{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26621834", "kind": "science-record", "revision": 7, "content_hash": "sha256:9fdf3eac4592798447fd6a67a0edb4d0250339179078514d3ee8712f9da05699", "created_at": "2026-11-01T15:40:14Z", "updated_at": "2026-11-01T21:20:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome-wide haplotype association study identify TNFRSF1A, CASP7, LRP1B, CDH1 and TG genes associated with Alzheimer's disease in Caribbean Hispanic individuals.", "doi": "10.18632/oncotarget.6391", "pmid": "26621834", "authors": ["Zhenwei Shang", "Hongchao Lv", "Mingming Zhang", "Lian Duan", "Situo Wang", "Jin Li", "Guiyou Liu", "Zhang Ruijie", "Yongshuai Jiang"], "journal": "Oncotarget", "year": 2015, "abstract": "Alzheimer's disease (AD) is an acquired disorder of cognitive and behavioral impairment. It is considered to be caused by variety of factors, such as age, environment and genetic factors. In order to identify the genetic affect factors of AD, we carried out a bioinformatic approach which combined genome-wide haplotype-based association study with gene prioritization. The raw SNP genotypes data was downloaded from GEO database (GSE33528). It contains 615 AD patients and 560 controls of Caribbean Hispanic individuals. Firstly, we identified the linkage disequilibrium (LD) haplotype blocks and performed genome-wide haplotype association study to screen significant haplotypes that were associated with AD. Then we mapped these significant haplotypes to genes and obtained candidate genes set for AD. At last, we prioritized AD candidate genes based on their similarity with 36 known AD genes, so as to identify AD related genes. The results showed that 141 haplotypes on 134 LD blocks were significantly associated with AD (P<1E-4), and these significant haplotypes were mapped to 132 AD candidate genes. After prioritizing these candidate genes, we found seven AD related genes: APOE, APOC1, TNFRSF1A, LRP1B, CDH1, TG and CASP7. Among these genes, APOE and APOC1 are known AD risk genes. For the other five genes TNFRSF1A, CDH1, CASP7, LRP1B and TG, this is the first genetic association study which showed the significant association between these five genes and AD susceptibility in Caribbean Hispanic individuals. We believe that our findings can provide a new perspective to understand the genetic affect factors of AD.", "claims": [{"id": "claim-method", "statement": "For each haplotype, we carried out a chi-square test to obtain its statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26621834", "locator": "sections[3] \"The results of genome-wide haplotype association study\" paragraph 2", "quote": "For each haplotype, we carried out a chi-square test to obtain its statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In our study, the raw SNP genotypes data was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), the GEO accession is GSE33528. It was released on May 01, 2012. The purpose of original study was to survey large rare copy number variations in late-onset AD, and they had found some meaningful results [56]. The datasets include 615 patients with late-onset AD and 560 controls of unrelated Caribbean Hispanic individuals. Its SNP chip platform is GPL14932 which includes 662,841 SNP markers.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26621834", "locator": "sections[13] \"Datasets\" paragraph 2", "quote": "In our study, the raw SNP genotypes data was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), the GEO accession is GSE33528. It was released on May 01, 2012. The purpose of original study was to survey large rare copy number variations in late-onset AD, and they had found some meaningful results [56]. The datasets include 615 patients with late-onset AD and 560 controls of unrelated Caribbean Hispanic individuals. Its SNP chip platform is GPL14932 which includes 662,841 SNP markers."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using chi-square testing of genome-wide haplotypes from GSE33528, the study identified 141 haplotypes on 134 LD blocks significantly associated with Alzheimer’s disease at P < 1E-4.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26621834", "locator": "sections[3] \"The results of genome-wide haplotype association study\" paragraph 2", "quote": "At last, we found 141 haplotypes that were significantly associated with AD (P < 1E-4, see Supplementary Table 2 in the website: http://www.bioapp.org/research/ADhaplotype). The 141 significant haplotypes were located on 134 block regions."}, {"asset": "source:pmid:26621834", "locator": "sections[14] \"Genome-wide haplotype association analysis\" paragraph 3", "quote": "Here we used the software Haploview to identify the LD blocks and performed association analysis. The method of identify LD blocks was Four Gamete Tests (FGT) which combined the impact of genetic factors into block construction. Then the Maximum Likelihood Estimation and Expectation Maximization algorithm were used to estimate the haplotypes and their frequencies. At last, the statistically significant haplotypes that associated with AD were obtained by chi-square test [57, 58]. A haplotype was considered associated with AD, if its P value of chi-square test was less than 1.0E-4."}, {"asset": "source:pmid:26621834", "locator": "sections[3] \"The results of genome-wide haplotype association study\" paragraph 2", "quote": "In this study, we carried out a genome-wide haplotype association study using SNP genotypes data of 1,175 Caribbean Hispanic individuals (GSE33528)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using chi-square testing of genome-wide haplotypes from GSE33528, the study identified 141 haplotypes on 134 LD blocks significantly associated with Alzheimer’s disease at P < 1E-4.", "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:26621834"], "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:GSE33528"], "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:GSE33528"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26621834", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.6391", "sha256": "sha256:2e56aaf0e13fabf6677e21b03400bc7d48f1710f4753c78c3046df8c76d4b2e1", "bytes": 37354, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.6391", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4767448", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE33528", "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=GSE33528", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33528", "version": null, "note": "In our study, the raw SNP genotypes data was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), the GEO accession is GSE33528. It was released on May 01, 2012. The purpose of original study was to survey large rare copy number variations in late-onset AD, and they had found some meaningful results [56]. The datasets include 615 patients with late-onset AD and 560 controls of unrelated Caribbean Hispanic individuals. Its SNP chip platform is GPL14932 which includes 662,841 SNP markers.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In our study, the raw SNP genotypes data was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), the GEO accession is GSE33528. It was released on May 01, 2012. The purpose of original study was to survey large rare copy number variations in late-onset AD, and they had found some meaningful results [56]. The datasets include 615 patients with late-onset AD and 560 controls of unrelated Caribbean Hispanic individuals. 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null, "platform": "14932", "taxon": "Homo sapiens", "title": "Genome-wide survey of large rare copy number variations in Alzheimer’s disease   among Caribbean Hispanics", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26621834:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:990593eaa2576a5d93e32509c90420a722db79b2d2561b3a7c036b6fdc7c32d4", "bytes": 549, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T1", "version": null, "note": "The top seven AD related genes of prioritization", "structure": {"pmcid": "PMC4767448", "section_index": 4, "section_title": "Mapping and prioritizing the AD candidate genes", "row_count": 8, "column_count": 4}, "table": {"label": "Table 1", "caption": "The top seven AD related genes of prioritization", "rows": [["Rank", "Ensembl gene ID", "Gene symbol", "P-value"], ["1", "ENSG00000130203", "APOE", "1.21E-09"], ["2", "ENSG00000130208", "APOC1", "1.09 E-06"], ["3", "ENSG00000067182", "TNFRSF1A", "3.63E-04"], ["4", "ENSG00000168702", "LRP1B", "3.84 E-04"], ["5", "ENSG00000039068", "CDH1", "4.88 E-04"], ["6", "ENSG00000042832", "TG", "6.21 E-04"], ["7", "ENSG00000165806", "CASP7", "9.5 E-04"]], "row_count": 8, "column_count": 4, "numeric_cells": 21, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:26621834:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0e133e1c9a4c4ad61e9e5a42b1c38845ce23abbcce557a19006be4a865745020", "bytes": 691, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T2", "version": null, "note": "The result of prioritization for reliability verification", "structure": {"pmcid": "PMC4767448", "section_index": 11, "section_title": "DISCUSSION", "row_count": 11, "column_count": 4}, "table": {"label": "Table 2", "caption": "The result of prioritization for reliability verification", "rows": [["Rank", "Ensembl gene ID", "Gene symbol", "P-value"], ["1", "ENSG00000130203", "APOE", "1.49E-05"], ["2", "ENSG00000168702", "LRP1B", "5.41E-05"], ["3", "ENSG00000067182", "TNFRSF1A", "2.09 E-04"], ["4", "ENSG00000039068", "CDH1", "4.4 E-04"], ["5", "ENSG00000042832", "TG", "4.84 E-04"], ["6", "ENSG00000184845", "DRD1", "8.55 E-04"], ["7", "ENSG00000165806", "CASP7", "1.28 E-03"], ["8", "ENSG00000130208", "APOC1", "3.63 E-03"], ["9", "ENSG00000101197", "BIRC7", "4.46 E-03"], ["10", "ENSG00000142515", "KLK3", "7.42 E-03"]], "row_count": 11, "column_count": 4, "numeric_cells": 30, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE33528 not downloaded", "asset:data:geo:GSE33528 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For each haplotype, we carried out a chi-square test to obtain its statistical significance."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["chi_square_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: chi_square."}, "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": ["GSE33528"], "resolved_accessions": ["GSE33528"], "statements": ["In our study, the raw SNP genotypes data was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), the GEO accession is GSE33528. It was released on May 01, 2012. The purpose of original study was to survey large rare copy number variations in late-onset AD, and they had found some meaningful results [56]. The datasets include 615 patients with late-onset AD and 560 controls of unrelated Caribbean Hispanic individuals. Its SNP chip platform is GPL14932 which includes 662,841 SNP markers."], "basis": "The paper names GSE33528 in GEO database (http://www.ncbi.nlm.nih.gov/geo) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["chi_square_test"], "assets": ["source:pmid:26621834", "data:geo:GSE33528", "asset:table:pmid:26621834:1", "asset:table:pmid:26621834:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE33528"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:18Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 86228, "completion_tokens": 2503, "cached_tokens": 22032}}, "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:26621834", "type": "paper", "label": "pmid:26621834"}, {"id": "source:pmid:26621834", "type": "manuscript", "label": "PMID 26621834 full text"}, {"id": "data:geo:GSE33528", "type": "dataset", "label": "GEO GSE33528"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26621834", "type": "paper", "label": "pmid:26621834"}, {"id": "source:pmid:26621834", "type": "manuscript", "label": "PMID 26621834 full text"}, {"id": "data:geo:GSE33528", "type": "dataset", "label": "GEO GSE33528"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26621834", "type": "extraction", "used": ["source:pmid:26621834"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE33528", "type": "accession_resolution", "used": ["data:geo:GSE33528"], "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:26621834", "parent_hash": "sha256:fe818594f46b45715c676ffdd2a6e2bdab2538db56ffa63acda9b117b26a894e", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE33528 licence not read", "asset:data:geo:GSE33528 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["7]. TNFRSF1A can activate NF-kappaB, mediate apoptosis, and its function as a regulator of inflamma", "central role in the execution-phase of cell apoptosis, and CASP7 is also involved in inflammation", "mber of the cysteine-aspartic acid protease (caspase) family. Studies have shown that sequential"], "order_basis": "paper_text_order:3306", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["lved in regulating microglia activation, and knockdown or chemical inhibition of it hindered microg"], "order_basis": "paper_text_order:8992", "id": "assay:2"}, {"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["For each haplotype, we carried out a chi-square test to obtain its statistical significance."], "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":"2026-11-04T01:48:49+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}}}