Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF)
PNAS · 2022 · PNAS 119(35):e2122636119 version-of-record PDF (10 pages) · Peer-reviewed
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Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
Claims
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- printed_value_conflict: dna-pathogen-20261012-bertax-source: Printed value conflict Results 'Performance of Final BERTax Model' prints 95.20% for BERTax phylum AveP on the final dataset; Table 1 and SI Table S7 print 95.10. (Results 'Performance of Final BERTax Model' paragraph 1; Table 1; SI Table S7)
- Relevance of the BERTax closely related dataset protocol (Mock et al. 2022) to "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) (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)
- Relevance of the BERTax distantly related dataset protocol (Mock et al. 2022) to "Select a DNA pathogen-identification workflow for diagnostic testing": Assessed by BERTax Distantly related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022) (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)
- Relevance of the BERTax final model dataset protocol (Mock et al. 2022) to "Select a DNA pathogen-identification workflow for diagnostic testing": Assessed by BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022) (dna-pathogen-20261012-bertax-source-pdf: Table 1; dna-pathogen-20261012-bertax-source-si: Details to PR-curve plots; dna-pathogen-20261012-bertax-source: Materials and Methods)
Models, benchmarks and other records
Protocols (3)
- BERTax Closely related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022)
- BERTax Distantly related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022)
- BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Evaluations (27)
- BERTax on the BERTax closely related dataset
- BERTax on the BERTax distantly related dataset
- BERTax on the BERTax final model dataset
- DeepMicrobes on the BERTax closely related dataset
- DeepMicrobes on the BERTax distantly related dataset
- DeepMicrobes on the BERTax final model dataset
- Kraken2 on the BERTax closely related dataset
- Kraken2 on the BERTax distantly related dataset
- Kraken2 on the BERTax final model dataset
- minimap2 on the BERTax closely related dataset
- minimap2 on the BERTax distantly related dataset
- minimap2 on the BERTax final model dataset
- MMseqs2 + BERTax on the BERTax closely related dataset
- MMseqs2 + BERTax on the BERTax distantly related dataset
- MMseqs2 + BERTax on the BERTax final model dataset
- MMseqs2 + DeepMicrobes on the BERTax closely related dataset
- MMseqs2 + DeepMicrobes on the BERTax distantly related dataset
- MMseqs2 + DeepMicrobes on the BERTax final model dataset
- MMseqs2 on the BERTax closely related dataset
- MMseqs2 on the BERTax distantly related dataset
- MMseqs2 on the BERTax final model dataset
- MMseqs2 taxonomy* on the BERTax closely related dataset
- MMseqs2 taxonomy* on the BERTax distantly related dataset
- MMseqs2 taxonomy* on the BERTax final model dataset
- sourmash on the BERTax closely related dataset
Evidence
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Evidence table
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32 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 7977424613ab5e5f4986745b527a270fd2c0427dbab40471813903eda85dcaec Source metadata | Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) No field-specific location recorded Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://www.pnas.org/doi/pdf/10.1073/pnas.2122636119 Source metadata | Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) No field-specific location recorded Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.1073/pnas.2122636119 Source metadata | Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) No field-specific location recorded Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Licence CC-BY-NC-ND-4.0 Source metadata | Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) No field-specific location recorded Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations1 values
| Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) No field-specific location recorded Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Media type application/pdf Source metadata | Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) No field-specific location recorded Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status peer_reviewed Source metadata | Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) No field-specific location recorded Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieval method Fetched in a Chrome session (Claude in Chrome) from the article page, because PNAS returns HTTP 403 to command-line clients; SHA-256 computed in the page with crypto.subtle; text layer read with pdf.js 4.0.379. Source metadata | Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) No field-specific location recorded Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieval note The bytes were not saved to disk. A reviewer must re-fetch the PDF through a browser and compare its SHA-256. Source metadata | Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) No field-specific location recorded Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-10-12T20:56:37Z Source metadata | Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) No field-specific location recorded Version: PNAS 119(35):e2122636119 version-of-record PDF (10 pages) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Version-of-record PDF, used for Table 1, whose PMC copy is an image.
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261012-bertax-source-pdf
- areas
- microbes-communities
- contexts
- research
- url
- https://doi.org/10.1073/pnas.2122636119
- artifact url
- https://www.pnas.org/doi/pdf/10.1073/pnas.2122636119
- version
- PNAS 119(35):e2122636119 version-of-record PDF (10 pages)
- retrieved at
- 2026-10-12T20:56:37Z
- artifact sha256
- 7977424613ab5e5f4986745b527a270fd2c0427dbab40471813903eda85dcaec
- doi
- 10.1073/pnas.2122636119
- publication status
- peer_reviewed
- licence
- CC-BY-NC-ND-4.0
- media type
- application/pdf
- venue
- PNAS
- year
- 2022
- retrieval method
- Fetched in a Chrome session (Claude in Chrome) from the article page, because PNAS returns HTTP 403 to command-line clients; SHA-256 computed in the page with crypto.subtle; text layer read with pdf.js 4.0.379.
- retrieval note
- The bytes were not saved to disk. A reviewer must re-fetch the PDF through a browser and compare its SHA-256.
- source locator
- Page 4, Table 1 'Comparison of the macro AveP on all three datasets'
- review artifact
- PMC open-access copy of the version-of-record PDF, https://pmc-oa-opendata.s3.amazonaws.com/PMC9436379.1/PMC9436379.1.pdf, SHA-256 725c99ba8bb95d9e5e73997cbbe45d3a889185163749f494673a084de534c835, retrieved 2026-10-12; Table 1 text identical to the pinned PDF's text layer as archived by the extractor
- review artifact matches original artifact sha256
- false
- limitations
- The reviewer could not re-fetch the pinned PNAS bytes (HTTP 403 to command-line clients) and did not use a browser, so the pinned SHA-256 is the extractor's in-browser hash, not independently re-verified. Table 1 values were checked against the PMC copy instead.
- review
- method: pdf-text-parse; independent-cell-check; 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: 725c99ba8bb95d9e5e73997cbbe45d3a889185163749f494673a084de534c835; retrieval url: https://pmc-oa-opendata.s3.amazonaws.com/PMC9436379.1/PMC9436379.1.pdf; note: Pinned hash not re-verified (PNAS HTTP 403). Values checked against the PMC copy named in review_artifact.