Relevance of genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024) to "Select a DNA pathogen-identification workflow for diagnostic testing"
- Use case
- Select a DNA pathogen-identification workflow for diagnostic testing
- Assessed by
- Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
- Relevance
- Proxy evidence
- Endpoint
- Genus-level sensitivity and F1 of read assignment, averaged across all 81 ONT bacterial isolates
Kraken2 and MMseqs2 are scored on real ONT reads from 81 bacterial isolates at genus level, with the same 516-genome reference. MetageNN is excluded because its printed values cover only one subset that no printed baseline value covers. It is proxy evidence: isolate reads, a 516-genome reference and genus-level calls, not patient specimens.
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.
21 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations1 values
| MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group metagenn2024-ont Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title MetageNN against alignment and k-mer classifiers on ONT reads (Peres da Silva et al. 2024) Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints2 values
| MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Genus-level sensitivity and F1 of read assignment, averaged across all 81 ONT bacterial isolates Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Excluded evaluations1 values
| MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field links:assessed_by:dna-pathogen-20261012-metagenn-protocol-isolates Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Headline metric recall Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations5 values
| MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records9 values
| MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed 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
1 source record and release history
- MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Original source · BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Technical metadata and extraction receipts
Stable ID: use-case-mapping-dna-pathogen-20261012-metagenn-isolates
- field
- links:assessed_by:dna-pathogen-20261012-metagenn-protocol-isolates
- value
- dna-pathogen-20261012-metagenn-protocol-isolates
- relevance
- proxy
- endpoint
- Genus-level sensitivity and F1 of read assignment, averaged across all 81 ONT bacterial isolates
- rationale
- Kraken2 and MMseqs2 are scored on real ONT reads from 81 bacterial isolates at genus level, with the same 516-genome reference. MetageNN is excluded because its printed values cover only one subset that no printed baseline value covers. It is proxy evidence: isolate reads, a 516-genome reference and genus-level calls, not patient specimens.
- 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; references and taxonomic ranks differ between sources.
- limitations
- Most per-tool accuracy values are only in Figures 3 and 4 and were not extracted.; Bacterial isolates only; no host DNA, viruses, fungi or clinical specimens.; A 516-genome reference and genus-level classification.; minimap2 is used only to produce MEGAN-LR's alignments, not scored on its own.; All tools were run by the MetageNN authors, who developed MetageNN (author_reported); no uncertainty is printed.
- citation locators
- source id: dna-pathogen-20261012-metagenn-source; locator: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings'
- source locator
- dna-pathogen-20261012-metagenn-source: Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings'
- 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 with corrections (docs/reviews/use-cases/dna-pathogen-ml-baseline-2026-10-12.md).
- comparison group
- metagenn2024-ont
- comparison title
- MetageNN against alignment and k-mer classifiers on ONT reads (Peres da Silva et al. 2024)
- headline metric
- recall
- stratum label
- ONT bacterial isolates
- 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: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11022314/fullTextXML; method note: Judgement drafted by the extracting agent from the pinned article.; note: Endpoint, proxy relevance and limitations checked against the use case's question, inputs and baseline. Every result on the listed evaluations was checked against the article XML.
- excluded evaluations
- id: dna-pathogen-20261012-metagenn-eval-metagenn-isolates; reason: MetageNN's printed values cover only out-of-database isolates in genera with more than three species, a subset with no printed baseline value; its full comparison is in Figure 3 only. Excluded at independent review 2026-10-12.
- reviewed evaluations
- dna-pathogen-20261012-metagenn-eval-kraken2-isolates; dna-pathogen-20261012-metagenn-eval-mmseqs2-isolates
- pins
- record id: dna-pathogen-20261012-metagenn-eval-kraken2-isolates; fields: status; links; attributes.origin; attributes.comparison; sha256: ce583906a91ae48a79f1ccd2ea0c3e124b8a81f185e68c5bb50f90c8d6077cb1; record id: dna-pathogen-20261012-metagenn-eval-mmseqs2-isolates; fields: status; links; attributes.origin; attributes.comparison; sha256: 85bdff0f1c7f326268a50716055c663e0285789c4636d8d35360f5e79da03cba; record id: dna-pathogen-20261012-metagenn-protocol-isolates; fields: status; name; description; facets; source_ids; links; attributes; sha256: 28481ee21f592aa2e82fa8dafcf76896085fe2c1e3865bb32dce1da29799352f; record id: dna-pathogen-20261012-metagenn-result-kraken2-isolates-all-f1; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: ffe8063bb713e1e006fa33aee9d810327a758b55210c05f12a4332228efc0cdc; record id: dna-pathogen-20261012-metagenn-result-kraken2-isolates-all-recall; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 99b853d78819134bf652a4bbb10b719c7b3990487f4fc8ea0d63fc9791fa888f; record id: dna-pathogen-20261012-metagenn-result-mmseqs2-isolates-all-f1; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 00e481267b4e05a3013c6102a15570ccb297520257ef480230b3b2fc76aaf8ff; record id: dna-pathogen-20261012-metagenn-result-mmseqs2-isolates-all-recall; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 44caca2c0db3d67d99604f55d09801038b60e0b545f206f364ea16e0da6fd5ed; record id: dna-pathogen-20261012-metagenn-source; fields: status; attributes.artifact_sha256; sha256: e8ab45945d6be94b2b510f47fec3f8847c209fbee7309ad4cfdd841f4ff6a331; record id: use-case-diagnostic-dna-pathogen-identification; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: fc133441f475bb23dafd0c0c55f4e16cd20302f9148b21b98de31077dfe16338