Evidence claim

Relevance of the BERTax closely related dataset protocol (Mock et al. 2022) to "Select a DNA pathogen-identification workflow for diagnostic testing"

Use case: Select a DNA pathogen-identification workflow for diagnostic testing
Assessed by: BERTax Closely related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022)
Relevance: Proxy evidence
Endpoint: Macro AveP, accuracy and proportion classified at superkingdom and phylum rank on 1,500-nt genome fragments

Machine-learning classifiers (BERTax, DeepMicrobes) and the baseline k-mer and alignment tools Kraken2 and minimap2 are scored on the same fragments with the same reference data. Tests whether a trained classifier matches reference-based tools when relatives are in the reference. It is proxy evidence: the inputs are simulated genome fragments, not specimen reads, and ranks stop at genus.

9 reviewed evaluations

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.

60 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Citation locations 3 values source id dna-pathogen-20261012-bertax-source-pdf locator Table 1 source id dna-pathogen-20261012-bertax-source-si locator Table S2 source id dna-pathogen-20261012-bertax-source locator Materials and Methods 'Three Evaluation Datasets', 'Comparison to Other Tools' Context-only references	Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks Original source ↗ dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PNAS 119(35):e2122636119, published 2022-08-26; PMC9436379 full-text XML Retrieved: 2026-10-12T20:51:54Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `c0bb2f1bba8680b300076292389b39346ae58bea4bdf28647dd9462333b3bcd7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 3 values source id dna-pathogen-20261012-bertax-source-pdf locator Table 1 source id dna-pathogen-20261012-bertax-source-si locator Table S2 source id dna-pathogen-20261012-bertax-source locator Materials and Methods 'Three Evaluation Datasets', 'Comparison to Other Tools' Context-only references	Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) Original source ↗ dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) Retrieved: 2026-10-12T20:56:37Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `7977424613ab5e5f4986745b527a270fd2c0427dbab40471813903eda85dcaec` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 3 values source id dna-pathogen-20261012-bertax-source-pdf locator Table 1 source id dna-pathogen-20261012-bertax-source-si locator Table S2 source id dna-pathogen-20261012-bertax-source locator Materials and Methods 'Three Evaluation Datasets', 'Comparison to Other Tools' Context-only references	BERTax SI Appendix (pnas.2122636119.sapp.pdf) Original source ↗ dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: SI Appendix as distributed with PMC9436379 (member pnas.2122636119.sapp.pdf of the Europe PMC supplementaryFiles ZIP) Retrieved: 2026-10-12T20:55:54Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `89a2f86f66cbb2ff17886d413cd89577285086fedd1009e1d9daf87b29fbc1c0` Hash scope: SHA-256 of the PDF member, not of the ZIP (the ZIP is rebuilt per request) Inspected artifact
Comparison group bertax2022-fragments Context-only references	Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks Original source ↗ dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PNAS 119(35):e2122636119, published 2022-08-26; PMC9436379 full-text XML Retrieved: 2026-10-12T20:51:54Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `c0bb2f1bba8680b300076292389b39346ae58bea4bdf28647dd9462333b3bcd7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group bertax2022-fragments Context-only references	Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) Original source ↗ dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) Retrieved: 2026-10-12T20:56:37Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `7977424613ab5e5f4986745b527a270fd2c0427dbab40471813903eda85dcaec` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group bertax2022-fragments Context-only references	BERTax SI Appendix (pnas.2122636119.sapp.pdf) Original source ↗ dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: SI Appendix as distributed with PMC9436379 (member pnas.2122636119.sapp.pdf of the Europe PMC supplementaryFiles ZIP) Retrieved: 2026-10-12T20:55:54Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `89a2f86f66cbb2ff17886d413cd89577285086fedd1009e1d9daf87b29fbc1c0` Hash scope: SHA-256 of the PDF member, not of the ZIP (the ZIP is rebuilt per request) Inspected artifact
Comparison title BERTax genome-fragment classification against database tools (Mock et al. 2022) Context-only references	Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks Original source ↗ dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PNAS 119(35):e2122636119, published 2022-08-26; PMC9436379 full-text XML Retrieved: 2026-10-12T20:51:54Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `c0bb2f1bba8680b300076292389b39346ae58bea4bdf28647dd9462333b3bcd7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title BERTax genome-fragment classification against database tools (Mock et al. 2022) Context-only references	Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) Original source ↗ dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) Retrieved: 2026-10-12T20:56:37Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `7977424613ab5e5f4986745b527a270fd2c0427dbab40471813903eda85dcaec` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title BERTax genome-fragment classification against database tools (Mock et al. 2022) Context-only references	BERTax SI Appendix (pnas.2122636119.sapp.pdf) Original source ↗ dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: SI Appendix as distributed with PMC9436379 (member pnas.2122636119.sapp.pdf of the Europe PMC supplementaryFiles ZIP) Retrieved: 2026-10-12T20:55:54Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `89a2f86f66cbb2ff17886d413cd89577285086fedd1009e1d9daf87b29fbc1c0` Hash scope: SHA-256 of the PDF member, not of the ZIP (the ZIP is rebuilt per request) Inspected artifact
Constraints 2 values Inspect every linked evaluation's source locator and preserved limitations before citing a result. Do not combine these results with another protocol's results; inputs, references and taxonomic ranks differ between sources. Context-only references	Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks Original source ↗ dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PNAS 119(35):e2122636119, published 2022-08-26; PMC9436379 full-text XML Retrieved: 2026-10-12T20:51:54Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `c0bb2f1bba8680b300076292389b39346ae58bea4bdf28647dd9462333b3bcd7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

3 source records and release history

Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks · Original source · PNAS 119(35):e2122636119, published 2022-08-26; PMC9436379 full-text XML
Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Original source · PNAS 119(35):e2122636119 version-of-record PDF (10 pages)
BERTax SI Appendix (pnas.2122636119.sapp.pdf) · Original source · SI Appendix as distributed with PMC9436379 (member pnas.2122636119.sapp.pdf of the Europe PMC supplementaryFiles ZIP)

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-dna-pathogen-20261012-bertax-closely

field: links:assessed_by:dna-pathogen-20261012-bertax-protocol-closely
value: dna-pathogen-20261012-bertax-protocol-closely
relevance: proxy
endpoint: Macro AveP, accuracy and proportion classified at superkingdom and phylum rank on 1,500-nt genome fragments
rationale: Machine-learning classifiers (BERTax, DeepMicrobes) and the baseline k-mer and alignment tools Kraken2 and minimap2 are scored on the same fragments with the same reference data. Tests whether a trained classifier matches reference-based tools when relatives are in the reference. It is proxy evidence: the inputs are simulated genome fragments, not specimen reads, and ranks stop at genus.
constraints: Inspect every linked evaluation's source locator and preserved limitations before citing a result.; Do not combine these results with another protocol's results; inputs, references and taxonomic ranks differ between sources.
limitations: Simulated 1,500-nt genome fragments from RefSeq genomes; no sequencing errors, host DNA or clinical specimens.; Superkingdom, phylum and genus only; pathogen identification usually needs species or strain.; Database tools were given only the training partition as reference, not whole genomes, which the authors call a necessary deviation from their designed use.; MEGAN-LR, the third named baseline, is not compared.; Macro AveP counts samples a tool leaves unclassified as random guesses. BERTax and DeepMicrobes classify every sample and the database tools fewer, so AveP partly reflects how many samples each tool classifies. Kraken2 and minimap2 classified 76.11% and 75.59% of this set at superkingdom (SI Table S2).; SI Table S2 accuracy is over the samples each tool classified; read it together with the proportion classified.; All tools were run by the BERTax authors, who developed BERTax (author_reported); no uncertainty is printed.
citation locators: source id: dna-pathogen-20261012-bertax-source-pdf; locator: Table 1; source id: dna-pathogen-20261012-bertax-source-si; locator: Table S2; source id: dna-pathogen-20261012-bertax-source; locator: Materials and Methods 'Three Evaluation Datasets', 'Comparison to Other Tools'
source locator: dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Tables S2 and S5; dna-pathogen-20261012-bertax-source: Materials and Methods
revision: 1
reason: Drafted by the extracting agent in the 2026-10-12 ML-versus-baseline pass (issue #121); reviewed by a separate Claude review agent on 2026-10-12, which added the AveP and accuracy caveats (docs/reviews/use-cases/dna-pathogen-ml-baseline-2026-10-12.md).
comparison group: bertax2022-fragments
comparison title: BERTax genome-fragment classification against database tools (Mock et al. 2022)
headline metric: macro-average-precision
stratum label: Closely related (test genera present in the reference)
stratum order: 1
review: method: source-hash-verification; independent-cell-check; scope-review; reviewer: claude; reviewer note: Separate Claude review agent (rev-mlvb), independent of the extracting agent; no human review claimed; date: 2026-10-12; artifact sha256: c0bb2f1bba8680b300076292389b39346ae58bea4bdf28647dd9462333b3bcd7; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9436379/fullTextXML; method note: Judgement drafted by the extracting agent from the pinned article and SI.; note: Endpoint, proxy relevance and limitations checked against the use case's question, inputs and baseline (Kraken2 and minimap2 with MEGAN-LR). Every result on the listed evaluations was checked against the SI and the PMC copy of the PDF.
reviewed evaluations: dna-pathogen-20261012-bertax-eval-bertax-closely; dna-pathogen-20261012-bertax-eval-deepmicrobes-closely; dna-pathogen-20261012-bertax-eval-kraken2-closely; dna-pathogen-20261012-bertax-eval-minimap2-closely; dna-pathogen-20261012-bertax-eval-mmseqs2-bertax-closely; dna-pathogen-20261012-bertax-eval-mmseqs2-closely; dna-pathogen-20261012-bertax-eval-mmseqs2-deepmicrobes-closely; dna-pathogen-20261012-bertax-eval-mmseqs2-taxonomy-closely; dna-pathogen-20261012-bertax-eval-sourmash-closely
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