10 true-positive-count
portik2022-ont-r10-zymo-d6300-kraken2-2-1-1-pluspf true-positive-count
- Tested configuration
- Kraken2 (Portik et al. 2022)
- Protocol
- ONT R10.3 ZymoBIOMICS D6300 standard, length-filtered (GridION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4)
- Dataset
- ONT R10.3 ZymoBIOMICS D6300 standard, length-filtered (GridION)
- Procedure
- dna-pathogen-20261009-protocol-portik2022-ont-r10-zymo-d6300-species
- Evaluation
- Kraken2 on ONT R10.3 ZymoBIOMICS D6300 standard, length-filtered (GridION)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedEvaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Table 4, dataset block 'ONT R10 Zymo D6300 (10 species, even)', row 'Kraken2' (table row 37), column 'True positives'
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 sequencing run
- Adaptation
- None; reference databases as listed in Table 2
- Scoring implementation
- Authors' scoring of species read counts against the community composition
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 10 Individual claims | Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets Table 4, dataset block 'ONT R10 Zymo D6300 (10 species, even)', row 'Kraken2' (table row 37), column 'True positives' Version: BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit detailsExtracted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
1 source records and release history
- Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Original source · BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261009-result-portik2022-ont-r10-zymo-d6300-kraken2-2-1-1-pluspf-tp
- metric
- true-positive-count
- metric direction
- higher
- unit
- count
- printed value
- 10
- numeric value
- 10
- source locator
- Table 4, dataset block 'ONT R10 Zymo D6300 (10 species, even)', row 'Kraken2' (table row 37), column 'True positives'
- unit detail
- species
- missing metadata
- uncertainty: reason: unreported
- 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: 42cf6834ec87e149752176a65247f3aab9873f7b215037a195175a8a3113c1fe; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9749362/fullTextXML; method note: Re-downloaded the article XML and matched its SHA-256. Read Portik Table 4 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. Recomputed precision, recall, F1 and F0.5 from the printed TP, FP and FN; ten printed two-decimal values differ from exact rounding by 0.005 to 0.009 (source rounding, see the dated review).; 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.