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The aim of this study was to explore the effects of OPCAB on the basis of the associated molecular mechanisms. GSE12486 expression profiles downloaded from the Gene Expression Omnibus database (GEO) were analyzed to identify the differentially expressed genes (DEGs). Principal component analysis (PCA) was conducted based on the expression profiles of DEGs. Function and pathway enrichment of upregulated DEGs was performed, followed by protein-protein interaction (PPI) network construction. Gene Set Enrichment Analysis (GSEA) was used for miRNA enrichment analysis based on expression profiles and prediction of their association with the disease. Cytoscape was applied to construct miRNA regulatory networks of DEGs. In total 64 DEGs were identified, including 63 upregulated and 1 downregulated gene. The first principal component in the PCA analysis was able to distinguish between pre- and post-OPCAB samples. Upregulated DEGs mainly enriched 20 Gene Ontology terms, such as chemokine activity, and 5 pathways including the chemokine signaling pathway. The constructed PPI network contained 234 edges and 55 nodes, and 10 upregulated hub nodes, including FBJ murine osteosarcoma viral oncogene homolog (FOS), were screened. A total of 36 miRNAs, including MIR-224 and MIR-7, were screened by GSEA enrichment analysis. A miRNA regulatory network including 176 edges and 97 nodes was constructed, showing the regulatory relationships between miRNAs and DEGs. For example, early growth response 2 (EGR2) was regulated by 8 miRNAs including MIR-150, MIR-142-3P, MIR-367 and MIR-224. The identified DEGs might play important roles in patients pre- and post-OPCAB surgery via the regulation of associated genes.", "claims": [{"id": "claim-method", "statement": "The limma multiple linear regression package (16) was applied for the calculation and analysis of DEGs, with further rectification by the Bayes method (17).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26998004", "locator": "sections[5] \"Data preprocessing and DEG screening\" paragraph 2", "quote": "The limma multiple linear regression package (16) was applied for the calculation and analysis of DEGs, with further rectification by the Bayes method (17)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profile GSE12486 was obtained from the Gene Expression Omnibus database (GEO; http://www.ncbi.nlm.nih.gov/geo/) (9).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26998004", "locator": "sections[4] \"Microarray data\" paragraph 2", "quote": "The gene expression profile GSE12486 was obtained from the Gene Expression Omnibus database (GEO; http://www.ncbi.nlm.nih.gov/geo/) (9)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used the limma multiple linear regression package with Bayes-method rectification for differential expression analysis, using GSE12486 expression profiles downloaded from the Gene Expression Omnibus (GEO) database as the source data; it identified 64 DEGs, including 63 upregulated and 1 downregulated gene.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26998004", "locator": "sections[5] \"Data preprocessing and DEG screening\" paragraph 2", "quote": "The limma multiple linear regression package (16) was applied for the calculation and analysis of DEGs, with further rectification by the Bayes method (17)."}, {"asset": "source:pmid:26998004", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "GSE12486 expression profiles downloaded from the Gene Expression Omnibus database (GEO) were analyzed to identify the differentially expressed genes (DEGs)."}, {"asset": "source:pmid:26998004", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In total 64 DEGs were identified, including 63 upregulated and 1 downregulated gene."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used the limma multiple linear regression package with Bayes-method rectification for differential expression analysis, using GSE12486 expression profiles downloaded from the Gene Expression Omnibus (GEO) database as the source data; it identified 64 DEGs, including 63 upregulated and 1 downregulated gene.", "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:26998004"], "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. 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"Chemotaxis", "2.21E-12", "CCL3, IL6, CCL2, C5AR1, IL8, CXCL2, S100A9, CCL8, CCL4, PROK2, CXCR4, CCL3L1, CCL3L3, CYR61"], ["BP", "GO:0006954", "Inflammatory response", "3.29E-12", "NFKBIZ, IL6, CCL3, CCL2, IL8, S100A8, CXCL2, S100A9, CCL8, CCL4, S100A12, FOS, PROK2, CXCR4, CCL3L1, CCL3L3, SELE"], ["BP", "GO:0007626", "Locomotory behavior", "8.03E-11", "CCL3, IL6, CCL2, C5AR1, IL8, CXCL2, S100A9, NR4A2, CCL8, CCL4, PROK2, CXCR4, CCL3L1, CCL3L3, CYR61"], ["BP", "GO:0006952", "Defense response", "3.10E-10", "NFKBIZ, IL6, CCL3, CCL2, C5AR1, IL8, S100A8, CXCL2, S100A9, CCL8, CCL4, S100A12, CD83, PROK2, FOS, CXCR4, CCL3L1, CCL3L3, SELE"], ["BP", "GO:0009611", "Response to wounding", "3.11E-09", "NFKBIZ, IL6, CCL3, CCL2, IL8, S100A8, CXCL2, S100A9, CCL8, CCL4, S100A12, FOS, PROK2, CXCR4, CCL3L1, CCL3L3, SELE"], ["BP", "GO:0010033", "Response to organic substance", "3.51E-09", "EGR1, IL6, EGR2, CCL2, PTGS2, SOCS3, NR4A2, NR4A3, PMAIP1, JUNB, CD83, FOS, DUSP1, BTG2, JUN, SELE, MYC, CYR61"], 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["hsa04010", "MAPK signaling pathway", "0.008586", "DUSP5, FOS, DUSP1, JUN, GADD45B, MYC"]], "row_count": 6, "column_count": 4, "numeric_cells": 11, "header_rows": 1, "locator": "section[15]/table-wrap[2]#tIII-etm-0-0-3003"}}, {"id": "asset:table:pmid:26998004:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:675960d9017851e499766d08bc72215f48259c31b83fcded9551b2595a201cdf", "bytes": 640, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#tIV-etm-0-0-3003", "version": null, "note": "Top 10 nodes in the protein-protein interaction network.", "structure": {"pmcid": "PMC4774345", "section_index": 16, "section_title": "PPI network construction", "row_count": 6, "column_count": 8}, "table": {"label": "Table IV.", "caption": "Top 10 nodes in the protein-protein interaction network.", "rows": [["Node", "Degree", "Log2FC", "P-value", 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enriched miRNAs.", "structure": {"pmcid": "PMC4774345", "section_index": 17, "section_title": "miRNA prediction analysis", "row_count": 37, "column_count": 6}, "table": {"label": "Table V.", "caption": "Significantly enriched miRNAs.", "rows": [["Namea", "Sizeb", "ES", "NES", "NOM P-value", "FDR q-value"], ["GTGACTT, MIR-224", "152", "0.562058", "1.822214", "0", "0.013101"], ["GTCTTCC, MIR-7", "163", "0.437548", "1.825578", "0", "0.013673"], ["CAGGTCC, MIR-492", "59", "0.559375", "1.757292", "0", "0.015391"], ["AGCGCTT, MIR-518F, MIR-518E, MIR-518A", "18", "0.632514", "1.786852", "0.019417", "0.015701"], ["CTGTTAC, MIR-194", "102", "0.514465", "1.748545", "0", "0.015956"], ["ATTACAT, MIR-380-3P", "100", "0.568861", "1.741315", "0", "0.01598"], ["CAGGGTC, MIR-504", "83", "0.447092", "1.763647", "0", "0.016012"], ["CACTGCC, MIR-34A, MIR-34C, MIR-449", "273", "0.327004", "1.722042", "0", "0.017363"], ["GTAAACC, MIR-299–5P", "51", "0.518946", "1.692057", "0", "0.018053"], ["ACACTAC, MIR-142–3P", "127", "0.5551", "1.722499", "0", "0.018404"], ["TCTATGA, MIR-376A, MIR-376B", "81", "0.461825", "1.694669", "0.007561", "0.018496"], ["TTGGGAG, MIR-150", "89", "0.463794", "1.681071", "0", "0.019215"], ["GGCACAT, MIR-455", "57", "0.545086", "1.868148", "0", "0.019345"], ["GCGCCTT, MIR-525, MIR-524", "15", "0.735336", "1.694803", "0.020121", "0.019371"], ["ACTGCCT, MIR-34B", "212", "0.400143", "1.70374", "0", "0.019561"], ["GGCACTT, MIR-519E", "120", "0.49198", "1.675179", "0", "0.020529"], ["AGGCACT, MIR-515–3P", "84", "0.428035", "1.666043", "0", "0.021838"], ["GACTGTT, MIR-212, MIR-132", "154", "0.457287", "1.655331", "0", "0.022945"], ["TATTATA, MIR-374", "282", "0.49871", "1.650721", "0", "0.023073"], ["CACCAGC, MIR-138", "217", "0.31838", "1.645393", "0", "0.024967"], ["CTACCTC, LET-7A, LET-7B, LET-7C, LET-7D, LET-7E, LET-7F, MIR-98, LET-7G, LET-7I", "375", "0.358576", "1.62671", "0", "0.03133"], ["GAGCCAG, MIR-149", "143", "0.30404", "1.62081", "0", "0.031399"], ["CCACACA, MIR-147", "59", "0.485473", "1.621963", "0", "0.032141"], ["ACTTTAT, MIR-142–5P", "283", "0.475001", "1.606214", "0", "0.034741"], ["AAAGGAT, MIR-501", "125", "0.459692", "1.600922", "0", "0.035487"], ["AGCACTT, MIR-93, MIR-302A, MIR-302B, MIR-302C, MIR-302D, MIR-372, MIR-373, MIR-520E, MIR-520A, MIR-526B, MIR-520B, MIR-520C, MIR-520D", "330", "0.465894", "1.606906", "0.005814", "0.035811"], ["CACTTTG, MIR-520G, MIR-520H", "230", "0.487052", "1.602", "0.003876", "0.036012"], ["CAATGCA, MIR-33", "91", "0.479179", "1.607379", "0", "0.036792"], ["GTGCAAT, MIR-25, MIR-32, MIR-92, MIR-363, MIR-367", "304", "0.440998", "1.581268", "0", "0.042634"], ["ATGTTTC, MIR-494", "155", "0.455721", "1.578166", "0.015717", "0.043117"], ["GCAAAAA, MIR-129", "182", "0.431128", "1.577369", "0.031558", "0.043279"], ["GACAATC, MIR-219", "138", "0.403393", "1.574232", "0", "0.0444"], ["CTAGGAA, MIR-384", "64", "0.439962", "1.566436", "0", "0.044528"], ["CACTGTG, MIR-128A, MIR-128B", "327", "0.344783", "1.567878", "0.005941", "0.045063"], ["TATCTGG, MIR-488", "60", "0.520626", "1.568708", "0", "0.045787"], ["GGGCATT, MIR-365", "107", "0.509769", "1.558457", "0.003883", "0.04858"]], "row_count": 37, "column_count": 6, "numeric_cells": 216, "header_rows": 1, "locator": "section[17]/table-wrap[1]#tV-etm-0-0-3003"}}], "gaps": ["asset:data:geo:GSE12486 not downloaded", "asset:data:geo:GSE12486 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The limma multiple linear regression package (16) was applied for the calculation and analysis of DEGs, with further rectification by the Bayes method (17)."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Principal component analysis"}}, {"id": "method-3", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "linear regression"}}, {"id": "method-4", "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-5", "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"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE12486"], "resolved_accessions": ["GSE12486"], "statements": ["The gene expression profile GSE12486 was obtained from the Gene Expression Omnibus database (GEO; http://www.ncbi.nlm.nih.gov/geo/) (9)."], "basis": "The paper names GSE12486 in Gene Expression Omnibus database (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:26998004", "data:geo:GSE12486", "asset:table:pmid:26998004:1", "asset:table:pmid:26998004:2", "asset:table:pmid:26998004:3", "asset:table:pmid:26998004:4", "asset:table:pmid:26998004:5", "asset:table:pmid:26998004:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12486"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:00Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 61504, "completion_tokens": 1923, "cached_tokens": 30720}}, "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:26998004", "type": "paper", "label": "pmid:26998004"}, {"id": "source:pmid:26998004", "type": "manuscript", "label": "PMID 26998004 full text"}, {"id": "data:geo:GSE12486", "type": "dataset", "label": "GEO GSE12486"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26998004", "type": "paper", "label": "pmid:26998004"}, {"id": "source:pmid:26998004", "type": "manuscript", "label": "PMID 26998004 full text"}, {"id": "data:geo:GSE12486", "type": "dataset", "label": "GEO GSE12486"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26998004", "type": "extraction", "used": ["source:pmid:26998004"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12486", "type": "accession_resolution", "used": ["data:geo:GSE12486"], "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:26998004", "parent_hash": "sha256:32a6e281f4cb27a862d7207277dd5cfab7228195711e792cedafbc2bd0f76523", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE12486 licence not read", "asset:data:geo:GSE12486 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Expression profile analysis based on DNA microarray for patients undergoing off-pump coronary ar"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["and 10 upregulated hub nodes, including FBJ murine osteosarcoma viral oncogene homolog (FOS), w"], "order_basis": "paper_text_order:1348", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The limma multiple linear regression package (16) was applied for the calculation and analysis of DEGs, with further rectification by the Bayes method (17)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:53:17+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}}}