{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36443762", "kind": "science-record", "revision": 2, "content_hash": "sha256:a3fdbe1cce851655f75e0ac794c197f7f9b96cdac2cfb61e8e6a37c852bdd75d", "created_at": "2026-11-01T19:00:55Z", "updated_at": "2026-11-01T21:29:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Blood DNA methylation signatures of lifestyle exposures: tobacco and alcohol consumption.", "doi": "10.1186/s13148-022-01376-7", "pmid": "36443762", "authors": ["Jonviea D Chamberlain", "Sébastien Nusslé", "Laurence Chapatte", "Cassandre Kinnaer", "Dusan Petrovic", "Sylvain Pradervand", "Murielle Bochud", "Sarah E Harris", "Janie Corley", "Simon R Cox", "Semira Gonseth Nusslé"], "journal": "Clinical epigenetics", "year": 2022, "abstract": "BACKGROUND: Smoking and alcohol consumption may compromise health by way of epigenetic modifications. Epigenetic signatures of alcohol and tobacco consumption could provide insights into the reversibility of phenotypic changes incurred with differing levels of lifestyle exposures. This study describes and validates two novel epigenetic signatures of tobacco (EpiTob) and alcohol (EpiAlc) consumption and investigates their association with disease outcomes.\nMETHODS: The epigenetic signatures, EpiTob and EpiAlc, were developed using data from the Swiss Kidney Project on Genes in Hypertension (SKIPOGH) (N = 689). Epigenetic and phenotypic data available from the 1921 (N = 550) and 1936 (N = 1091) Lothian Birth Cohort (LBC) studies, and two publicly available datasets on GEO Accession (GSE50660, N = 464; and GSE110043, N = 94) were used to validate the signatures. A multivariable logistic regression model, adjusting for age and sex, was used to assess the association between self-reported tobacco or alcohol consumption and the respective epigenetic signature, as well as to estimate the association between CVD and epigenetic signatures. A Cox proportional hazard model was used to estimate the risk of mortality in association with the EpiTob and EpiAlc signatures.\nRESULTS: The EpiTob signature was positively associated with self-reported tobacco consumption for current or never smokers with explained variance ranging from 0.49 (LBC1921) to 0.72 (LBC1936) (pseudo-R2). In the SKIPOGH, LBC1921 and LBC1936 cohorts, the epigenetic signature for alcohol consumption explained limited variance in association with self-reported alcohol status [i.e., non-drinker, moderate drinker, and heavy drinker] (pseudo-R2 = 0.05, 0.03 and 0.03, respectively), although this improved considerably when measuring self-reported alcohol consumption with standardized units consumed per week (SKIPOGH R2 = 0.21; LBC1921 R2 = 0.31; LBC1936 R2 = 0.41). Both signatures were associated with history of CVD in SKIPOGH and LBC1936, but not in LBC1921. The EpiTob signature was associated with increased risk of all-cause and lung-cancer specific mortality in the 1936 and 1921 LBC cohorts.\nCONCLUSIONS: This study found the EpiTob and EpiAlc signatures to be well-correlated with self-reported exposure status and associated with long-term health outcomes. Epigenetic signatures of lifestyle exposures may reduce measurement issues and biases and could aid in risk stratification for informing early-stage targeted interventions.", "claims": [{"id": "claim-method", "statement": "Logistic regression models were used to investigate the association between EpiTob and EpiAlc and CVD, individually.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36443762", "locator": "sections[9] \"Statistical analyses\" paragraph 3", "quote": "Logistic regression models were used to investigate the association between EpiTob and EpiAlc and CVD, individually."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data for the SKIPOGH cohort is available upon formal request submitted to the SKIPOGH steering committee (https://www.maelstrom-research.org/study/skipogh). Data for both LBC studies are available upon formal request, additional information can be found on the website: https://www.ed.ac.uk/lothian-birth-cohorts/data-access-collaboration. All epigenetic signatures are available upon request for non-commercial use by contacting genknowme at labo@genknowme.com.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36443762", "locator": "sections[28] \"notes\" paragraph 1", "quote": "Data for the SKIPOGH cohort is available upon formal request submitted to the SKIPOGH steering committee (https://www.maelstrom-research.org/study/skipogh). Data for both LBC studies are available upon formal request, additional information can be found on the website: https://www.ed.ac.uk/lothian-birth-cohorts/data-access-collaboration. All epigenetic signatures are available upon request for non-commercial use by contacting genknowme at labo@genknowme.com."}], "state": "complete"}, {"id": "claim-target-result", "statement": "When adjusting for age, sex, BMI, self-reported drinking status and education, a one standard deviation increase in the EpiTob signature was associated with a 31% higher odds of CVD in the SKIPOGH cohort (OR = 1.31, 95% CI 1.04–1.64), and a 16% increased odds in the LBC1936 cohort, albeit not significant (OR = 1.16, 95% CI 0.99–1.35).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36443762", "locator": "sections[14] \"Association with cardiovascular disease\" paragraph 2", "quote": "When adjusting for age, sex, BMI, self-reported drinking status and education, a one standard deviation increase in the EpiTob signature was associated with a 31% higher odds of CVD in the SKIPOGH cohort (OR = 1.31, 95% CI 1.04–1.64), and a 16% increased odds in the LBC1936 cohort, albeit not significant (OR = 1.16, 95% CI 0.99–1.35)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "When adjusting for age, sex, BMI, self-reported drinking status and education, a one standard deviation increase in the EpiTob signature was associated with a 31% higher odds of CVD in the SKIPOGH cohort (OR = 1.31, 95% CI 1.04–1.64), and a 16% increased odds in the LBC1936 cohort, albeit not significant (OR = 1.16, 95% CI 0.99–1.35).", "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:36443762"], "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:GSE110043"], "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:GSE110043"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36443762", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13148-022-01376-7", "sha256": "sha256:d250c7213bffa0f2cfc592ee7e1b1c777464ed5d347ed6f7a87facff0e1e5460", "bytes": 44488, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13148-022-01376-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9706852", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE110043", "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=GSE110043", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE110043", "version": null, "note": "Data for the SKIPOGH cohort is available upon formal request submitted to the SKIPOGH steering committee (https://www.maelstrom-research.org/study/skipogh). Data for both LBC studies are available upon formal request, additional information can be found on the website: https://www.ed.ac.uk/lothian-birth-cohorts/data-access-collaboration. All epigenetic signatures are available upon request for non-commercial use by contacting genknowme at labo@genknowme.com.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data for the SKIPOGH cohort is available upon formal request submitted to the SKIPOGH steering committee (https://www.maelstrom-research.org/study/skipogh). Data for both LBC studies are available upon formal request, additional information can be found on the website: https://www.ed.ac.uk/lothian-birth-cohorts/data-access-collaboration. All epigenetic signatures are available upon request for non-commercial use by contacting genknowme at labo@genknowme.com.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2976871", "GSM2976872", "GSM2976873", "GSM2976874", "GSM2976875", "GSM2976876", "GSM2976877", "GSM2976878", "GSM2976879", "GSM2976880", "GSM2976881", "GSM2976882", "GSM2976883", "GSM2976884", "GSM2976885", "GSM2976886", "GSM2976887", "GSM2976888", "GSM2976889", "GSM2976890", "GSM2976891", "GSM2976892", "GSM2976893", "GSM2976894", "GSM2976895", "GSM2976896", "GSM2976897", "GSM2976898", "GSM2976899", "GSM2976900", "GSM2976901", "GSM2976902", "GSM2976903", "GSM2976904", "GSM2976905", "GSM2976906", "GSM2976907", "GSM2976908", "GSM2976909", "GSM2976910", "GSM2976911", "GSM2976912", "GSM2976913", "GSM2976914", "GSM2976915", "GSM2976916", "GSM2976917", "GSM2976918", "GSM2976919", "GSM2976920", "GSM2976921", "GSM2976922", "GSM2976923", "GSM2976924", "GSM2976925", "GSM2976926", "GSM2976927", "GSM2976928", "GSM2976929", "GSM2976930", "GSM2976931", "GSM2976932", "GSM2976933", "GSM2976934", "GSM2976935", "GSM2976936", "GSM2976937", "GSM2976938", "GSM2976939", "GSM2976940", "GSM2976941", "GSM2976942", "GSM2976943", "GSM2976944", "GSM2976945", "GSM2976946", "GSM2976947", "GSM2976948", "GSM2976949", "GSM2976950", "GSM2976951", "GSM2976952", "GSM2976953", "GSM2976954", "GSM2976955", "GSM2976956", "GSM2976957", "GSM2976958", "GSM2976959", "GSM2976960", "GSM2976961", "GSM2976962", "GSM2976963", "GSM2976964"], "sample_count": 94, "group_sizes": null, "group_sizes_basis": null, "platform": "13534", "taxon": "Homo sapiens", "title": "Epigenome analysis of alcohol consumption in whole blood (WB) samples", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE50660", "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=GSE50660", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE50660", "version": null, "note": "Data for the SKIPOGH cohort is available upon formal request submitted to the SKIPOGH steering committee (https://www.maelstrom-research.org/study/skipogh). Data for both LBC studies are available upon formal request, additional information can be found on the website: https://www.ed.ac.uk/lothian-birth-cohorts/data-access-collaboration. All epigenetic signatures are available upon request for non-commercial use by contacting genknowme at labo@genknowme.com.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data for the SKIPOGH cohort is available upon formal request submitted to the SKIPOGH steering committee (https://www.maelstrom-research.org/study/skipogh). Data for both LBC studies are available upon formal request, additional information can be found on the website: https://www.ed.ac.uk/lothian-birth-cohorts/data-access-collaboration. All epigenetic signatures are available upon request for non-commercial use by contacting genknowme at labo@genknowme.com.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1225377", "GSM1225378", "GSM1225379", "GSM1225380", "GSM1225381", "GSM1225382", "GSM1225383", "GSM1225384", "GSM1225385", "GSM1225386", "GSM1225387", "GSM1225388", "GSM1225389", "GSM1225390", "GSM1225391", "GSM1225392", "GSM1225393", "GSM1225394", "GSM1225395", "GSM1225396", "GSM1225397", "GSM1225398", "GSM1225399", "GSM1225400", "GSM1225401", "GSM1225402", "GSM1225403", "GSM1225404", "GSM1225405", "GSM1225406", "GSM1225407", "GSM1225408", "GSM1225409", "GSM1225410", "GSM1225411", "GSM1225412", "GSM1225413", "GSM1225414", "GSM1225415", "GSM1225416", "GSM1225417", "GSM1225418", "GSM1225419", "GSM1225420", "GSM1225421", "GSM1225422", "GSM1225423", "GSM1225424", "GSM1225425", "GSM1225426", "GSM1225427", "GSM1225428", "GSM1225429", "GSM1225430", "GSM1225431", "GSM1225432", "GSM1225433", 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"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:GSE110043 not downloaded", "asset:data:geo:GSE110043 licence not read", "asset:data:geo:GSE50660 not downloaded", "asset:data:geo:GSE50660 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Logistic regression models were used to investigate the association between EpiTob and EpiAlc and CVD, individually."}}], "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": ["glm_logit_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: logistic."}, "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": ["GSE50660", "GSE110043"], "resolved_accessions": ["GSE50660", "GSE110043"], "statements": ["Data for the SKIPOGH cohort is available upon formal request submitted to the SKIPOGH steering committee (https://www.maelstrom-research.org/study/skipogh). Data for both LBC studies are available upon formal request, additional information can be found on the website: https://www.ed.ac.uk/lothian-birth-cohorts/data-access-collaboration. All epigenetic signatures are available upon request for non-commercial use by contacting genknowme at labo@genknowme.com."], "basis": "The paper names GSE50660, GSE110043 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["glm_logit_fit"], "assets": ["source:pmid:36443762", "data:geo:GSE110043"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE110043"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:17:27Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11724, "completion_tokens": 2600, "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:36443762", "type": "paper", "label": "pmid:36443762"}, {"id": "source:pmid:36443762", "type": "manuscript", "label": "PMID 36443762 full text"}, {"id": "data:geo:GSE110043", "type": "dataset", "label": "GEO GSE110043"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36443762", "type": "paper", "label": "pmid:36443762"}, {"id": "source:pmid:36443762", "type": "manuscript", "label": "PMID 36443762 full text"}, {"id": "data:geo:GSE110043", "type": "dataset", "label": "GEO GSE110043"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36443762", "type": "extraction", "used": ["source:pmid:36443762"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE110043", "type": "accession_resolution", "used": ["data:geo:GSE110043"], "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:36443762", "parent_hash": "sha256:765a1a89ce18c3fbfe0efef619b39065765c20e299cf6e6212e8c043416b3e30", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE110043 licence not read", "asset:data:geo:GSE110043 not downloaded", "asset:data:geo:GSE50660 licence not read", "asset:data:geo:GSE50660 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Logistic regression models were used to investigate the association between EpiTob and EpiAlc and CVD, individually."], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T00:38:08+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}}}