Specificity (negative percent agreement; organism level; organisms: fungi; reference: composite reference standard (CRS)) of Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) on 62 residual BALF specimens with culture results (Hu et al. 2026)
91.7% Specificity (negative percent agreement; organism level; organisms: fungi; reference: composite reference standard (CRS))
Methods
- Tested configuration
- Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)
- Protocol
- Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026)
- Dataset
- 62 residual BALF specimens with culture results (Hu et al. 2026)
- Procedure
- Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026)
- Evaluation
- Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against composite reference standard (CRS)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Author-reported evaluation · source checkedHu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "TGS", column group "Composite reference standard (CRS)", row "NPA"
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 clinical set
- Adaptation
- Workflow as stated per configuration
- Scoring implementation
- Organism-level 2x2 counts; PPA and NPA
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 91.70% Individual claims | Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Supplemental Table 7, block "TGS", column group "Composite reference standard (CRS)", row "NPA" Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-11 author reported Audit detailsRe-downloaded the pinned artifact and matched its SHA-256; compared every value with a separate stdlib parser written for this review (the extractor's script was not run) and checked a stratified sample by hand against the rendered table. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Original source · spectrum.03993-25-s0001.docx as distributed with PMC13339908
- Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Original source · Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261011-hu2026-result-crs-hdont-fungi-npa
- metric
- specificity
- metric direction
- higher
- unit
- percent
- printed value
- 91.70%
- numeric value
- 91.70
- metric qualifier
- negative percent agreement; organism level; organisms: fungi; reference: composite reference standard (CRS)
- source locator
- Supplemental Table 7, block "TGS", column group "Composite reference standard (CRS)", row "NPA"
- missing metadata
- uncertainty: reason: unreported
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; reviewer: claude; reviewer note: Separate Claude review agent (reviewer-path), independent of the extractor; no human review claimed; date: 2026-10-11; artifact sha256: 7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13339908/supplementaryFiles; method note: Extracted by deterministic parse of the pinned supplementary DOCX (word/document.xml) (extract/extract_hu2026.py), with block, row and column labels asserted. printed_value is the cell text exactly.; note: Re-downloaded the pinned artifact and matched its SHA-256; compared every value with a separate stdlib parser written for this review (the extractor's script was not run) and checked a stratified sample by hand against the rendered table.