{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38342795", "kind": "science-record", "revision": 4, "content_hash": "sha256:c2ff0d3a734f0be4013a721f61975efa5a5119bb12b4c59f047b14752f3f9398", "created_at": "2026-11-01T19:20:16Z", "updated_at": "2026-11-01T22:53:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "FOXM1 promote the growth and metastasis of uveal melanoma cells by regulating CDK2 expression.", "doi": "10.1007/s10792-024-02943-y", "pmid": "38342795", "authors": ["Xue Bai", "Shan Li", "Yan Luo"], "journal": "International ophthalmology", "year": 2024, "abstract": "BACKGROUND: Uveal melanoma (UVM) is an aggressive malignant tumor originating from melanocytes in the eye. Here, we screened the possible genes involved in the development and prognosis of UVM, and identified that FOXM1 and MET were associated with the prognosis of UVM patients. Forkhead box protein M1 (FOXM1) is a transcription factor that regulates the expression of cell cycle-related genes that are necessary for DNA duplication. However, the regulatory mechanism of FOXM1 in UVM was still not clear. Here, we investigated the regulation of FOXM1 in the malignant phenotype of UVM cells and its effect on the prognosis of UVM patients.\nMETHODS: UVM gene expression profiles were obtained using GSE22138 data from the gene expression omnibus (GEO). Weighted gene co-expression network analysis (WGCNA) was used to construct a key module gene for metastasis, which was strongly correlated with UVM prognosis. The latent biological pathways were identified through gene ontology analysis. Protein-protein interaction (PPI) networks and hub shared gene authentication were performed. GEPIA and UALCAN databases were used for the analysis of relationship between candidate genes (FOXM1 or MET) and the prognosis of UVM patients. The abundance of FOXM1 was examined by quantitative real time polymerase chain reaction (qRT-PCR) and western blot. Colony formation and cell counting kit-8 (CCK-8) assays for cell proliferation, wound healing assay for migration, and transwell invasion analysis for invasion were performed.\nRESULTS: GEO database showed the differentially expressed genes between UVM samples with or without metastasis, and a key module gene for metastasis was constructed by WGCNA. The PPI network revealed that seven candidate genes (VEGFA, KRAS, MET, SRC, EZR, FOXM1, and CCNB1) were closely associated with UVM metastasis. GEPIA and UALCAN analyzes suggested that FOXM1 and MET are related to the prognosis of patients with UVM. These experimental results suggested that FOXM1 was highly expressed in UVM cells. FOXM1 deficiency represses the proliferative, migratory, and invasive abilities of UVM cells.\nCONCLUSIONS: FOXM1 silencing may hinder UVM cell progression, providing a novel theoretical basis and new insights for UVM treatment.", "claims": [{"id": "claim-method", "statement": "The limma R package (Version 3.38.3; http://www.bioconductor.org/packages/release/bioc/html/limma.html) was utilized to explore the differentially expressed genes between tumor tissues of “No” group (28 cases) and the “Yes” (35 cases), the threshold was set to: |log2FC|> 0 and P value < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38342795", "locator": "sections[4] \"Weighted gene co-expression network analysis (WGCNA) and functional annotation\" paragraph 2", "quote": "The limma R package (Version 3.38.3; http://www.bioconductor.org/packages/release/bioc/html/limma.html) was utilized to explore the differentially expressed genes between tumor tissues of “No” group (28 cases) and the “Yes” (35 cases), the threshold was set to: |log2FC|> 0 and P value < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profile matrix file from GSE22138 based on the platform GPL570 (including transcription profile data of 63 UVM tissue samples and matching clinically relevant information) was acquired from the gene expression omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). GEO is an international public repository that archives and freely distributes high-throughput microarray and other functional genomic data sets submitted by the research community [17, 18].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38342795", "locator": "sections[3] \"Microarray data download and preprocessing\" paragraph 2", "quote": "The gene expression profile matrix file from GSE22138 based on the platform GPL570 (including transcription profile data of 63 UVM tissue samples and matching clinically relevant information) was acquired from the gene expression omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/)."}, {"asset": "source:pmid:38342795", "locator": "sections[22] \"Discussion\" paragraph 3", "quote": "GEO is an international public repository that archives and freely distributes high-throughput microarray and other functional genomic data sets submitted by the research community [17, 18]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "FOXM1 deficiency represses the proliferative, migratory, and invasive abilities of UVM cells.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38342795", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "FOXM1 deficiency represses the proliferative, migratory, and invasive abilities of UVM cells."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "FOXM1 deficiency represses the proliferative, migratory, and invasive abilities of UVM cells.", "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:38342795"], "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:GSE22138"], "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:GSE22138"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38342795", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s10792-024-02943-y", "sha256": "sha256:609e5a6cc1119398e210a01c51ae8f64e70e7ad4c68a403fe99904497f2e638a", "bytes": 31674, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s10792-024-02943-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10859341", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE22138", "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=GSE22138", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22138", "version": null, "note": "The gene expression profile matrix file from GSE22138 based on the platform GPL570 (including transcription profile data of 63 UVM tissue samples and matching clinically relevant information) was acquired from the gene expression omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). GEO is an international public repository that archives and freely distributes high-throughput microarray and other functional genomic data sets submitted by the research community [17, 18].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profile matrix file from GSE22138 based on the platform GPL570 (including transcription profile data of 63 UVM tissue samples and matching clinically relevant information) was acquired from the gene expression omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). GEO is an international public repository that archives and freely distributes high-throughput microarray and other functional genomic data sets submitted by the research community [17, 18].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM550623", "GSM550624", "GSM550625", "GSM550626", "GSM550627", "GSM550628", "GSM550629", "GSM550630", "GSM550631", "GSM550632", "GSM550633", "GSM550634", "GSM550635", "GSM550636", "GSM550637", "GSM550638", "GSM550639", "GSM550640", "GSM550641", "GSM550642", "GSM550643", "GSM550644", "GSM550645", "GSM550646", "GSM550647", "GSM550648", "GSM550649", "GSM550650", "GSM550651", "GSM550652", "GSM550653", "GSM550654", "GSM550655", "GSM550656", "GSM550657", "GSM550658", "GSM550659", "GSM550660", "GSM550661", "GSM550662", "GSM550663", "GSM550664", "GSM550665", "GSM550666", "GSM550667", "GSM550668", "GSM550669", "GSM550670", "GSM550671", "GSM550672", "GSM550673", "GSM550674", "GSM550675", "GSM550676", "GSM550677", "GSM550678", "GSM550679", "GSM550680", "GSM550681", "GSM550682", "GSM550683", "GSM550684", "GSM550685"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression Data from Uveal Melanoma primary tumors.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE22138 not downloaded", "asset:data:geo:GSE22138 licence not read"]}, "analysis": {"state": "partial", "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": "The limma R package (Version 3.38.3; http://www.bioconductor.org/packages/release/bioc/html/limma.html) was utilized to explore the differentially expressed genes between tumor tissues of “No” group (28 cases) and the “Yes” (35 cases), the threshold was set to: |log2FC|> 0 and P value < 0.05."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Protein-protein interaction"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE22138"], "resolved_accessions": ["GSE22138"], "statements": ["The gene expression profile matrix file from GSE22138 based on the platform GPL570 (including transcription profile data of 63 UVM tissue samples and matching clinically relevant information) was acquired from the gene expression omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). GEO is an international public repository that archives and freely distributes high-throughput microarray and other functional genomic data sets submitted by the research community [17, 18]."], "basis": "The paper names GSE22138 in 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:38342795", "data:geo:GSE22138"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE22138"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:08:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 9702, "completion_tokens": 3116, "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:38342795", "type": "paper", "label": "pmid:38342795"}, {"id": "source:pmid:38342795", "type": "manuscript", "label": "PMID 38342795 full text"}, {"id": "data:geo:GSE22138", "type": "dataset", "label": "GEO GSE22138"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38342795", "type": "paper", "label": "pmid:38342795"}, {"id": "source:pmid:38342795", "type": "manuscript", "label": "PMID 38342795 full text"}, {"id": "data:geo:GSE22138", "type": "dataset", "label": "GEO GSE22138"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38342795", "type": "extraction", "used": ["source:pmid:38342795"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE22138", "type": "accession_resolution", "used": ["data:geo:GSE22138"], "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:38342795", "parent_hash": "sha256:128ffd1e03cff2965370c69d642aa018fec0015bb0fa39ce7aae0723b0387a15", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE22138 licence not read", "asset:data:geo:GSE22138 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["time polymerase chain reaction (qRT-PCR) and western blot. Colony formation and cell counting kit-8 (C"], "order_basis": "paper_text_order:1382", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["t. Colony formation and cell counting kit-8 (CCK-8) assays for cell proliferation, wound healin"], "order_basis": "paper_text_order:1438", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["(Beijing, China). PIG1 and MUM-2B cells were cultured in 90% DMEM (Procell) and M619 cells were propa", "(Beijing, China). PIG1 and MUM-2B cells were cultured in 90% DMEM (Procell) and M619 cells were pr"], "order_basis": "paper_text_order:3487", "id": "assay:3"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The limma R package (Version 3.38.3; http://www.bioconductor.org/packages/release/bioc/html/limma.html) was utilized to explore the differentially expressed genes between tumor tissues of “No” group (28 cases) and the “Yes” (35 cases), the threshold was set to: |log2FC|> 0 and P value < 0.05."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]},"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":"2026-11-04T02:50:29+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}}}