889853", "GSM2889854", "GSM2889855", "GSM2889856", "GSM2889857", "GSM2889858", "GSM2889859", "GSM2889860", "GSM2889861", "GSM2889862", "GSM2889863", "GSM2889864", "GSM2889865", "GSM2889866", "GSM2889867", "GSM2889868", "GSM2889869", "GSM2889870", "GSM2889871", "GSM2889872", "GSM2889873", "GSM2889874", "GSM2889875", "GSM2889876", "GSM2889877", "GSM2889878", "GSM2889879", "GSM2889880", "GSM2889881", "GSM2889882", "GSM2889883", "GSM2889884", "GSM2889885", "GSM2889886", "GSM2889887", "GSM2889888", "GSM2889889", "GSM2889890", "GSM2889891", "GSM2889892", "GSM2889893", "GSM2889894", "GSM2889895", "GSM2889896", "GSM2889897", "GSM2889898", "GSM2889899", "GSM2889900", "GSM2889901", "GSM2889902", "GSM2889903", "GSM2889904", "GSM2889905", "GSM2889906", "GSM2889907", "GSM2889908", "GSM2889909", "GSM2889910", "GSM2889911", "GSM2889912", "GSM2889913", "GSM2889914", "GSM2889915", "GSM2889916", "GSM2889917", "GSM2889918", "GSM2889919", "GSM2889920", "GSM2889921", "GSM2889922", "GSM2889923", "GSM2889924", "GSM2889925", "GSM2889926", "GSM2889927", "GSM2889928", "GSM2889929", "GSM2889930", "GSM2889931", "GSM2889932", "GSM2889933", "GSM2889934", "GSM2889935", "GSM2889936", "GSM2889937", "GSM2889938", "GSM2889939", "GSM2889940", "GSM2889941", "GSM2889942", "GSM2889943", "GSM2889944", "GSM2889945", "GSM2889946", "GSM2889947", "GSM2889948", "GSM2889949", "GSM2889950", "GSM2889951", "GSM2889952", "GSM2889953", "GSM2889954", "GSM2889955", "GSM2889956", "GSM2889957", "GSM2889958", "GSM2889959"], "sample_count": 111, "group_sizes": null, "group_sizes_basis": null, "platform": "19983", "taxon": "Homo sapiens", "title": "Shared molecular targets in the glomerular transcriptome from patients with nephrotic syndrome and ANCA-associated vasculitis", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE108113", "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=GSE108113", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE108113", "version": null, "note": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2889849", "GSM2889850", "GSM2889851", "GSM2889852", "GSM2889853", "GSM2889854", "GSM2889855", "GSM2889856", "GSM2889857", "GSM2889858", "GSM2889859", "GSM2889860", "GSM2889861", "GSM2889862", "GSM2889863", "GSM2889864", "GSM2889865", "GSM2889866", "GSM2889867", "GSM2889868", "GSM2889869", "GSM2889870", "GSM2889871", "GSM2889872", "GSM2889873", "GSM2889874", "GSM2889875", "GSM2889876", "GSM2889877", "GSM2889878", "GSM2889879", "GSM2889880", "GSM2889881", "GSM2889882", "GSM2889883", "GSM2889884", "GSM2889885", "GSM2889886", "GSM2889887", "GSM2889888", "GSM2889889", "GSM2889890", "GSM2889891", "GSM2889892", "GSM2889893", "GSM2889894", "GSM2889895", "GSM2889896", "GSM2889897", "GSM2889898", "GSM2889899", "GSM2889900", "GSM2889901", "GSM2889902", "GSM2889903", "GSM2889904", "GSM2889905", "GSM2889906", "GSM2889907", "GSM2889908", "GSM2889909", "GSM2889910", "GSM2889911", "GSM2889912", "GSM2889913", "GSM2889914", "GSM2889915", "GSM2889916", "GSM2889917", "GSM2889918", "GSM2889919", "GSM2889920", "GSM2889921", "GSM2889922", "GSM2889923", "GSM2889924", "GSM2889925", "GSM2889926", "GSM2889927", "GSM2889928", "GSM2889929", "GSM2889930", "GSM2889931", "GSM2889932", "GSM2889933", "GSM2889934", "GSM2889935", "GSM2889936", "GSM2889937", "GSM2889938", "GSM2889939", "GSM2889940", "GSM2889941", "GSM2889942", "GSM2889943", "GSM2889944", "GSM2889945", "GSM2889946", "GSM2889947", "GSM2889948", "GSM2889949", "GSM2889950", "GSM2889951", "GSM2889952", "GSM2889953", "GSM2889954", "GSM2889955", "GSM2889956", "GSM2889957", "GSM2889958", "GSM2889959", "GSM2890019", "GSM2890020", "GSM2890021", "GSM2890022", "GSM2890023", "GSM2890024", "GSM2890025", "GSM2890026", "GSM2890027", "GSM2890028", "GSM2890029", "GSM2890030", "GSM2890031", "GSM2890032", "GSM2890033", "GSM2890034", "GSM2890035", "GSM2890036", "GSM2890037", "GSM2890038", "GSM2890039", "GSM2890040", "GSM2890041", "GSM2890042", "GSM2890043", "GSM2890044", "GSM2890045", "GSM2890046", "GSM2890047", "GSM2890048", "GSM2890049", "GSM2890050", "GSM2890051", "GSM2890052", "GSM2890053", "GSM2890054", "GSM2890055", "GSM2890056", "GSM2890057", "GSM2890058", "GSM2890059", "GSM2890060", "GSM2890061", "GSM2890062", "GSM2890063", "GSM2890064", "GSM2890065", "GSM2890066", "GSM2890067", "GSM2890068", "GSM2890069", "GSM2890070", "GSM2890071", "GSM2890072", "GSM2890073", "GSM2890074", "GSM2890075", "GSM2890076", "GSM2890077", "GSM2890078", "GSM2890079", "GSM2890080", "GSM2890081", "GSM2890082", "GSM2890083", "GSM2890084", "GSM2890085", "GSM2890086", "GSM2890087", "GSM2890088", "GSM2890089", "GSM2890090", "GSM2890091", "GSM2890092", "GSM2890093", "GSM2890094", "GSM2890095", "GSM2890096", "GSM2890097", "GSM2890098", "GSM2890099", "GSM2890100", "GSM2890101", "GSM2890102", "GSM2890103", "GSM2890104", "GSM2890105", "GSM2890106", "GSM2890107", "GSM2890108", "GSM2890109", "GSM2890110", "GSM2890111", "GSM2890112", "GSM2890113", "GSM2890114", "GSM2890115", "GSM2890116", "GSM2890117", "GSM2890118", "GSM2890119", "GSM2890120", "GSM2890121", "GSM2890122", "GSM2890123", "GSM2890124", "GSM2890125", "GSM2890126", "GSM2890127", "GSM2890128", "GSM2890129", "GSM2890130", "GSM2890131", "GSM2890132", "GSM2890133", "GSM2890134", "GSM2890135", "GSM2890136", "GSM2890137", "GSM2890138", "GSM2890139", "GSM2890140", "GSM2890141", "GSM2890142", "GSM2890143", "GSM2890144", "GSM2890145", "GSM2890146", "GSM2890147", "GSM2890148", "GSM2890149", "GSM2890150", "GSM2890151", "GSM2890152", "GSM2890153", "GSM2890154", "GSM2890155", "GSM2890156", "GSM2890157", "GSM2890158", "GSM2890159", "GSM2890160", "GSM2890161", "GSM2890162", "GSM2890163", "GSM2890164", "GSM2890165", "GSM2890166", "GSM2890167", "GSM2890168", "GSM2890169", "GSM2890170", "GSM2890171", "GSM2890172", "GSM2890173", "GSM2890174", "GSM2890175", "GSM2890176", "GSM2890177", "GSM2890178", "GSM2890179", "GSM2890180", "GSM2890181", "GSM2890182", "GSM2890183", "GSM2890184", "GSM2890185", "GSM2890186", "GSM2890187"], "sample_count": 280, "group_sizes": null, "group_sizes_basis": null, "platform": "19983", "taxon": "Homo sapiens", "title": "Shared molecular targets in the glomerular and tubulointerstitial transcriptomes from patients with nephrotic syndrome and ANCA-associated vasculitis", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE51674", "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=GSE51674", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE51674", "version": null, "note": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1581506", "GSM1581507", "GSM1581508", "GSM1581509", "GSM1581510", "GSM1581511", "GSM1581512", "GSM1581513", "GSM1581514", "GSM1581517", "GSM3181593", "GSM3181594", "GSM3181595", "GSM3181596", "GSM3181597", "GSM3181598"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "10656", "taxon": "Homo sapiens", "title": "miRNA-27b-3p and miRNA-1228-3p correlate with the progression of Kidney Fibrosis in Diabetic Nephropathy", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE108109 not downloaded", "asset:data:geo:GSE108109 licence not read", "asset:data:geo:GSE108113 not downloaded", "asset:data:geo:GSE108113 licence not read", "asset:data:geo:GSE51674 not downloaded", "asset:data:geo:GSE51674 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": "PPI"}}, {"id": "method-2", "family": null, "specific": null, "label": "Differential expression analysis using GEO2R with adj. p value <0.01 and |log2 fold change (FC)| > 1.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The online analysis tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) from NCBI's GEO online analysis tool was used to obtain differential mRNAs and miRNAs and screen the differential genes. The standard setting is adj. p value <0.01 and |log2 fold change (FC)| > 1."}}], "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": ["GSE51674", "GSE108109", "GSE108113"], "resolved_accessions": ["GSE51674", "GSE108109", "GSE108113"], "statements": ["The simulation experiment data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE51674, GSE108109, GSE108113 in GEO (Gene Expression Omnibus) database of NCBI 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:34824764", "data:geo:GSE108109"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE108109"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:08:55Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10526, "completion_tokens": 1557, "cached_tokens": 128}}, "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:34824764", "type": "paper", "label": "pmid:34824764"}, {"id": "source:pmid:34824764", "type": "manuscript", "label": "PMID 34824764 full text"}, {"id": "data:geo:GSE108109", "type": "dataset", "label": "GEO GSE108109"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34824764", "type": "paper", "label": "pmid:34824764"}, {"id": "source:pmid:34824764", "type": "manuscript", "label": "PMID 34824764 full text"}, {"id": "data:geo:GSE108109", "type": "dataset", "label": "GEO GSE108109"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34824764", "type": "extraction", "used": ["source:pmid:34824764"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE108109", "type": "accession_resolution", "used": ["data:geo:GSE108109"], "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:34824764", "parent_hash": "sha256:3907a95f3d2b1c157c0e7ae41f4776341489b88648c967acd8db31d2913d2f50", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE108109 licence not read", "asset:data:geo:GSE108109 not downloaded", "asset:data:geo:GSE108113 licence not read", "asset:data:geo:GSE108113 not downloaded", "asset:data:geo:GSE51674 licence not read", "asset:data:geo:GSE51674 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": ["PPI"], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:59:14+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}}}