{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40820106", "kind": "science-record", "revision": 4, "content_hash": "sha256:dfdc5be8a4ddef38c3df569603865c331573f69769591a805fde1bf3699438ab", "created_at": "2026-11-01T20:30:54Z", "updated_at": "2026-11-01T22:57:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Regulatory role of LncRNA FMR1-AS1 in the pathogenesis of alzheimer's disease based on bioinformatics and in vitro experimental validation.", "doi": "10.1038/s41598-025-15242-y", "pmid": "40820106", "authors": ["Xiang Yu", "Hao Cai", "Cai He", "Zhong Ouyang", "Yongchang Li", "Liang Chen"], "journal": "Scientific reports", "year": 2025, "abstract": "Alzheimer's disease (AD) is a major cause of dementia, characterized by β-amyloid (Aβ) plaque accumulation and Tau protein hyperphosphorylation. Although long non-coding RNAs (lncRNAs) have been implicated in neurodegenerative diseases, their roles in AD remain unclear. This study analyzed RNA sequencing data from the brain tissues of 17 AD patients and 19 healthy controls (GEO: GSE138260) to construct a gene co-expression network and identified eight lncRNAs strongly associated with AD. FMR1-AS1 was selected for functional validation. In an Aβ1-42-induced SH-SY5Y neuronal injury model, overexpression of FMR1-AS1 significantly increased cell viability ([Formula: see text]), inhibited apoptosis ([Formula: see text]), and reduced Tau hyperphosphorylation ([Formula: see text]). FMR1-AS1 also alleviated oxidative stress by lowering reactive oxygen species (ROS) levels ([Formula: see text]), enhanced superoxide dismutase (SOD) activity ([Formula: see text]), and decreased malondialdehyde (MDA) content ([Formula: see text]). Knockdown of FMR1-AS1 exacerbated neuronal damage. These results demonstrate that FMR1-AS1 exerts neuroprotective effects by regulating apoptosis, oxidative stress, and Tau pathology. The study highlights FMR1-AS1 as a potential therapeutic target for AD and may advance the understanding of lncRNA-mediated regulatory mechanisms in neurodegeneration.", "claims": [{"id": "claim-method", "statement": "One-way analysis of variance (ANOVA) was used to evaluate differences among multiple groups, followed by Tukey’s or Dunnett’s post hoc multiple comparisons test. For comparisons between two groups, an unpaired two-tailed Student’s t-test was applied.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40820106", "locator": "sections[17] \"Statistical analysis\" paragraph 2", "quote": "One-way analysis of variance (ANOVA) was used to evaluate differences among multiple groups, followed by Tukey’s or Dunnett’s post hoc multiple comparisons test. For comparisons between two groups, an unpaired two-tailed Student’s t-test was applied."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analysed during this study are included in this published article and its supplementary information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40820106", "locator": "sections[38] \"notes\" paragraph 1", "quote": "All data generated or analysed during this study are included in this published article and its supplementary information files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "FMR1-AS1 exerts neuroprotective effects by regulating apoptosis, oxidative stress, and Tau pathology.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40820106", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "These results demonstrate that FMR1-AS1 exerts neuroprotective effects by regulating apoptosis, oxidative stress, and Tau pathology."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "FMR1-AS1 exerts neuroprotective effects by regulating apoptosis, oxidative stress, and Tau pathology.", "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:40820106"], "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:GSE138260"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE138260"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40820106", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-15242-y", "sha256": "sha256:0f00e2c4e72ba26c5b998cc444e31e41a2f0e0c073fbea066860e3c9c1273c06", "bytes": 81762, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-15242-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12358618", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE138260", "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=GSE138260", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE138260", "version": null, "note": "All data generated or analysed during this study are included in this published article and its supplementary information files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analysed during this study are included in this published article and its supplementary information files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4103849", "GSM4103850", "GSM4103851", "GSM4103852", "GSM4103853", "GSM4103854", "GSM4103855", "GSM4103856", "GSM4103857", "GSM4103858", "GSM4103859", "GSM4103860", "GSM4103861", "GSM4103862", "GSM4103863", "GSM4103864", "GSM4103865", "GSM4103866", "GSM4103867", "GSM4103868", "GSM4103869", "GSM4103870", "GSM4103871", "GSM4103872", "GSM4103873", "GSM4103874", "GSM4103875", "GSM4103876", "GSM4103877", "GSM4103878", "GSM4103879", "GSM4103880", "GSM4103881", "GSM4103882", "GSM4103883", "GSM4103884"], "sample_count": 36, "group_sizes": null, "group_sizes_basis": null, "platform": "27556", "taxon": "Homo sapiens", "title": "Differential expression analysis of human brain samples with Alzheimer disease versus healthy control samples", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE138260 not downloaded", "asset:data:geo:GSE138260 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "One-way analysis of variance (ANOVA) was used to evaluate differences among multiple groups, followed by Tukey’s or Dunnett’s post hoc multiple comparisons test. For comparisons between two groups, an unpaired two-tailed Student’s t-test was applied."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-3", "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": "pathway enrichment"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE138260"], "resolved_accessions": ["GSE138260"], "statements": ["All data generated or analysed during this study are included in this published article and its supplementary information files."], "basis": "The paper names GSE138260 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": [], "assets": ["source:pmid:40820106", "data:geo:GSE138260"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE138260"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:59:34Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 22323, "completion_tokens": 974, "cached_tokens": 264}}, "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:40820106", "type": "paper", "label": "pmid:40820106"}, {"id": "source:pmid:40820106", "type": "manuscript", "label": "PMID 40820106 full text"}, {"id": "data:geo:GSE138260", "type": "dataset", "label": "GEO GSE138260"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40820106", "type": "paper", "label": "pmid:40820106"}, {"id": "source:pmid:40820106", "type": "manuscript", "label": "PMID 40820106 full text"}, {"id": "data:geo:GSE138260", "type": "dataset", "label": "GEO GSE138260"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40820106", "type": "extraction", "used": ["source:pmid:40820106"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE138260", "type": "accession_resolution", "used": ["data:geo:GSE138260"], "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:40820106", "parent_hash": "sha256:d9b6158180159f93c57ed7773992ca407cd8d491034586ace5662f6a80851ce2", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE138260 licence not read", "asset:data:geo:GSE138260 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "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": ["es in AD remain unclear. This study analyzed RNA sequencing data from the brain tissues of 17 AD patient", "lysis, and experimental validation. Based on transcriptomic data from the Gene Expression Omnibus (GEO)"], "order_basis": "paper_text_order:386", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["functional validation. In an Aβ1-42-induced SH-SY5Y neuronal injury model, overexpression of FMR", "Y27 (SNL-092, Sean Biotechnology, China) was cultured in DMEM/F12 medium (12660-012, Gibco) supplemen", "51). To establish an in vitro AD cell model, SH-SY5Y cells were treated with A\\documentclass[12pt", "\\end{document}1-42 treatment on apoptosis in SH-SY5Y cells, flow cytometry was performed using an"], "order_basis": "paper_text_order:659", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["l viability ([Formula: see text]), inhibited apoptosis ([Formula: see text]), and reduced Tau hyper", "exerts neuroprotective effects by regulating apoptosis, oxidative stress, and Tau pathology. The st", "ts regulatory effects on neuronal viability, apoptosis, Tau protein phosphorylation, and oxidative", "aggregation. Flow cytometry analysis of cell apoptosis To evaluate the effect of A\\documentclass[12"], "order_basis": "paper_text_order:788", "id": "assay:3"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ldehyde (MDA) content ([Formula: see text]). Knockdown of FMR1-AS1 exacerbated neuronal damage. The", "48-F, Sino Biological Inc., Beijing, China). Transfected cells were harvested and centrifuged at 300"], "order_basis": "paper_text_order:1130", "id": "assay:4"}, {"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": ["tion Quantitative Polymerase Chain Reaction (RT-qPCR), Western blotting, MTT assay, TUNEL stainin", "n Quantitative Polymerase Chain Reaction (RT-qPCR), Western blotting, MTT assay, TUNEL stainin", "8813, Applied Biosystems, USA). Quantitative real-time PCR was performed using SYBR® Green PCR Master M", "ctions were conducted on a CFX Opus Deepwell Real-Time PCR System with the following cycling conditions"], "order_basis": "paper_text_order:2888", "id": "assay:5"}, {"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": ["itative Polymerase Chain Reaction (RT-qPCR), Western blotting, MTT assay, TUNEL staining, flow cytometry,", "ly and late apoptotic cells were quantified. Western blot analysis of Tau protein expression To invest", "of FMR1-AS1 on Tau protein phosphorylation, Western blot analysis was performed. Total proteins were"], "order_basis": "paper_text_order:2898", "id": "assay:6"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Western blotting, MTT assay, TUNEL staining, flow cytometry, and measurements of ROS, SOD, and MDA level", "ocument}$$\\beta$$\\end{document} aggregation. Flow cytometry analysis of cell apoptosis To evaluate the e", "-42 treatment on apoptosis in SH-SY5Y cells, flow cytometry was performed using an Annexin V-FITC/PI dou"], "order_basis": "paper_text_order:2943", "id": "assay:7"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["i-phospho-Tau (ab109390, 1:1000, Abcam, UK), mouse anti-Tau (ab80579, 1:1000, Abcam, UK), and r"], "order_basis": "paper_text_order:9405", "id": "assay:8"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["One-way analysis of variance (ANOVA) was used to evaluate differences among multiple groups, followed by Tukey’s or Dunnett’s post hoc multiple comparisons test. For comparisons between two groups, an unpaired two-tailed Student’s t-test was applied."], "order_basis": "consumes_earlier_output", "id": "assay:9"}]},"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":"2026-11-04T02:16:11+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}}}