13.4% top-5-accuracy
yuan2022-kmcgd-phenolyzer-top5 top-5-accuracy
- Tested configuration
- Phenolyzer default, singleton (Yuan et al. 2022)
- Protocol
- Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3)
- Dataset
- KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)
- Procedure
- rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default
- Evaluation
- Phenolyzer default singleton on KMCGD 209
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedEvaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 5(%)'
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
- Default parameters
- Scoring implementation
- Rank of the causal gene per case
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 13.4 Individual claims | Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 5(%)' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit detailsDeterministic parse of the pinned docx table XML (extract/extract_rare_ranking.py) with the caption paragraph, header row, dataset labels and method labels asserted. Independent review 2026-10-09: matches SM Table 3 (word/document.xml of the docx). The row is monotone from top 1 to top 50, and the percentage equals a whole number of cases out of the cohort size (305 DDD or 209 KMCGD) at the printed precision. The docx is a member of the Europe PMC supplementaryFiles zip, which is assembled per request (this retrieval: zip SHA-256 b1c6092b3b199b1aa3c7e847e7e4cd2c1faef3c18d5db50be67104859afb86a0); the member matches the pinned hash. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 13.4 Individual claims | Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 5(%)' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: sm_table_3_r1_bbac019.docx inside the Europe PMC supplementaryFiles zip for PMC8921623 | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit detailsDeterministic parse of the pinned docx table XML (extract/extract_rare_ranking.py) with the caption paragraph, header row, dataset labels and method labels asserted. Independent review 2026-10-09: matches SM Table 3 (word/document.xml of the docx). The row is monotone from top 1 to top 50, and the percentage equals a whole number of cases out of the cohort size (305 DDD or 209 KMCGD) at the printed precision. The docx is a member of the Europe PMC supplementaryFiles zip, which is assembled per request (this retrieval: zip SHA-256 b1c6092b3b199b1aa3c7e847e7e4cd2c1faef3c18d5db50be67104859afb86a0); the member matches the pinned hash. Field: Source artifact SHA-256: Hash scope: SHA-256 of the docx member (zip SHA-256 2477ed033ada78ae776a159b0cf0a0daa15231a71a6f87ea705e6e4d3d996d41; assembled per request). Extraction artifact SHA-256: |
Sources and history
Release 2026-10-10-6e93f504adfc · Record review: source checked
2 source records and release history
- Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases · Original source · Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML
- Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · Original source · sm_table_3_r1_bbac019.docx inside the Europe PMC supplementaryFiles zip for PMC8921623
Technical metadata and extraction receipts
Stable ID: rare-ranking-20261009-result-yuan2022-kmcgd-phenolyzer-top5
- metric
- top-5-accuracy
- metric direction
- higher
- unit
- percent
- printed value
- 13.4
- numeric value
- 13.4
- source locator
- SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 5(%)'
- missing metadata
- uncertainty: reason: unreported
- metric qualifier
- proportion of solved cases with the causal gene within the tool's top-ranked genes
- review
- method: source-hash-verification; deterministic-table-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: 5a49ff00fe9b6ed8a92786c83cee79da7b2c9b958a6784d41e496ef59f17e707; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8921623/supplementaryFiles; note: Deterministic parse of the pinned docx table XML (extract/extract_rare_ranking.py) with the caption paragraph, header row, dataset labels and method labels asserted. Independent review 2026-10-09: matches SM Table 3 (word/document.xml of the docx). The row is monotone from top 1 to top 50, and the percentage equals a whole number of cases out of the cohort size (305 DDD or 209 KMCGD) at the printed precision. The docx is a member of the Europe PMC supplementaryFiles zip, which is assembled per request (this retrieval: zip SHA-256 b1c6092b3b199b1aa3c7e847e7e4cd2c1faef3c18d5db50be67104859afb86a0); the member matches the pinned hash.
Related records
- evaluation: Phenolyzer default singleton on KMCGD 209