{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40964109", "kind": "science-record", "revision": 2, "content_hash": "sha256:0216b2951f7b2d73bd011e1857dc5f60a10df643b8e7c2f04d6b3e03f023dabc", "created_at": "2026-11-01T20:31:03Z", "updated_at": "2026-11-01T21:35:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "[Regulatory Role of the AKT1/AMPK Pathway in Oxidative Stress of Lens Epithelial Cells in Cataract Patients].", "doi": "10.12182/20250560203", "pmid": "40964109", "authors": ["Yan Huang", "Bingjing Lyu", "Kunyuan Tang", "Ke Hu"], "journal": "Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition", "year": 2025, "abstract": "Objective: To elucidate the regulatory role and the underlying molecular mechanisms of serine/threonine protein kinase 1 (AKT1) in the lens epithelium of patients with age-related cataract (ARC).\nMethods: 1) Differentially expressed genes in ARC were screened using bioinformatics analysis (Genecard and GEO database GSE213546), and key genes were identified through functional enrichment analysis (KEGG and GO). 2) An oxidative stress model of lens epithelial cells was established by treating HLE-B3 cells with 200 μmol/L H2O2 for 24 h. RT-qPCR and Western blot were performed to assess AKT1 gene and protein expression changes. 3) Model cells were randomly divided into a si-NC group transfected with si-NC plasmids and 3 parallel si-AKT1 groups transfected with 3 types of si-AKT1 plasmids. A control + si-NC group was also set up, in which HLE-B3 cells not treated with H2O2 were transfected with si-NC empty plasmids. The AKT1 gene and protein expression levels in the si-NC and si-AKT1 groups were determined by RT-qPCR and Western blot. Two si-AKT1 parallel groups demonstrating the most significant changes in expression levels were selected for further experiments. The protein expression levels of AMPK and phosphorylated AMPK (p-AMPK) in the si-NC group, the two selected si-AKT1 parallel groups, and the control + si-NC group were determined by Western blot. A si-AKT1 parallel group demonstrating significant changes in p-AMPK/AMPK values was selected and treated with Acadesine (AICAR), an AMPK agonist, to verify the role of the AMPK pathway. Western blot was performed to determine Bcl-2 and Bax protein levels in the si-NC group, the control + si-NC group, and the si-AKT1 group before and after the administration of AICAR. Flow cytometry was performed to measure apoptosis and reactive oxygen species (ROS) levels, while ELISA kits were used to assess the levels of superoxide dismutase (SOD), malondialdehyde (MDA), and reduced glutathione (GSH).\nResults: 1) Through bioinformatics analysis, 78 differentially expressed genes were identified, with AKT1 significantly upregulated in ARC samples (P < 0.05) and enriched in the AMPK pathway. 2) Compared with cells not treated with H2O2, AKT1 mRNA and protein expression increased in the oxidative stress model cells. 3) The p-AMPK/AMPK ratio was higher in the si-NC group than that in the control + si-NC group. In contrast, AKT1 knockdown suppressed AMPK pathway activity, with all the si-AKT1 groups showing a significantly decreased p-AMPK/AMPK ratio compared to that of the si-NC group (P < 0.05). Compared with the control + si-NC group, the si-NC group exhibited elevated ROS and MDA levels, increased apoptosis rate, reduced SOD and GSH levels, downregulated Bcl-2, and upregulated Bax (all P < 0.05). Compared to those in the si-NC group, these indicators were improved in the si-AKT1 group (all P < 0.05). However, compared with the findings before AICAR treatment, these effects were antagonized after AICAR treatment in the si-AKT1 group (all P < 0.05).\nConclusion: The oxidative stress-related gene AKT1 may be a key pathogenic factor in cataract, and AKT1 induces oxidative stress and apoptosis in lens epithelial cells by modulating AMPK pathway activity.", "claims": [{"id": "claim-method", "statement": "使用GEO2R标准化数据（limma包）的normalizeBetweenArrays函数依据表达中位数对样本进行标准化处理。通过比较白内障组织和对照组的基因表达值，采用Bonferroni法调整P值，并将调整后的P值（adj.p.Value）<0.05且差异倍数logFC> 2 的基因定义为差异表达基因。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40964109", "locator": "sections[6] \"数据获取、标准化及差异表达分析\" paragraph 2", "quote": "使用GEO2R标准化数据（limma包）的normalizeBetweenArrays函数依据表达中位数对样本进行标准化处理。通过比较白内障组织和对照组的基因表达值，采用Bonferroni法调整P值，并将调整后的P值（adj.p.Value）<0.05且差异倍数logFC> 2 的基因定义为差异表达基因。"}], "state": "complete"}, {"id": "claim-data-access", "statement": "通过Genecard（https://www.genecards.org/Search/Keyword?queryString=fibrosis）检索oxidative stress and fibrosis相关基因。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40964109", "locator": "sections[6] \"数据获取、标准化及差异表达分析\" paragraph 2", "quote": "通过Genecard（https://www.genecards.org/Search/Keyword?queryString=fibrosis）检索oxidative stress and fibrosis相关基因。"}], "state": "complete"}, {"id": "claim-target-result", "statement": "氧化应激相关基因AKT1可能是白内障的关键致病基因，且AKT1通过影响AMPK通路活性诱导晶状体上皮细胞氧化应激和凋亡。", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40964109", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "氧化应激相关基因AKT1可能是白内障的关键致病基因，且AKT1通过影响AMPK通路活性诱导晶状体上皮细胞氧化应激和凋亡。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "氧化应激相关基因AKT1可能是白内障的关键致病基因，且AKT1通过影响AMPK通路活性诱导晶状体上皮细胞氧化应激和凋亡。", "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:40964109"], "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:GSE213546"], "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:GSE213546"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40964109", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12182/20250560203", "sha256": "sha256:a6f73a81860ae7343b1c54c53f1f214e85142eec80d622b0ecd6bb7a229136f0", "bytes": 13374, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12182/20250560203", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12439649", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE213546", "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=GSE213546", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE213546", "version": null, "note": "通过Genecard（https://www.genecards.org/Search/Keyword?queryString=fibrosis）检索oxidative stress and fibrosis相关基因。", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "通过Genecard（https://www.genecards.org/Search/Keyword?queryString=fibrosis）检索oxidative stress and fibrosis相关基因。", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM6588927", "GSM6588928", "GSM6588929", "GSM6588930", "GSM6588931", "GSM6588932"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Transcriptomic analysis of human lens and age-related cataract", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE213546 not downloaded", "asset:data:geo:GSE213546 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "使用GEO2R的limma包及normalizeBetweenArrays函数进行标准化，并采用Bonferroni法调整P值。", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "使用GEO2R标准化数据（limma包）的normalizeBetweenArrays函数依据表达中位数对样本进行标准化处理。通过比较白内障组织和对照组的基因表达值，采用Bonferroni法调整P值，并将调整后的P值（adj.p.Value）<0.05且差异倍数logFC> 2 的基因定义为差异表达基因。"}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (使用GEO2R的limma包及normalizeBetweenArrays函数进行标准化，并采用Bonferroni法调整P值。), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE213546"], "resolved_accessions": ["GSE213546"], "statements": ["通过Genecard（https://www.genecards.org/Search/Keyword?queryString=fibrosis）检索oxidative stress and fibrosis相关基因。"], "basis": "The paper names GSE213546 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40964109", "data:geo:GSE213546"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE213546"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:01:36Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 8822, "completion_tokens": 1783, "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:40964109", "type": "paper", "label": "pmid:40964109"}, {"id": "source:pmid:40964109", "type": "manuscript", "label": "PMID 40964109 full text"}, {"id": "data:geo:GSE213546", "type": "dataset", "label": "GEO GSE213546"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40964109", "type": "paper", "label": "pmid:40964109"}, {"id": "source:pmid:40964109", "type": "manuscript", "label": "PMID 40964109 full text"}, {"id": "data:geo:GSE213546", "type": "dataset", "label": "GEO GSE213546"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40964109", "type": "extraction", "used": ["source:pmid:40964109"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE213546", "type": "accession_resolution", "used": ["data:geo:GSE213546"], "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:40964109", "parent_hash": "sha256:b33b05273fa09233a7a00acd09b00ef5759251d50d85ee1c027c0ac638b4463e", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE213546 licence not read", "asset:data:geo:GSE213546 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["HLE-B3 cells with 200 μmol/L H2O2 for 24 h. RT-qPCR and Western blot were performed to assess AK", "si-NC and si-AKT1 groups were determined by RT-qPCR and Western blot. Two si-AKT1 parallel group", "E-B3 cells with 200 μmol/L H2O2 for 24 h. RT-qPCR and Western blot were performed to assess AK", "-NC and si-AKT1 groups were determined by RT-qPCR and Western blot. Two si-AKT1 parallel group"], "order_basis": "paper_text_order:605", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s with 200 μmol/L H2O2 for 24 h. RT-qPCR and Western blot were performed to assess AKT1 gene and prote", "i-AKT1 groups were determined by RT-qPCR and Western blot. Two si-AKT1 parallel groups demonstrating t", "the control + si-NC group were determined by Western blot. A si-AKT1 parallel group demonstrating sign", "ist, to verify the role of the AMPK pathway. Western blot was performed to determine Bcl-2 and Bax pro"], "order_basis": "paper_text_order:616", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lls were randomly divided into a si-NC group transfected with si-NC plasmids and 3 parallel si-AKT1 g", "si-NC plasmids and 3 parallel si-AKT1 groups transfected with 3 types of si-AKT1 plasmids. A control", "hich HLE-B3 cells not treated with H2O2 were transfected with si-NC empty plasmids. The AKT1 gene and", "the control + si-NC group. In contrast, AKT1 knockdown suppressed AMPK pathway activity, with all t"], "order_basis": "paper_text_order:752", "id": "assay:3"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["efore and after the administration of AICAR. Flow cytometry was performed to measure apoptosis and react"], "order_basis": "paper_text_order:1808", "id": "assay:4"}, {"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": ["CAR. Flow cytometry was performed to measure apoptosis and reactive oxygen species (ROS) levels, wh", "bited elevated ROS and MDA levels, increased apoptosis rate, reduced SOD and GSH levels, downregula", "aract, and AKT1 induces oxidative stress and apoptosis in lens epithelial cells by modulating AMPK"], "order_basis": "paper_text_order:1848", "id": "assay:5"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["reactive oxygen species (ROS) levels, while ELISA kits were used to assess the levels of super"], "order_basis": "paper_text_order:1907", "id": "assay:6"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:14:35+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}}}