{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32528308", "kind": "science-record", "revision": 8, "content_hash": "sha256:a864d0a98bf74d2c1af7a5e1e82304ea47365a14b1f5b1b899d654a45a783496", "created_at": "2026-11-01T15:41:03Z", "updated_at": "2026-11-01T22:44:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic Analysis of Myocardia Containing the Obscurin R4344Q Mutation Linked to Hypertrophic Cardiomyopathy.", "doi": "10.3389/fphys.2020.00478", "pmid": "32528308", "authors": ["Li-Yen R Hu", "Aikaterini Kontrogianni-Konstantopoulos"], "journal": "Frontiers in physiology", "year": 2020, "abstract": "Obscurin is a giant cytoskeletal protein with structural and regulatory roles encoded by the OBSCN gene. Recently, mutations in OBSCN were associated with the development of different forms of cardiomyopathies, including hypertrophic cardiomyopathy (HCM). We previously reported that homozygous mice carrying the HCM-linked R4344Q obscurin mutation develop arrhythmia by 1-year of age under sedentary conditions characterized by increased heart rate, frequent incidents of premature ventricular contractions, and episodes of spontaneous ventricular tachycardia. In an effort to delineate the molecular mechanisms that contribute to the observed arrhythmic phenotype, we subjected protein lysates prepared from left ventricles of 1-year old R4344Q and wild-type mice to comparative proteomics analysis using tandem mass spectrometry; raw data are available via ProteomeXchange with identifier PXD017314. We found that the expression levels of proteins involved in cardiac function and disease, cytoskeletal organization, electropotential regulation, molecular transport and metabolism were significantly altered. Moreover, phospho-proteomic evaluation revealed changes in the phosphorylation profile of Ca2+ cycling proteins, including sAnk1.5, a major binding partner of obscurin localized in the sarcoplasmic reticulum; notably, this is the first report indicating that sAnk1 undergoes phosphorylation. Taken together, our findings implicate obscurin in diverse cellular processes within the myocardium, which is consistent with its multiple binding partners, localization in different subcellular compartments, and disease association.", "claims": [{"id": "claim-method", "statement": "A two-tailed t-test using a one-way ANOVA model was applied to evaluate the adjusted modified peptides between wild-type and R4344Q LV samples using the Partek Genomics Suite 6.6 analytic platform (Partek Inc. 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"row_count": 38, "column_count": 7}, "table": {"label": "TABLE 3", "caption": "Altered expression levels of proteins involved in cytoskeleton organization, cellular assembly and maintenance.", "rows": [["Gene", "Protein", "% Change (95% Confidence interval)", "P-value", "Unique peptides", "Total peptides", "Function"], ["CLIP1", "CAP-GLY domain containing linker protein 1", "−16.3 (−29.3, −0.8)", "0.0435", "1", "46", "Stabilization of filaments"], ["EML2", "Echinoderm microtubule associated protein like 2", "−28.9 (−40.7, −14.7)", "0.0065", "9", "9", ""], ["GALK2", "Galactokinase 2", "−6.8 (−11.1, −2.4)", "0.0138", "2", "2", ""], ["GAP43", "Growth associated protein 43", "−32.0 (−44.5, −16.6)", "0.0063", "4", "4", ""], ["KIFC3", "Kinesin family member C3", "15.8 (1.4, 32.2)", "0.0373", "1", "1", ""], ["MAP1B", "Microtubule-associated protein 1B", "−16.9 (−28.1, −3.9)", "0.0242", "9", "9", ""], ["ACTB", "Actin, beta", "−11.7 (−22.0, −0.1)", "0.0485", "8", "28", "Microtubule dynamics"], ["CCL21A", "Chemokine (C-C motif) ligand 21A", "−21.9 (−35.9, −4.7)", "0.0260", "1", "1", ""], ["CLIP1", "CAP-GLY domain containing linker protein 1", "−16.3 (−29.3, −0.8)", "0.0435", "1", "46", ""], ["CRK", "v-crk avian sarcoma CT10 oncogene homolog", "22.2 (4.4, 43.0)", "0.0242", "10", "10", ""], ["CTNND1", "Catenin, delta 1", "−10.0 (−18.4, −0.8)", "0.0397", "1", "13", ""], ["CTSS", "Cathepsin S", "−16.6 (−30.2, −0.4)", "0.0470", "1", "1", ""], ["DDAH1", "Dimethylarginine dimethylaminohydrolase 1", "45.5 (24.1, 70.6)", "0.0028", "2", "3", ""], ["EIF4G2", "Eukaryotic translation initiation factor 4, gamma 2", "24.2 (7.9, 43.1)", "0.0130", "14", "14", ""], ["EML2", "Echinoderm microtubule associated protein like 2", "−28.9 (−40.7, −14.7)", "0.0065", "9", "9", ""], ["EPHA4", "Eph receptor A4", "14.9 (2.1, 29.3)", "0.0312", "3", "3", ""], ["GALK2", "Galactokinase 2", "−6.8 (−11.1, −2.4)", "0.0138", "2", "2", ""], ["GAP43", "Growth associated protein 43", "−32.0 (−44.5, −16.6)", "0.0063", "4", "4", ""], ["GAPDH", "Glyceraldehyde-3-phosphate dehydrogenase", "−11.8 (−21.3, −1.2)", "0.0371", "22", "22", ""], ["GIT1", "G protein-coupled receptor kinase-interactor 1", "−10.2 (−17.3, −2.4)", "0.0232", "5", "5", ""], ["HDAC6", "Histone deacetylase 6", "−14.0 (−24.5, −2.0)", "0.0324", "5", "5", ""], ["IDE", "Insulin degrading enzyme", "6.4 (1.7, 11.4)", "0.0188", "8", "8", ""], ["KIF1C", "Kinesin family member 1C", "52.6 (18.3, 96.8)", "0.0100", "5", "6", ""], ["KIFC3", "Kinesin family member C3", "15.8 (1.4, 32.2)", "0.0373", "1", "1", ""], ["MAP1B", "Microtubule-associated protein 1B", "−16.9 (−28.1, −3.9)", "0.0242", "9", "9", ""], ["MAPK8IP3", "Mitogen-activated protein kinase 8 interacting protein 3", "22.5 (2.8, 46.0)", "0.0325", "7", "12", ""], ["MGLL", "Monoglyceride lipase", "−14.6 (−27.0, −0.1)", "0.0488", "3", "3", ""], ["PKG1", "Protein kinase, cGMP-dependent, type 1 (PKG1)", "43.6 (1.5, 103.1)", "0.0444", "1", "5", ""], ["PRPH", "Peripherin", "−26.1 (−39.3, −10.1)", "0.0129", "9", "13", ""], ["PRUNE2", "Prune homolog 2", "23.1 (6.9, 41.7)", "0.0148", "7", "7", ""], ["PTPN11", "Protein tyrosine phosphatase, non-receptor type 11", "20.8 (9.1, 33.8)", "0.0067", "21", "21", ""], ["SIRPA", "Signal-regulatory protein alpha", "17.8 (5.7, 31.3)", "0.0138", "2", "2", ""], ["SLK", "Ste20-like kinase", "10.1 (2.8, 18.0)", "0.0180", "15", "16", ""], ["TUBB3", "Tubulin, beta 3", "−31.4 (−49.5, −6.9)", "0.0266", "2", "13", ""], ["VLDLR", "Very low density lipoprotein receptor", "7.6 (1.2, 14.3)", "0.0291", "8", "8", ""], ["DYSF", "Dysferlin", "−34.2 (−49.5, −14.2)", "0.0118", "40", "42", "Damage of transverse tubule"], ["FHL2", "Four and a half LIM domains 2", "−56.0 (−79.7, −4.6)", "0.0422", "5", "5", "Cell growth and differentiation; HCM and DCM"]], "row_count": 38, "column_count": 7, "numeric_cells": 179, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:32528308:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:df7e34dc1e48bb90484cdced89ffcf365bd877eee18369c1fa011d9aadaca6c3", "bytes": 2225, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T6", "version": null, "note": "Altered expression levels of proteins involved in various molecular pathways.", "structure": {"pmcid": "PMC7247546", "section_index": 14, "section_title": "Metabolism", "row_count": 18, "column_count": 7}, "table": {"label": "TABLE 6", "caption": "Altered expression levels of proteins involved in various molecular pathways.", "rows": [["Gene", "Protein", "% Change (95% Confidence interval)", "P-value", "Unique peptides", "Total peptides", "Molecular Pathways"], ["CYB5A", "Cytochrome b5 type A (microsomal)", "−39.6 (−62.2, −3.5)", "0.0405", "4", "4", "γ-linolenate biosynthesis II"], ["SLC27A4", "Solute carrier family 27 (fatty acid transporter), member 4", "19.4 (0.9, 41.2)", "0.0428", "3", "4", ""], ["ACOT2", "Acyl-CoA thioesterase 2", "20.4 (4.3, 39.1)", "0.0231", "8", "15", "Stearate biosynthesis I"], ["ACOT7", "Acyl-CoA thioesterase 7", "22.0 (1.2, 47.2)", "0.0418", "5", "5", ""], ["SLC27A4", "Solute carrier family 27 (fatty acid transporter), member 4", "19.4 (0.9, 41.2)", "0.0428", "3", "4", ""], ["ACOT2", "Acyl-CoA thioesterase 2", "20.4 (4.3, 39.1)", "0.0231", "8", "15", "Acyl-CoA hydrolysis"], ["ACOT7", "Acyl-CoA thioesterase 7", "22.0 (1.2, 47.2)", "0.0418", "5", "5", ""], ["NUDT12", "Nudix (nucleoside diphosphate linked moiety X)-type motif 12", "66.5 (15.9, 139.1)", "0.0174", "4", "4", "NAD salvage pathway II"], ["NMNAT3", "Nicotinamide nucleotide adenylyltransferase 3", "18.9 (7.1, 32.0)", "0.0100", "4", "4", "NAD salvage pathway II and III"], ["IVD", "Isovaleryl coenzyme A dehydrogenase", "−12.5 (−20.2, −4.1)", "0.0156", "19", "19", "Leucine degradation I"], ["MCCC2", "Methylcrotonoyl-coenzyme A carboxylase 2", "−12.2 (−20.3, −3.4)", "0.0198", "22", "22", ""], ["HSD17B10", "Hydroxysteroid (17-beta) dehydrogenase 10", "−10.2 (−15.3, −4.8)", "0.0070", "14", "14", "Fatty Acid β-oxidation"], ["IVD", "Isovaleryl coenzyme A dehydrogenase", "−12.5 (−20.2, −4.1)", "0.0156", "19", "19", ""], ["SLC27A4", "Solute carrier family 27 (fatty acid transporter), member 4", "19.4 (0.9, 41.2)", "0.0428", "3", "4", ""], ["PTPN11", "Protein tyrosine phosphatase, non-receptor type 11", "20.8 (9.1, 33.8)", "0.0067", "21", "21", "Role of JAK2 in hormone-like cytokine signaling"], ["SIRPA", "Signal-regulatory protein alpha", "17.8 (5.7, 31.3)", "0.0138", "2", "2", ""], ["NR1D1", "Nuclear receptor subfamily 1, group D, member 1", "42.0 (2.2, 97.3)", "0.0414", "2", "2", "Circadian rhythm signaling"]], "row_count": 18, "column_count": 7, "numeric_cells": 88, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T6"}}, {"id": "asset:table:pmid:32528308:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6f8848e4fd17d6396510b72159922b41062f7496852bcd1aa0639f78fc14fb6c", "bytes": 779, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T7", "version": null, "note": "Altered phosphorylation levels of identified proteins.", "structure": {"pmcid": "PMC7247546", "section_index": 15, "section_title": "Altered Phosphorylation Levels", "row_count": 6, "column_count": 6}, "table": {"label": "TABLE 7", "caption": "Altered phosphorylation levels of identified proteins.", "rows": [["Gene", "Protein", "Site", "Domain", "% Change (95% Confidence interval)", "P-value"], ["ANK1", "Small ankyrin 1.5", "Ser55", "Non-modular", "38.3 (4.7, 82.8)", "0.0319"], ["KLHDC7A", "Kelch domain containing 7A", "Ser361", "Non-modular", "194.1 (70.2, 408.2)", "0.0054"], ["MYH6", "Myosin, heavy polypeptide 6, cardiac muscle, alpha", "Ser1309", "Light meromyosin (LMM)", "24.9 (3.6, 50.5)", "0.0299"], ["UBAP2l", "Ubiquitin-associated protein 2-like", "Ser487", "Non-modular", "−53.4 (−72.3, −21.6)", "0.0152"], ["JPH2", "Junctophilin 2", "Ser597", "Non-modular", "−38.4 (−61.1, −2.5)", "0.0428"]], "row_count": 6, "column_count": 6, "numeric_cells": 21, "header_rows": 1, "locator": "section[15]/table-wrap[1]#T7"}}], "gaps": ["asset:data:geo:PXD017314 not downloaded", "asset:data:geo:PXD017314 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "A two-tailed t-test using a one-way ANOVA model was applied to evaluate the adjusted modified peptides between wild-type and R4344Q LV samples using the Partek Genomics Suite 6.6 analytic platform (Partek Inc. St. Louis, MO, United States)."}}], "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD017314"], "resolved_accessions": ["PXD017314"], "statements": ["The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation, to any qualified researcher."], "basis": "The paper names PXD017314 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:32528308", "data:geo:PXD017314", "asset:table:pmid:32528308:1", "asset:table:pmid:32528308:2", "asset:table:pmid:32528308:3", "asset:table:pmid:32528308:4", "asset:table:pmid:32528308:5", "asset:table:pmid:32528308:6", "asset:table:pmid:32528308:7"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD017314"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:35Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 55552, "completion_tokens": 1682, "cached_tokens": 18696}}, "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:32528308", "type": "paper", "label": "pmid:32528308"}, {"id": "source:pmid:32528308", "type": "manuscript", "label": "PMID 32528308 full text"}, {"id": "data:geo:PXD017314", "type": "dataset", "label": "GEO PXD017314"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32528308", "type": "paper", "label": "pmid:32528308"}, {"id": "source:pmid:32528308", "type": "manuscript", "label": "PMID 32528308 full text"}, {"id": "data:geo:PXD017314", "type": "dataset", "label": "GEO PXD017314"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32528308", "type": "extraction", "used": ["source:pmid:32528308"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD017314", "type": "accession_resolution", "used": ["data:geo:PXD017314"], "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:32528308", "parent_hash": "sha256:7826e0c45ac25dcf61a99ebb6baaa2a721e6aaeaec1085ec59492654eabc9473", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD017314 licence not read", "asset:data:geo:PXD017314 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Proteomic Analysis of Myocardia Containing the Obscuri", "old R4344Q and wild-type mice to comparative proteomics analysis using tandem mass spectrometry; raw", "ere significantly altered. Moreover, phospho-proteomic evaluation revealed changes in the phosphory", "comparative proteomics analysis using tandem mass spectrometry; raw data are available via ProteomeXchange"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["A two-tailed t-test using a one-way ANOVA model was applied to evaluate the adjusted modified peptides between wild-type and R4344Q LV samples using the Partek Genomics Suite 6.6 analytic platform (Partek Inc. St. Louis, MO, United States)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T01:33:54+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}}}