Result

43 true-positive-count

riepe2021-abca4-ncss-spidex-1-0-tp true-positive-count

Tested configuration: Spidex (Riepe et al. 2021)
Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3)
Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)
Procedure: splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss
Evaluation: Spidex on ABCA4 noncanonical splice-site variants
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedBenchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Spidex', column 'TP'

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 split
Adaptation: Per-data-set cutoff
Scoring implementation: Not reported

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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

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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.

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1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance
Reported result 43 Individual claims	Benchmarking deep learning splice prediction tools using functional splice assays Original source ↗ Table 3 row 'Spidex', column 'TP' Version: Human Mutation 42(7):799, published online 2021-05-20; PMC8360004 full-text XML Retrieved: 2026-10-09T20:52:02Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit details Deterministic parse of the pinned article XML table (extract/extract_splicing_follow_up.py) with caption, column headers and tool labels asserted. Independent review 2026-10-09: value and identity match the source. The printed rates and MCC reproduce from the row's confusion matrix (62.5% is printed as 63). Spidex has 5 (ABCA4 NCSS) or 3 (MYBPC3) unscored variants, yet its TP, FP, TN and FN sum to the same total as every other tool, so the unscored variants were counted in one of the cells; the article does not say which (Methods P16 sets missing scores to zero only for the Alamut tools). Field: `attributes.printed_value` Source artifact SHA-256: `595be5360a9d3d421c4d4b6adda30175b4048e1aa0b563eb7afd2b7850277112` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `595be5360a9d3d421c4d4b6adda30175b4048e1aa0b563eb7afd2b7850277112` Extraction artifact

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Sources and history

Release 2026-10-10-6e93f504adfc · Record review: source checked

1 source records and release history

Benchmarking deep learning splice prediction tools using functional splice assays · Original source · Human Mutation 42(7):799, published online 2021-05-20; PMC8360004 full-text XML

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Technical metadata and extraction receipts

Stable ID: splicing-follow-up-20261009-result-riepe2021-abca4-ncss-spidex-1-0-tp

metric: true-positive-count
metric direction: higher
unit: count
printed value: 43
numeric value: 43
source locator: Table 3 row 'Spidex', column 'TP'
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the article XML and matched its SHA-256. Read tables humu24212-tbl-0003 to -0005 with a separate stdlib XML reader written for this review; the extractor's scripts were not imported or run. Built each cell's identity from the header row and tool label, checked printed value, numeric value, metric, qualifier, unit, direction and the linked evaluation's configuration, protocol and dataset, and recomputed accuracy, PPV, sensitivity, specificity, NPV and MCC from the printed TP, FP, TN and FN.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: 595be5360a9d3d421c4d4b6adda30175b4048e1aa0b563eb7afd2b7850277112; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8360004/fullTextXML; note: Deterministic parse of the pinned article XML table (extract/extract_splicing_follow_up.py) with caption, column headers and tool labels asserted. Independent review 2026-10-09: value and identity match the source. The printed rates and MCC reproduce from the row's confusion matrix (62.5% is printed as 63). Spidex has 5 (ABCA4 NCSS) or 3 (MYBPC3) unscored variants, yet its TP, FP, TN and FN sum to the same total as every other tool, so the unscored variants were counted in one of the cells; the article does not say which (Methods P16 sets missing scores to zero only for the Alamut tools).
missing metadata: uncertainty: reason: unreported
unit detail: variants

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evaluation: Spidex on ABCA4 noncanonical splice-site variants

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