{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27293547", "kind": "science-record", "revision": 4, "content_hash": "sha256:127b9938e85e90e3639c0d048f7b3bb0bf6f412e07e12d8927382dce2de60cba", "created_at": "2026-11-01T15:40:18Z", "updated_at": "2026-11-01T21:20:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic analysis reveals the expression of unique transcriptomic signatures in Zika virus infected human neural stem cells.", "doi": "10.1186/s13578-016-0110-x", "pmid": "27293547", "authors": ["Alyssa J Rolfe", "Dale B Bosco", "Jingying Wang", "Richard S Nowakowski", "Jianqing Fan", "Yi Ren"], "journal": "Cell & bioscience", "year": 2016, "abstract": "BACKGROUND: The single-stranded RNA Flavivirus, Zika virus (ZIKV), has recently re-emerged and spread rapidly across the western hemisphere's equatorial countries, primarily through Aedes mosquito transmission. While symptoms in adult infections appear to be self-limiting and mild, severe birth defects, such as microcephaly, have been linked to infection during early pregnancy. Recently, Tang et al. (Cell Stem Cell 2016, doi: 10.1016/j.stem.2016.02.016) demonstrated that ZIKV efficiently infects induced pluripotent stem cell (iPSC) derived human neural progenitor cells (hNPCs), resulting in cell cycle abnormalities and apoptosis. Consequently, hNPCs are a suggested ZIKV target.\nMETHODS: We analyzed the transcriptomic sequencing (RNA-seq) data (GEO: GSE78711) of ZIKV (Strain: MR766) infected hNPCs. For comparison to the ZIKV-infected hNPCs, the expression data from hNPCs infected with human cytomegalovirus (CMV) (Strain: AD169) was used (GEO: GSE35295). Utilizing a combination of Gene Ontology, database of human diseases, and pathway analysis, we generated a putative systemic model of infection supported by known molecular pathways of other highly related viruses.\nRESULTS: We analyzed RNA-sequencing data for transcript expression alterations in ZIKV-infected hNPCs, and then compared them to expression patterns of iPSC-derived hNPCs infected with CMV, a virus that can also induce severe congenital neurological defects in developing fetuses. We demonstrate for the first time that many of cellular pathways correlate with clinical pathologies following ZIKV infection such as microcephaly, congenital nervous system disorders and epilepsy. Furthermore, ZIKV activates several inflammatory signals within infected hNPCs that are implicated in innate and acquired immune responses, while CMV-infected hNPCs showed limited representation of these pathways. Moreover, several genes related to pathogen responses are significantly upregulated upon ZIKV infection, but not perturbed in CMV-infected hNPCs.\nCONCLUSION: The presented study is the first to report enrichment of numerous pro-inflammatory pathways in ZIKV-infected hNPCs, indicating that hNPCs are capable of signaling through canonical pro-inflammatory pathways following viral infection. By defining gene expression profiles, new factors in the pathogenesis of ZIKV were identified which could help develop new therapeutic strategies.", "claims": [{"id": "claim-method", "statement": "Comparison of the mock-infected samples to the ZIKV-infected samples using a modified t-test yields a total of 3443 genes up-regulated and 3421 down-regulated.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27293547", "locator": "sections[3] \"Comprehensive gene set gene ontology analysis\" paragraph 2", "quote": "Comparison of the mock-infected samples to the ZIKV-infected samples using a modified t-test yields a total of 3443 genes up-regulated and 3421 down-regulated."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusions of this article are available in the gene expression omnibus (GEO) repository, http://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27293547", "locator": "sections[13] \"Availability of data and materials\" paragraph 2", "quote": "The datasets supporting the conclusions of this article are available in the gene expression omnibus (GEO) repository, http://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using a modified t-test on ZIKV-infected hNPC RNA-seq data from GEO GSE78711, with GEO GSE35295 used for CMV comparison, the study found broad enrichment of pro-inflammatory and congenital nervous system pathways in ZIKV-infected hNPCs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27293547", "locator": "sections[3] \"Comprehensive gene set gene ontology analysis\" paragraph 2", "quote": "Comparison of the mock-infected samples to the ZIKV-infected samples using a modified t-test yields a total of 3443 genes up-regulated and 3421 down-regulated."}, {"asset": "source:pmid:27293547", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We analyzed the transcriptomic sequencing (RNA-seq) data (GEO: GSE78711) of ZIKV (Strain: MR766) infected hNPCs."}, {"asset": "source:pmid:27293547", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "For comparison to the ZIKV-infected hNPCs, the expression data from hNPCs infected with human cytomegalovirus (CMV) (Strain: AD169) was used (GEO: GSE35295)."}, {"asset": "source:pmid:27293547", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We demonstrate for the first time that many of cellular pathways correlate with clinical pathologies following ZIKV infection such as microcephaly, congenital nervous system disorders and epilepsy."}, {"asset": "source:pmid:27293547", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The presented study is the first to report enrichment of numerous pro-inflammatory pathways in ZIKV-infected hNPCs, indicating that hNPCs are capable of signaling through canonical pro-inflammatory pathways following viral infection."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using a modified t-test on ZIKV-infected hNPC RNA-seq data from GEO GSE78711, with GEO GSE35295 used for CMV comparison, the study found broad enrichment of pro-inflammatory and congenital nervous system pathways in ZIKV-infected hNPCs.", "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:27293547"], "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. 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http://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusions of this article are available in the gene expression omnibus (GEO) repository, http://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM480450", "GSM480451", "GSM480452", "GSM480453", "GSM480454", "GSM480455", "GSM480456", "GSM480457"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Human Cytomegalovirus Infection Causes Premature and Abnormal Differentiation of Human Neural Progenitor Cells", "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:GSE35295", "role": "raw", "format": "geo-series", "media_type": 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viral oncogene homolog B", "2.52167", "0.00005"], ["BHLHE40", "8553", "Basic helix-loop-helix family, member e40", "2.50278", "0.00005"], ["INHBE", "83729", "Inhibin, beta E", "2.48416", "0.00005"], ["XBP1", "7494", "X-box binding protein 1", "2.48392", "0.00005"], ["SELPLG", "6404", "Selectin P ligand", "2.47628", "0.00005"], ["SLC7A5", "8140", "Solute carrier family 7 (amino acid transporter light chain, L system), member 5", "2.44283", "0.00005"], ["ARHGAP9", "64333", "Rho GTPase activating protein 9", "2.42899", "0.00005"], ["HERPUD1", "9709", "Homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1", "2.38525", "0.00005"], ["KLF15", "28999", "Kruppel-like factor 15", "2.36633", "0.00005"], ["CDC42EP1", "11135", "CDC42 effector protein (Rho GTPase binding) 1", "2.35073", "0.00005"], ["CEBPD", "1052", "CCAAT/enhancer binding protein (C/EBP), delta", "2.34979", "0.00025"], ["GAL3ST2", "64090", "Galactose-3-O-sulfotransferase 2", "2.31589", "0.0021"], ["FAM129A", "116496", "Family with sequence similarity 129, member A", "2.28808", "0.00005"]], "row_count": 31, "column_count": 5, "numeric_cells": 125, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:27293547:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cde5113c2dcb987bedc2be7005632cc7054cc3c5ffead8c090cb1247810a8051", "bytes": 2607, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#Tab2", "version": null, "note": "Top 30 genes down-regulated in ZIKV infected hNPCs compared to controls", "structure": {"pmcid": "PMC4902960", "section_index": 3, "section_title": "Comprehensive gene set gene ontology analysis", "row_count": 31, "column_count": 5}, "table": {"label": "Table 2", "caption": "Top 30 genes down-regulated in ZIKV infected hNPCs compared to controls", "rows": [["Gene 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null, "note": "Neurological clinical phenotypes associated with ZIKV DEGs", "structure": {"pmcid": "PMC4902960", "section_index": 4, "section_title": "ZIKV DEGs represented in canonical human neurological diseases", "row_count": 62, "column_count": 3}, "table": {"label": "Table 3", "caption": "Neurological clinical phenotypes associated with ZIKV DEGs", "rows": [["Disease", "Gene symbol", "Gene name"], ["Microcephaly", "DYRK1A", "Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A"], ["MCPH1", "Microcephalin 1"], ["CASK", "Calcium/calmodulin-dependent serine protein kinase (MAGUK family)"], ["PHGDH", "Phosphoglycerate dehydrogenase"], ["ARFGEF2", "ADP-ribosylation factor guanine nucleotide-exchange factor 2"], ["ASPM", "Asp (abnormal spindle) homolog, microcephaly associated"], ["CENPJ", "Centromere protein J"], ["CEP152", "Centrosomal protein 152 kDa"], ["SLC25A19", "Solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19"], ["WDR62", "WD repeat domain 62"], ["CDK5RAP2", "CDK5 regulatory subunit associated protein 2"], ["CASC5", "Cancer susceptibility candidate 5"], ["NBN", "Nibrin"], ["EFTUD2", "Elongation factor Tu GTP binding domain containing 2"], ["IER3IP1", "Immediate early response 3 interacting protein 1"], ["STIL", "SCL/TAL1 interrupting locus"], ["CEP135", "Centrosomal protein 135 kDa"], ["ZNF335", "Zinc finger protein 335"], ["NDE1", "nudE nuclear distribution E homolog 1"], ["DIAPH1", "Diaphanous homolog 1"], ["KIF11", "Kinesin family member 11"], ["Congenital nervous system disorders", "MCPH1", "Microcephalin 1"], ["ARFGEF2", "ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)"], ["TGIF1", "TGFB-induced factor homeobox 1"], ["GRIN2B", "Glutamate receptor, ionotropic, N-methyl d-aspartate 2B"], ["SLC12A5", "Solute carrier family 12 (potassium/chloride transporter), member 5"], ["FLNA", "Filamin A, alpha"], ["SIX3", "SIX homeobox 3"], ["SHH", "Sonic hedgehog"], ["CDK5RAP2", 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"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 (Modified t-test), 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": ["GSE78711", "GSE35295", "GSE19345"], "resolved_accessions": ["GSE78711", "GSE35295", "GSE19345"], "statements": ["The datasets supporting the conclusions of this article are available in the gene expression omnibus (GEO) repository, http://www.ncbi.nlm.nih.gov/geo/."], "basis": "The paper names GSE78711, GSE35295, GSE19345 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": [], "assets": ["source:pmid:27293547", "data:geo:GSE19345", "asset:table:pmid:27293547:1", "asset:table:pmid:27293547:2", "asset:table:pmid:27293547:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19345"]}, "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": "2026-10-31T18:28:44Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 77399, "completion_tokens": 4328, "cached_tokens": 19984}}, "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:27293547", "type": "paper", "label": "pmid:27293547"}, {"id": "source:pmid:27293547", "type": "manuscript", "label": "PMID 27293547 full text"}, {"id": "data:geo:GSE19345", "type": "dataset", "label": "GEO GSE19345"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27293547", "type": "paper", "label": "pmid:27293547"}, {"id": "source:pmid:27293547", "type": "manuscript", "label": "PMID 27293547 full text"}, {"id": "data:geo:GSE19345", "type": "dataset", "label": "GEO GSE19345"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27293547", "type": "extraction", "used": ["source:pmid:27293547"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19345", "type": "accession_resolution", "used": ["data:geo:GSE19345"], "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:27293547", "parent_hash": "sha256:9c602ea4cf4246d66e75ba6b40e461a5f709434076344b86ced2aa01179ae949", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE19345 licence not read", "asset:data:geo:GSE19345 not downloaded", "asset:data:geo:GSE35295 licence not read", "asset:data:geo:GSE35295 not downloaded", "asset:data:geo:GSE78711 licence not read", "asset:data:geo:GSE78711 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ic analysis reveals the expression of unique transcriptomic signatures in Zika virus infected human neur", ": We analyzed the transcriptomic sequencing (RNA-seq) data (GEO: GSE78711) of ZIKV (Strain: MR766", "highly related viruses. RESULTS: We analyzed RNA-sequencing data for transcript expression alterations i", "gested ZIKV target. METHODS: We analyzed the transcriptomic sequencing (RNA-seq) data (GEO: GSE78711) of"], "order_basis": "paper_text_order:11", "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": 0.69, "evidence": ["), resulting in cell cycle abnormalities and apoptosis. Consequently, hNPCs are a suggested ZIKV ta"], "order_basis": "paper_text_order:712", "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":"2026-11-04T01:50:32+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}}}