{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36618351", "kind": "science-record", "revision": 4, "content_hash": "sha256:480b2110c305259c47a181bebc6a8d6d957059d6ee34d13a8146d3ba53852160", "created_at": "2026-11-01T19:01:10Z", "updated_at": "2026-11-01T22:51:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "NR4A2 may be a potential diagnostic biomarker for myocardial infarction: A comprehensive bioinformatics analysis and experimental validation.", "doi": "10.3389/fimmu.2022.1061800", "pmid": "36618351", "authors": ["Dongsheng Wei", "Jiajie Qi", "Yuxuan Wang", "Luzhen Li", "Guanlin Yang", "Xinyong He", "Zhe Zhang"], "journal": "Frontiers in immunology", "year": 2022, "abstract": "Background: Myocardial infarction is a well-established severe consequence of coronary artery disease. However, the lack of effective early biomarkers accounts for the lag time before clinical diagnosis of myocardial infarction. The present study aimed to predict critical genes for the diagnosis of MI by immune infiltration analysis and establish a nomogram.\nMethods: Gene microarray data were downloaded from Gene Expression Omnibus (GEO). Differential expression analysis, single-cell sequencing, and disease ontology (DO) enrichment analysis were performed to determine the distribution of Differentially Expressed Genes (DEGs) in cell subpopulations and their correlation with MI. Next, the level of infiltration of 16 immune cells and immune functions and their hub genes were analyzed using a Single-sample Gene Set Enrichment Analysis (ssGSEA). In addition, the accuracy of critical markers for the diagnosis of MI was subsequently assessed using receiver operating characteristic curves (ROC). One datasets were used to test the accuracy of the model. Finally, the genes with the most diagnostic value for MI were screened and experimentally validated.\nResults: 335 DEGs were identified in GSE66360, including 280 upregulated and 55 downregulated genes. Single-cell sequencing results demonstrated that DEGs were mainly distributed in endothelial cells. DO enrichment analysis suggested that DEGs were highly correlated with MI. In the MI population, macrophages, neutrophils, CCR, and Parainflammation were significantly upregulated compared to the average population. NR4A2 was identified as the gene with the most significant diagnostic value in the immune scoring and diagnostic model. 191 possible drugs for the treatment of myocardial infarction were identified by drug prediction analysis. Finally, our results were validated by Real-time Quantitativepolymerase chain reaction and Western Blot of animal samples.\nConclusion: Our comprehensive in silico analysis revealed that NR4A2 has huge prospects for application in diagnosing patients with MI.", "claims": [{"id": "claim-method", "statement": "Finally, the eligible DEGs were screening and electing by the linear models for microarray (LIMMA) data package; P-value < 0.05, and |log2 FC| > 1 (16).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36618351", "locator": "sections[4] \"Characteristics of differentially expressed genes from dataset GSE66360\" paragraph 2", "quote": "Finally, the eligible DEGs were screening and electing by the linear models for microarray (LIMMA) data package; P-value < 0.05, and |log2 FC| > 1 (16)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36618351", "locator": "sections[27] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential expression analysis using Limma on the GEO dataset GSE66360 identified 335 DEGs, including 280 upregulated and 55 downregulated genes.", "kind": "quantitative", "target": {"value": 4.1, "unit": "correlation coefficient", "tolerance": null, "source": "Dataset GSE66360 was selected and underwent differential expression analysis using the “Limma” package in R 4.1.3 software. Three hundred thirty-five DEGs were identified, including 280 up- and 55 downregulated genes (log2FC > 1 and P-value <0.05)."}, "evidence": [{"asset": "source:pmid:36618351", "locator": "sections[16] \"Identification of DEGs\" paragraph 2", "quote": "Dataset GSE66360 was selected and underwent differential expression analysis using the “Limma” package in R 4.1.3 software. Three hundred thirty-five DEGs were identified, including 280 up- and 55 downregulated genes (log2FC > 1 and P-value <0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential expression analysis using Limma on the GEO dataset GSE66360 identified 335 DEGs, including 280 upregulated and 55 downregulated genes.", "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:36618351"], "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:GSE180678"], "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:GSE180678"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36618351", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2022.1061800", "sha256": "sha256:c050bfb17405dbdfa2f0d6976a77a60b040060062639b74f62b6c649fb842645", "bytes": 36855, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2022.1061800", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9815548", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE180678", "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=GSE180678", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE180678", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5467651"], "sample_count": 1, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Hypoxia inducible factors individually facilitate inflammatory myeloid metabolism and inefficient cardiac repair", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE62646", "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=GSE62646", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62646", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1530765", "GSM1530766", "GSM1530767", "GSM1530768", "GSM1530769", "GSM1530770", "GSM1530771", "GSM1530772", "GSM1530773", "GSM1530774", "GSM1530775", "GSM1530776", "GSM1530777", "GSM1530778", "GSM1530779", "GSM1530780", "GSM1530781", "GSM1530782", "GSM1530783", "GSM1530784", "GSM1530785", "GSM1530786", "GSM1530787", "GSM1530788", "GSM1530789", "GSM1530790", "GSM1530791", "GSM1530792", "GSM1530793", "GSM1530794", "GSM1530795", "GSM1530796", "GSM1530797", "GSM1530798", "GSM1530799", "GSM1530800", "GSM1530801", "GSM1530802", "GSM1530803", "GSM1530804", "GSM1530805", "GSM1530806", "GSM1530807", "GSM1530808", "GSM1530809", "GSM1530810", "GSM1530811", "GSM1530812", "GSM1530813", "GSM1530814", "GSM1530815", "GSM1530816", "GSM1530817", "GSM1530818", "GSM1530819", "GSM1530820", "GSM1530821", "GSM1530822", "GSM1530823", "GSM1530824", "GSM1530825", "GSM1530826", "GSM1530827", "GSM1530828", "GSM1530829", "GSM1530830", "GSM1530831", "GSM1530832", "GSM1530833", "GSM1530834", "GSM1530835", "GSM1530836", "GSM1530837", "GSM1530838", "GSM1530839", "GSM1530840", "GSM1530841", "GSM1530842", "GSM1530843", "GSM1530844", "GSM1530845", "GSM1530846", "GSM1530847", "GSM1530848", "GSM1530849", "GSM1530850", "GSM1530851", "GSM1530852", "GSM1530853", "GSM1530854", "GSM1530855", "GSM1530856", "GSM1530857", "GSM1530858", "GSM1530859", "GSM1530860", "GSM1530861", "GSM1530862"], "sample_count": 98, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Altered gene expression pattern in peripheral blood mononuclear cells in patients with acute myocardial infarction", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE66360", "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=GSE66360", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66360", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1620819", "GSM1620820", "GSM1620821", "GSM1620822", "GSM1620823", "GSM1620824", "GSM1620825", "GSM1620826", "GSM1620827", "GSM1620828", "GSM1620829", "GSM1620830", "GSM1620831", "GSM1620832", "GSM1620833", "GSM1620834", "GSM1620835", "GSM1620836", "GSM1620837", "GSM1620838", "GSM1620839", "GSM1620840", "GSM1620841", "GSM1620842", "GSM1620843", "GSM1620844", "GSM1620845", "GSM1620846", "GSM1620847", "GSM1620848", "GSM1620849", "GSM1620850", "GSM1620851", "GSM1620852", "GSM1620853", "GSM1620854", "GSM1620855", "GSM1620856", "GSM1620857", "GSM1620858", "GSM1620859", "GSM1620860", "GSM1620861", "GSM1620862", "GSM1620863", "GSM1620864", "GSM1620865", "GSM1620866", "GSM1620867", "GSM1620868", "GSM1620869", "GSM1620870", "GSM1620871", "GSM1620872", "GSM1620873", "GSM1620874", "GSM1620875", "GSM1620876", "GSM1620877", "GSM1620878", "GSM1620879", "GSM1620880", "GSM1620881", "GSM1620882", "GSM1620883", "GSM1620884", "GSM1620885", "GSM1620886", "GSM1620887", "GSM1620888", "GSM1620889", "GSM1620890", "GSM1620891", "GSM1620892", "GSM1620893", "GSM1620894", "GSM1620895", "GSM1620896", "GSM1620897", "GSM1620898", "GSM1620899", "GSM1620900", "GSM1620901", "GSM1620902", "GSM1620903", "GSM1620904", "GSM1620905", "GSM1620906", "GSM1620907", "GSM1620908", "GSM1620909", "GSM1620910", "GSM1620911", "GSM1620912", "GSM1620913", "GSM1620914", "GSM1620915", "GSM1620916", "GSM1620917"], "sample_count": 99, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A Whole Blood Molecular Signature for the Identification of Acute Myocardial Infarction Without Relying Upon Myonecrosis (microarray)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE180678 not downloaded", "asset:data:geo:GSE180678 licence not read", "asset:data:geo:GSE62646 not downloaded", "asset:data:geo:GSE62646 licence not read", "asset:data:geo:GSE66360 not downloaded", "asset:data:geo:GSE66360 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Finally, the eligible DEGs were screening and electing by the linear models for microarray (LIMMA) data package; P-value < 0.05, and |log2 FC| > 1 (16)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 4.1, "unit": "correlation coefficient", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE66360", "GSE62646", "GSE180678"], "resolved_accessions": ["GSE66360", "GSE62646", "GSE180678"], "statements": ["Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article."], "basis": "The paper names GSE66360, GSE62646, GSE180678 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36618351", "data:geo:GSE180678"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE180678"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:22:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9966, "completion_tokens": 1625, "cached_tokens": 188}}, "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:36618351", "type": "paper", "label": "pmid:36618351"}, {"id": "source:pmid:36618351", "type": "manuscript", "label": "PMID 36618351 full text"}, {"id": "data:geo:GSE180678", "type": "dataset", "label": "GEO GSE180678"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36618351", "type": "paper", "label": "pmid:36618351"}, {"id": "source:pmid:36618351", "type": "manuscript", "label": "PMID 36618351 full text"}, {"id": "data:geo:GSE180678", "type": "dataset", "label": "GEO GSE180678"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36618351", "type": "extraction", "used": ["source:pmid:36618351"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE180678", "type": "accession_resolution", "used": ["data:geo:GSE180678"], "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:36618351", "parent_hash": "sha256:4842d327c738f5391c12f66949650f4e429ecb1d06fd291e1a6cce6a0287c846", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE180678 licence not read", "asset:data:geo:GSE180678 not downloaded", "asset:data:geo:GSE62646 licence not read", "asset:data:geo:GSE62646 not downloaded", "asset:data:geo:GSE66360 licence not read", "asset:data:geo:GSE66360 not downloaded", "execution.not_run", "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": 0.99, "evidence": ["ysis and establish a nomogram. Methods: Gene microarray data were downloaded from Gene Expression Om", "Materials and methods Microarray data extracted from gene expression omnibus", "in Figure 1 . Dataset GSE66360 based on the Affymetrix platform ( Table 1 ) was downloaded from the"], "order_basis": "paper_text_order:472", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["me Quantitativepolymerase chain reaction and Western Blot of animal samples. Conclusion: Our comprehen"], "order_basis": "paper_text_order:1995", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s. Experimental animal preparation Twenty SD rats were divided into an experimental group (n=17) an", "uccessful modeling. After the operation, the rats were fed for seven days. The rat’s abdominal aort", "s. Experimental animal preparation Twenty SD rats were divided into an experimental group (n=1", "group (n=3). After 7 days of adaptation, the rats underwent ligation of the anterior descendin"], "order_basis": "paper_text_order:4165", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["o two groups for quantitative real-time PCR (qPCR) and WB (MI=3, control=3). This study was ap", "tration analysis, immune-related gene model, QPCR, WB experimental results data analysis, and", "ided 6 rats into two groups for quantitative real-time PCR (qPCR) and WB (MI=3, control=3). This study"], "order_basis": "paper_text_order:4821", "id": "assay:4"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Finally, the eligible DEGs were screening and electing by the linear models for microarray (LIMMA) data package; P-value < 0.05, and |log2 FC| > 1 (16)."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"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":"2026-11-04T02:10:31+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}}}