{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40685483", "kind": "science-record", "revision": 4, "content_hash": "sha256:a61253e2b0c5c0e0809e44ef52b3e227c25dbcd681674a4c29d63044b10bbe60", "created_at": "2026-11-01T20:30:47Z", "updated_at": "2026-11-01T22:56:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration of common pathogenic genes between cerebral amyloid angiopathy and insomnia based on bioinformatics and experimental validation.", "doi": "10.1038/s41598-025-12553-y", "pmid": "40685483", "authors": ["Xin-Yu Li", "Kun Li", "Yi-Han Wei", "Wen-Kai Yu", "Jing-Hao Wu", "Kai Gao", "Wen-Jun He", "Peng-Peng Niu", "Chan Zhang", "Yu-Nan Cheng", "Yu-Sheng Li"], "journal": "Scientific reports", "year": 2025, "abstract": "Cerebral amyloid angiopathy (CAA) and insomnia are age-related neurological disorders increasingly recognized as being closely associated. However, research on the shared genes and their biological mechanisms remains limited. This study aims to identify common genes between CAA and insomnia and explore their potential molecular mechanisms, offering new insights for diagnosis and treatment. Blood samples were collected from 11 CAA patients and 11 healthy controls, followed by RNA sequencing (RNA-seq). Additionally, the microarray dataset GSE208668 for the insomnia cohort was downloaded from the Gene Expression Omnibus (GEO) database. Differential expression analysis was performed to identify common differentially expressed genes (DEGs). Protein-protein interaction (PPI) networks and machine learning methods Random Forest (RF) and Extreme Gradient Boosting (XGBoost) were used to narrow down key genes. We explored the biological functions of these genes through immune cell infiltration, metabolic and Hallmark pathway analyses, and clinical correlation analysis. Co-expression networks, drug-mRNA networks, transcription factor (TF)-mRNA-miRNA networks, and competing endogenous RNA (ceRNA) networks were also constructed. Finally, hub gene expression patterns were analyzed using the Human Protein Atlas (HPA) database, and validation was performed in clinical samples and animal models using quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) and Western blot. Differential expression analysis identified 185 DEGs. PPI network construction and machine learning methods identified CBX5 and POLR1B as common hub genes for both insomnia and CAA. Immune infiltration, metabolic, and Hallmark pathway analyses revealed these hub genes play distinct roles in each disease. Various network models were constructed to explore their regulatory mechanisms. The reliability of the hub genes was validated using bioinformatics analyses and experimental approaches. This study, combining bioinformatics and experimental validation, identifies CBX5 and POLR1B as shared hub genes for CAA and insomnia. These findings offer new molecular targets for the diagnosis and treatment of both diseases, providing a foundation for future research.", "claims": [{"id": "claim-method", "statement": "DEGs were identified between 11 CAA samples and 11 controls, as well as between 17 insomnia samples and 25 control samples from the GSE208668 dataset, using the R package ‘limma‘(v3.54.2)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40685483", "locator": "sections[5] \"Public data provenance and differential expression analysis\" paragraph 2", "quote": "DEGs were identified between 11 CAA samples and 11 controls, as well as between 17 insomnia samples and 25 control samples from the GSE208668 dataset, using the R package ‘limma‘(v3.54.2)"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40685483", "locator": "sections[36] \"notes\" paragraph 1", "quote": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials."}], "state": "complete"}, {"id": "claim-target-result", "statement": "CBX5 and POLR1B were identified as shared hub genes for both cerebral amyloid angiopathy and insomnia.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40685483", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "PPI network construction and machine learning methods identified CBX5 and POLR1B as common hub genes for both insomnia and CAA."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "CBX5 and POLR1B were identified as shared hub genes for both cerebral amyloid angiopathy and insomnia.", "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:40685483"], "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:GSE208668"], "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:GSE208668"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40685483", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-12553-y", "sha256": "sha256:70d33cf486a423b8e525b528aec47c21c4443ebc59dac7328949b27938d1195e", "bytes": 51914, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-12553-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12277429", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE208668", "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=GSE208668", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE208668", "version": null, "note": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. 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These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T20:16:20Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE208668 not downloaded", "asset:data:geo:GSE208668 licence not read", "asset:data:geo:GSE289809 not downloaded", "asset:data:geo:GSE289809 licence not read", "asset:data:geo:GSE39445 not downloaded", "asset:data:geo:GSE39445 licence not read", "asset:data:geo:PRJNA1220702 not downloaded", "asset:data:geo:PRJNA1220702 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": "DEGs were identified between 11 CAA samples and 11 controls, as well as between 17 insomnia samples and 25 control samples from the GSE208668 dataset, using the R package ‘limma‘(v3.54.2)"}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "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": 0.8, "band": "high", "quote": "Principal component analysis"}}, {"id": "method-4", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Random Forest"}}, {"id": "method-5", "family": "machine_learning", "specific": "gradient_boosting", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Gradient Boosting"}}, {"id": "method-6", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman rank correlation"}}, {"id": "method-7", "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-8", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO 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": ["PRJNA1220702", "GSE289809", "GSE208668", "GSE39445"], "resolved_accessions": ["GSE289809", "GSE208668", "GSE39445"], "statements": ["The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials."], "basis": "The paper names GSE289809, GSE208668, GSE39445 in NCBI Sequence Read Archive (SRA) 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:40685483", "data:geo:GSE208668"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE208668"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:57:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12631, "completion_tokens": 1620, "cached_tokens": 256}}, "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:40685483", "type": "paper", "label": "pmid:40685483"}, {"id": "source:pmid:40685483", "type": "manuscript", "label": "PMID 40685483 full text"}, {"id": "data:geo:GSE208668", "type": "dataset", "label": "GEO GSE208668"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40685483", "type": "paper", "label": "pmid:40685483"}, {"id": "source:pmid:40685483", "type": "manuscript", "label": "PMID 40685483 full text"}, {"id": "data:geo:GSE208668", "type": "dataset", "label": "GEO GSE208668"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40685483", "type": "extraction", "used": ["source:pmid:40685483"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE208668", "type": "accession_resolution", "used": ["data:geo:GSE208668"], "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:40685483", "parent_hash": "sha256:c7460208726d559d74d81f913d118a4d404394101af9900193b101a6f8887fa0", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE208668 licence not read", "asset:data:geo:GSE208668 not downloaded", "asset:data:geo:GSE289809 licence not read", "asset:data:geo:GSE289809 not downloaded", "asset:data:geo:GSE39445 licence not read", "asset:data:geo:GSE39445 not downloaded", "asset:data:geo:PRJNA1220702 licence not read", "asset:data:geo:PRJNA1220702 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": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ealthy controls, followed by RNA sequencing (RNA-seq). Additionally, the microarray dataset GSE20", "atients and 11 healthy controls, followed by RNA sequencing (RNA-seq). Additionally, the microarray data", "from all 22 participants were collected for RNA-seq. The clinical characteristics of the groups", "11 age- and sex-matched healthy controls for RNA-seq. Principal component analysis demonstrated c"], "order_basis": "paper_text_order:576", "id": "assay:1"}, {"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": ["RNA sequencing (RNA-seq). Additionally, the microarray dataset GSE208668 for the insomnia cohort wa"], "order_basis": "paper_text_order:621", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tion Polymerase Chain Reaction (qRT-PCR) and Western blot. Differential expression analysis identified", "d age- and sex-matched controls. qRT-PCR and Western blot analyses were conducted to assess the transc", "CAA and insomnia patients. Both qRT-PCR and Western blot results demonstrated significantly reduced e", "AA and insomnia model mice using qRT-PCR and Western blotting. The results revealed a decrease in CBX5 exp"], "order_basis": "paper_text_order:1577", "id": "assay:3"}, {"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s of DEGs We collected blood samples from 11 patients with CAA and 11 age- and sex-matched healthy cont", "ex between the two groups. Peripheral venous blood samples from all 22 participants were collected for RNA-s", "nal enrichment analysis of DEGs We collected blood samples from 11 patients with CAA and 11 age- and sex-mat", "urther validate our bioinformatics findings, we recruited 5 CAA patients, 5 insomnia patients, and age"], "order_basis": "paper_text_order:2886", "id": "assay:4"}, {"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": ["ermates were utilized. The TgSWDI transgenic mice were sourced from Jackson Laboratory. In addition", "on, five 12-week-old male C57BL/6J wild-type mice were subjected to sleep deprivation in a transpar", "e from sleeping for 20 h daily. Five control mice were housed in the same apparatus with unrestrict", "ne week of continuous sleep deprivation, the mice were used for subsequent experimental procedures."], "order_basis": "paper_text_order:4641", "id": "assay:5"}, {"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": ["DEGs were identified between 11 CAA samples and 11 controls, as well as between 17 insomnia samples and 25 control samples from the GSE208668 dataset, using the R package ‘limma‘(v3.54.2)"], "order_basis": "consumes_earlier_output", "id": "assay:6"}]},"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":"2026-11-04T02:38:44+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}}}