Result

80% recall

devries2021-hit-one-codex recall (hit level, 15 PCR-positive hits)

Tested configuration: One Codex as run by an ENNGS laboratory (de Vries et al. 2021)
Protocol: Virus hits against RT-PCR: true and false positives, PPV and hit-level sensitivity (de Vries et al. 2021 Supplementary Table 4)
Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)
Procedure: rna-pathogen-20261009-protocol-devries2021-hit-level
Evaluation: One Codex: virus hits against RT-PCR (ENNGS)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedde Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 4, cell T37, row 'One Codex', column 'Sensitivity [%], hit level'

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: Each laboratory's own database and reporting criteria
Scoring implementation: Organisers' scoring of reported hits against RT-PCR

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 80 Individual claims	de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 Original source ↗ Supplementary Table 4, cell T37, row 'One Codex', column 'Sensitivity [%], hit level' Version: medRxiv 2021.05.04.21256618 version 1, supplementary file media-1.xlsx (sheets SuppS2, SuppS3, SuppS4) Retrieved: 2026-10-09T20:15:56Z	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 XLSX cell XML (extract/extract_rna_pathogen.py), with row and column labels asserted. printed_value is the cell text, or the shortest decimal that round-trips to the stored number; displayed spreadsheet formatting was not applied. Pending independent review. Independent review 2026-10-09: value and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `be0ea61fcffe8ea580077467ca19ef1ac39e88bbc82d916bc65b58a6683214f6` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `be0ea61fcffe8ea580077467ca19ef1ac39e88bbc82d916bc65b58a6683214f6` Extraction artifact

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Sources and history

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

2 source records and release history

de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Original source · medRxiv 2021.05.04.21256618 version 1, supplementary file media-1.xlsx (sheets SuppS2, SuppS3, SuppS4)
Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples · Original source · medRxiv 2021.05.04.21256618 version 1 (2021-05-08), JATS XML; published as J Clin Virol 141:104908 (doi:10.1016/j.jcv.2021.104908)

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Technical metadata and extraction receipts

Stable ID: rna-pathogen-20261009-result-devries2021-hit-one-codex-sensitivity

metric: recall
metric direction: higher
unit: percent
printed value: 80
numeric value: 80
source locator: Supplementary Table 4, cell T37, row 'One Codex', column 'Sensitivity [%], hit level'
missing metadata: uncertainty: reason: unreported
metric qualifier: hit level, 15 PCR-positive hits
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: be0ea61fcffe8ea580077467ca19ef1ac39e88bbc82d916bc65b58a6683214f6; retrieval url: https://www.medrxiv.org/content/medrxiv/early/2021/05/08/2021.05.04.21256618/DC1/embed/media-1.xlsx; method note: Re-downloaded the workbook and matched its SHA-256. Read de Vries et al. Supplementary Tables 2 and 4 (medRxiv v1 workbook) with a separate stdlib OOXML reader written for this review (the extractor's script was not run). Checked printed and numeric value, locator, metric, unit and direction from the headers, and the evaluation's configuration, protocol and dataset. Recomputed PPV, sensitivity, TP + FN and TP + FP for every row.; note: Extracted by deterministic parse of the pinned XLSX cell XML (extract/extract_rna_pathogen.py), with row and column labels asserted. printed_value is the cell text, or the shortest decimal that round-trips to the stored number; displayed spreadsheet formatting was not applied. Pending independent review. Independent review 2026-10-09: value and identity match the source.

Related records

evaluation: One Codex: virus hits against RT-PCR (ENNGS)

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