{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35154514", "kind": "science-record", "revision": 9, "content_hash": "sha256:bd356c38bbe2c0c0ed0e0bb7a87b40932edc3197f328a7975f3a644424ef7226", "created_at": "2026-11-01T17:36:54Z", "updated_at": "2026-11-01T23:46:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Atrial Fibrillation-Related lncRNA Based on Bioinformatic Analysis.", "doi": "10.1155/2022/8307975", "pmid": "35154514", "authors": ["Liangzhen Xie", "GuanShen Huang", "Mingjian Gao", "Jianming Huang", "Hai Li", "Hao Xia", "Xiuting Xiang", "Saizhu Wu", "Yunjun Ruan"], "journal": "Disease markers", "year": 2022, "abstract": "BACKGROUND: Atrial fibrillation (AF) is the most common arrhythmia in the world. Long noncoding RNA (lncRNA) has been found to play an important role in cardiovascular diseases including heart failure, myocardial infarction, and atherosclerosis. However, the role of lncRNA in AF has rarely been studied. The purpose of this study is to identify the expression profile of lncRNA in AF patients, explore the function of lncRNA in AF, and provide a potential scientific basis for the treatment of AF in the future.\nMETHODS: The lncRNA and mRNA expression profiles were obtained from the atrial appendage samples of GSE31821, GSE411774, GSE79768, and GSE115574 in the Gene Expression Omnibus (GEO) database. Functional analysis was performed via Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Variation Analysis (GSVA). The \"CIBERSORT\" R kit was used to analyze 22 immune cell infiltrates in AF and sinus rhythm (SR) patients. The \"CORRPLOT\" R package was used to analyze the immune correlation between lncRNA and immune cells.\nRESULTS: A total of 6 differentially expressed lncRNAs and 45 differentially expressed mRNAs were identified in the AF and SR groups. GO, KEGG, and GSVA results showed that abnormally expressed lncRNAs were involved in signaling pathways related to the atrium, including the Toll-like receptor signaling pathway and calcium signaling pathway. Immune cell infiltration analysis revealed that native B cells, follicular helper T cells, and resting dendritic cells may be involved in the AF process. In addition, LINC00844 was negatively correlated with resting dendritic cells.\nCONCLUSION: The expression profile of lncRNA in AF patients was different from that in normal controls. The physiological functions of these differentially expressed lncRNAs may be related to the pathogenesis of AF, which provide a scientific basis for the prognosis and treatment of patients with AF.", "claims": [{"id": "claim-method", "statement": "In order to evaluate the differential expression, the standard error was adjusted by using the “limma” package of R software, linear model fitting, and a simple empirical Bayes model [16]. For each comparison of each gene, a moderate t statistic and the logarithm of differential expression were calculated. We then adopted the Benjamini and Hochberg (BH) method to adjust the P value to reduce false-positive errors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35154514", "locator": "sections[5] \"2.3. Identification of Differentially Expressed lncRNAs and mRNAs\" paragraph 2", "quote": "In order to evaluate the differential expression, the standard error was adjusted by using the “limma” package of R software, linear model fitting, and a simple empirical Bayes model [16]. For each comparison of each gene, a moderate t statistic and the logarithm of differential expression were calculated. We then adopted the Benjamini and Hochberg (BH) method to adjust the P value to reduce false-positive errors."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35154514", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 6 lncRNAs were differentially expressed between the SR group and the AF group, while 45 differentially expressed mRNAs were identified.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "A total of 6 lncRNAs were differentially expressed between the SR group and the AF group (log2FC > 0.58 and P < 0.05), compared with SR groups: 4 lncRNAs were upregulated and 2 were downregulated in AF groups (Figures 2(a) and 2(b))."}, "evidence": [{"asset": "source:pmid:35154514", "locator": "sections[12] \"3.1. Identification of Differentially lncRNA and mRNA Expression Profile\" paragraph 2", "quote": "A total of 6 lncRNAs were differentially expressed between the SR group and the AF group (log2FC > 0.58 and P < 0.05), compared with SR groups: 4 lncRNAs were upregulated and 2 were downregulated in AF groups (Figures 2(a) and 2(b))."}, {"asset": "source:pmid:35154514", "locator": "sections[12] \"3.1. Identification of Differentially lncRNA and mRNA Expression Profile\" paragraph 2", "quote": "In addition, we also found 45 differentially expressed mRNAs, of which 31 mRNAs were downregulated and 14 were upregulated in AR groups compared with SR groups (Figures 3(a) and 3(b))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 6 lncRNAs were differentially expressed between the SR group and the AF group, while 45 differentially expressed mRNAs were identified.", "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:35154514"], "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:GSE115574"], "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:GSE115574"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35154514", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/8307975", "sha256": "sha256:484e39f88cd165ff0d527cc73800b95711b58807c1336da2d2726c20faa5f904", "bytes": 22341, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/8307975", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8837454", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE115574", "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=GSE115574", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE115574", "version": null, "note": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3182680", "GSM3182681", "GSM3182682", "GSM3182683", "GSM3182684", "GSM3182685", "GSM3182686", "GSM3182687", "GSM3182688", "GSM3182689", "GSM3182690", "GSM3182691", "GSM3182692", "GSM3182693", "GSM3182694", "GSM3182695", "GSM3182696", "GSM3182697", "GSM3182698", "GSM3182699", "GSM3182700", "GSM3182701", "GSM3182702", "GSM3182703", "GSM3182704", "GSM3182705", "GSM3182706", "GSM3182707", "GSM3182708", "GSM3182709", "GSM3182710", "GSM3182711", "GSM3182712", "GSM3182713", "GSM3182714", "GSM3182715", "GSM3182716", "GSM3182717", "GSM3182718", "GSM3182719", "GSM3182720", "GSM3182721", "GSM3182722", "GSM3182723", "GSM3182724", "GSM3182725", "GSM3182726", "GSM3182727", "GSM3182728", "GSM3182729", "GSM3182730", "GSM3182731", "GSM3182732", "GSM3182733", "GSM3182734", "GSM3182735", "GSM3182736", "GSM3182737", "GSM3182738"], "sample_count": 59, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data from human left and right atrial tissues in patients with degenerative MR in SR and AFib.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE31821", "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=GSE31821", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31821", "version": null, "note": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM789270", "GSM789271", "GSM789272", "GSM789273", "GSM789274", "GSM789275"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression and miRNA profiles in atrial fibrillation. Role of miR-21.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE411774", "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=GSE411774", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE411774", "version": null, "note": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T23:38:31Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE115574 not downloaded", "asset:data:geo:GSE115574 licence not read", "asset:data:geo:GSE31821 not downloaded", "asset:data:geo:GSE31821 licence not read", "asset:data:geo:GSE411774 not downloaded", "asset:data:geo:GSE411774 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In order to evaluate the differential expression, the standard error was adjusted by using the “limma” package of R software, linear model fitting, and a simple empirical Bayes model [16]. For each comparison of each gene, a moderate t statistic and the logarithm of differential expression were calculated. We then adopted the Benjamini and Hochberg (BH) method to adjust the P value to reduce false-positive errors."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE31821", "GSE411774", "GSE115574"], "resolved_accessions": ["GSE31821", "GSE115574"], "statements": ["The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE31821, GSE115574 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:35154514", "data:geo:GSE115574"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE115574"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:34:01Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 7310, "completion_tokens": 1910, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35154514", "type": "paper", "label": "pmid:35154514"}, {"id": "source:pmid:35154514", "type": "manuscript", "label": "PMID 35154514 full text"}, {"id": "data:geo:GSE115574", "type": "dataset", "label": "GEO GSE115574"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35154514", "type": "paper", "label": "pmid:35154514"}, {"id": "source:pmid:35154514", "type": "manuscript", "label": "PMID 35154514 full text"}, {"id": "data:geo:GSE115574", "type": "dataset", "label": "GEO GSE115574"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35154514", "type": "extraction", "used": ["source:pmid:35154514"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE115574", "type": "accession_resolution", "used": ["data:geo:GSE115574"], "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:35154514", "parent_hash": "sha256:a7bcbce9a68ad693eadef26ac6eca169b4fb03502b00716676ccf8091824767e", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE115574 licence not read", "asset:data:geo:GSE115574 not downloaded", "asset:data:geo:GSE31821 licence not read", "asset:data:geo:GSE31821 not downloaded", "asset:data:geo:GSE411774 licence not read", "asset:data:geo:GSE411774 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["into the gene symbol code. 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We then adopted the Benjamini and Hochberg (BH) method to adjust the P value to reduce false-positive errors."], "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. 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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}}}