5 true-positive-count
vestito2024-dh9-vs4 true-positive-count (diagnosed variants flagged)
- Tested configuration
- Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.9, variant score 0.4 (Vestito et al. 2024)
- Protocol
- Flagging new reanalysis candidates from Exomiser score changes across database releases (Vestito et al. 2024 Supplementary Table 1)
- Dataset
- 100,000 Genomes Project: 37 cases unsolved in February 2019 and later diagnosed through a new disease-gene association (Vestito et al. 2024)
- Procedure
- rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging
- Evaluation
- Exomiser reanalysis flag 0.9/0.4: later-diagnosed 100kGP cases
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Author-reported evaluation · source checkedVestito et al. 2024, Supplementary Table 1 · Supplementary Table 1 line 78 (Diff human score 0.9, Var score 0.4), 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
- Threshold pair as stated per configuration
- Scoring implementation
- Variant-level confusion counts in R 4.2.1
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 5 Individual claims | Vestito et al. 2024, Supplementary Table 1 Supplementary Table 1 line 78 (Diff human score 0.9, Var score 0.4), column 'TP' Version: 41525_2024_456_MOESM1_ESM.pdf from the Europe PMC supplementary bundle (PDF title 'Supplementary_table_S1 copy', 4 pages) | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-09 author reported Audit detailsExtracted by deterministic parse of `pdftotext -layout` output of the pinned supplementary PDF (extract/extract_rare_reanalysis.py), with row and column labels asserted. printed_value is the token as printed. Independent review 2026-10-09: matches Supplementary Table 1 (pdftotext -layout, poppler 26.08.0). Recall, precision, F1 and F2 recomputed from the TP, FN and FP cells of the same row agree with the printed values to within 5e-10; TP + FN = 37 and TP + FN + FP + TN = 1846 on the row. The Europe PMC supplementaryFiles bundle returned HTTP 500 on 2026-10-09; the same file was retrieved from the publisher URL given here and its bytes match the pinned SHA-256. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-10-6e93f504adfc · Record review: source checked
2 source records and release history
- Vestito et al. 2024, Supplementary Table 1 · Original source · 41525_2024_456_MOESM1_ESM.pdf from the Europe PMC supplementary bundle (PDF title 'Supplementary_table_S1 copy', 4 pages)
- Efficient reinterpretation of rare disease cases using Exomiser · Original source · npj Genomic Medicine 9:65, published 2024-12-18; PMC11655964 full-text XML
Technical metadata and extraction receipts
Stable ID: rare-reanalysis-20261009-result-vestito2024-dh9-vs4-tp
- metric
- true-positive-count
- metric direction
- higher
- unit
- count
- printed value
- 5
- numeric value
- 5
- source locator
- Supplementary Table 1 line 78 (Diff human score 0.9, Var score 0.4), column 'TP'
- missing metadata
- uncertainty: reason: unreported
- metric qualifier
- diagnosed variants flagged
- unit detail
- variants
- review
- method: source-hash-verification; pdf-text-parse; independent-cell-check; method note: Re-downloaded the artifact and matched its SHA-256. Read the cell with a separate parser written for this review; the extractor script was not imported or run. Checked printed and numeric value, locator, metric, qualifier, unit, direction and the linked evaluation, configuration, protocol and dataset.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: d761ccee3944cd762d1c07e5388ed2810bd57634e1fc2c23a054b547a710a5ad; retrieval url: https://static-content.springer.com/esm/art%3A10.1038%2Fs41525-024-00456-2/MediaObjects/41525_2024_456_MOESM1_ESM.pdf; note: Extracted by deterministic parse of `pdftotext -layout` output of the pinned supplementary PDF (extract/extract_rare_reanalysis.py), with row and column labels asserted. printed_value is the token as printed. Independent review 2026-10-09: matches Supplementary Table 1 (pdftotext -layout, poppler 26.08.0). Recall, precision, F1 and F2 recomputed from the TP, FN and FP cells of the same row agree with the printed values to within 5e-10; TP + FN = 37 and TP + FN + FP + TN = 1846 on the row. The Europe PMC supplementaryFiles bundle returned HTTP 500 on 2026-10-09; the same file was retrieved from the publisher URL given here and its bytes match the pinned SHA-256.