0.607 negative-predictive-value
drost2025-cagi6-al4-negative-predictive-value negative-predictive-value
- Tested configuration
- At least 4 of 4 splice predictors (Drost et al.)
- Protocol
- Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1)
- Dataset
- CAGI6 Splicing VUS variants as scored by Drost et al.
- Procedure
- rna-splicing-20261009-protocol-drost2025-cagi6
- Evaluation
- At least 4 of 4 splice predictors on 56 CAGI6 Splicing VUS variants
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Author-reported evaluation · source checkedRoutine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell H28; row AtLeast4, column Neg Pred Value
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- No training split
- Adaptation
- None; pretrained predictors with literature thresholds
- Scoring implementation
- R: plotROC 2.3.1 (ROC), yardstick 1.2.0 (PR), caret 6.0.94 (binary statistics)
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.607142857142857 Individual claims | Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools Data S1 Table S4 'CAGI6 dataset', cell H28; row AtLeast4, column Neg Pred Value Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: HGG Advances 7(1):100521, published online 2025-09-22; PMC12547740 full-text XML | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 author reported Audit detailsDeterministic parse of the pinned XLSX cell XML (extract/extract_rna_splicing.py) with sheet title, block titles, column headers and row labels asserted; printed_value is the shortest round-trip decimal of the stored double, raw_xml_value keeps the stored text. Pending independent review. Independent review 2026-10-09: value and identity match the source. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 0.607142857142857 Individual claims | Drost et al. 2025, Data S1 (Tables S1-S6) Data S1 Table S4 'CAGI6 dataset', cell H28; row AtLeast4, column Neg Pred Value Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: mmc2.xlsx (Data S1. Tables S1-S6) inside the Europe PMC supplementaryFiles zip for PMC12547740 | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 author reported Audit detailsDeterministic parse of the pinned XLSX cell XML (extract/extract_rna_splicing.py) with sheet title, block titles, column headers and row labels asserted; printed_value is the shortest round-trip decimal of the stored double, raw_xml_value keeps the stored text. Pending independent review. Independent review 2026-10-09: value and identity match the source. Field: Source artifact SHA-256: Hash scope: SHA-256 of mmc2.xlsx as extracted from the supplementaryFiles zip (zip SHA-256 1c89a7ebc0bf686c6087d0fee86ba6f364a6d754d5bc7eb9c446b7db017f1ebc; the zip is re-built by Europe PMC on each request, so only the member hash is stable). Extraction artifact SHA-256: |
Sources and history
Release 2026-10-09-ba02f2f4a36e · Record review: source checked
2 source records and release history
- Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools · Original source · HGG Advances 7(1):100521, published online 2025-09-22; PMC12547740 full-text XML
- Drost et al. 2025, Data S1 (Tables S1-S6) · Original source · mmc2.xlsx (Data S1. Tables S1-S6) inside the Europe PMC supplementaryFiles zip for PMC12547740
Technical metadata and extraction receipts
Stable ID: rna-splicing-20261009-result-drost2025-cagi6-al4-negative-predictive-value
- metric
- negative-predictive-value
- metric direction
- higher
- unit
- fraction
- printed value
- 0.607142857142857
- numeric value
- 0.607142857142857
- source locator
- Data S1 Table S4 'CAGI6 dataset', cell H28; row AtLeast4, column Neg Pred Value
- missing metadata
- uncertainty: reason: unreported
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: a3a69202b8f0d9ecb7fa22a16991d5e4d583b5ae72fd598206ea5c2b4c5c14ca; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12547740/supplementaryFiles; method note: Re-downloaded the artifact and matched its SHA-256. Read Drost Data S1 Table S4 with a separate reader written for this review (the extractor's scripts were not run). Checked printed and numeric value, locator, metric, unit and direction, and the evaluation's configuration, protocol and dataset. Recovered integer TP and TN for each row and confirmed that the Entire Dataset counts equal CAGI6 plus In House for every tool.; note: Deterministic parse of the pinned XLSX cell XML (extract/extract_rna_splicing.py) with sheet title, block titles, column headers and row labels asserted; printed_value is the shortest round-trip decimal of the stored double, raw_xml_value keeps the stored text. Pending independent review. Independent review 2026-10-09: value and identity match the source.
- metric qualifier
- at-least-N consensus of four thresholded tools
- raw xml value
- 0.60714285714285698