Result

0.0548 youden-index

hall2024-sim-illumina-kraken2-standard-8 youden-index

Tested configuration: kraken standard-8 (Hall and Coin 2024)
Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7)
Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)
Procedure: dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina
Evaluation: kraken standard-8 on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)
Coverage: Not reported scored / Not reported eligible
Uncertainty: 95% CI 0.0541 to 0.0556. Wilson score interval (table footnote)
Evidence: Independent external evaluation · source checkedPangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard-8', column 'Youden’s index (95% CI)'

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: Single dataset
Adaptation: Database as stated per configuration
Scoring implementation: Per-read confusion counts against known read origin

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

Claims, original sources and review scope · Release 2026-10-09-8cc1db47c7f9
Property and statement	Original source and location	Review and provenance
Reported result 0.0548 Individual claims	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Original source ↗ Table 7, row 'kraken standard-8', column 'Youden’s index (95% CI)' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML Retrieved: 2026-10-09T19:55:15Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit details Extracted by deterministic parse of the pinned Europe PMC full-text XML (extract/extract_pathogen.py), with every row and column label asserted. printed_value is the table cell text exactly as in the XML. Pending independent review. Independent review 2026-10-09: value and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554` Extraction artifact

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Sources and history

Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

1 source records and release history

Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Original source · GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML

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Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261009-result-hall2024-sim-illumina-kraken2-standard-8-youden

metric: youden-index
metric direction: higher
unit: fraction
printed value: 0.0548
numeric value: 0.0548
source locator: Table 7, row 'kraken standard-8', column 'Youden’s index (95% CI)'
uncertainty: type: confidence_interval; printed: (0.0541–0.0556); lower: 0.0541; upper: 0.0556; level: 0.95; method: analytic; note: Wilson score interval (table footnote)
printed source cell: 0.0548 (0.0541–0.0556)
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: ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10993716/fullTextXML; method note: Re-downloaded the article XML and matched its SHA-256. Read Hall Tables 5-8 with a separate parser written for this review (row and column spans expanded; the extractor's script was not run). Checked printed and numeric value, locator, metric, qualifier, unit and direction from the headers, and the evaluation's configuration, protocol and dataset. Checked the interval bounds, level and Wilson method against the cell and table footnote.; note: Extracted by deterministic parse of the pinned Europe PMC full-text XML (extract/extract_pathogen.py), with every row and column label asserted. printed_value is the table cell text exactly as in the XML. Pending independent review. Independent review 2026-10-09: value and identity match the source.

Related records

evaluation: kraken standard-8 on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)

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