rewirebio.iobenchmarks
Dataset

30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)

Pseudo-mock communities built from the isolate reads of species out of the database, 20 to 34 species each, up to 100,000 reads log-distributed across species.

Evaluation results

5 evaluations · 5 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: Kraken2 (main database, Peres da Silva et al. 2024)Protocol: Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
Dataset: 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
64.9% Proportion (share of reads assigned at genus level (correct or not); mean across 30 pseudo-mock communities of out-of-database species)
percent · unknown

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

Kraken2 on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)

dna-pathogen-20261012-metagenn-protocol-mocks

Aggregation: Not reported

MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Read classification results' paragraph 1 (values shown in Fig. 4a)
Configuration: MEGAN-LR (main database, Peres da Silva et al. 2024)Protocol: Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
Dataset: 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
53.1% Proportion (share of reads assigned at genus level (correct or not); mean across 30 pseudo-mock communities of out-of-database species)
percent · unknown

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

MEGAN-LR on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)

dna-pathogen-20261012-metagenn-protocol-mocks

Aggregation: Not reported

MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Read classification results' paragraph 1 (values shown in Fig. 4a)
Configuration: MetageNN (main database, Peres da Silva et al. 2024)Protocol: Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
Dataset: 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
93.3% Proportion (share of reads assigned at genus level (correct or not); mean across 30 pseudo-mock communities of out-of-database species)
percent · unknown

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

MetageNN on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)

dna-pathogen-20261012-metagenn-protocol-mocks

Aggregation: Not reported

MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Read classification results' paragraph 1 (values shown in Fig. 4a)
Configuration: MetaMaps (main database, Peres da Silva et al. 2024)Protocol: Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
Dataset: 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
37.3% Proportion (share of reads assigned at genus level (correct or not); mean across 30 pseudo-mock communities of out-of-database species)
percent · unknown

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

MetaMaps on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)

dna-pathogen-20261012-metagenn-protocol-mocks

Aggregation: Not reported

MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Read classification results' paragraph 1 (values shown in Fig. 4a)
Configuration: MMseqs2 (main database, Peres da Silva et al. 2024)Protocol: Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
Dataset: 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
85.5% Proportion (share of reads assigned at genus level (correct or not); mean across 30 pseudo-mock communities of out-of-database species)
percent · unknown

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

MMseqs2 on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)

dna-pathogen-20261012-metagenn-protocol-mocks

Aggregation: Not reported

MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Read classification results' paragraph 1 (values shown in Fig. 4a)

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

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.

7 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statementOriginal source and locationReview and provenance
Access
Not released; built from the listed SRA runs
Context-only references
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes

Original source ↗

Results 'MetageNN is more sensitive ... at the community-level for ONT pseudo-mock communities' Experimental setup

Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Retrieved: 2026-10-12T20:50:20Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.access

Source artifact SHA-256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Population
30 pseudo-mock communities
Context-only references
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes

Original source ↗

Results 'MetageNN is more sensitive ... at the community-level for ONT pseudo-mock communities' Experimental setup

Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Retrieved: 2026-10-12T20:50:20Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.population

Source artifact SHA-256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Source location
Results 'MetageNN is more sensitive ... at the community-level for ONT pseudo-mock communities' Experimental setup
Context-only references
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes

Original source ↗

Results 'MetageNN is more sensitive ... at the community-level for ONT pseudo-mock communities' Experimental setup

Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Retrieved: 2026-10-12T20:50:20Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.source_locator

Source artifact SHA-256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Split
Test only
Context-only references
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes

Original source ↗

Results 'MetageNN is more sensitive ... at the community-level for ONT pseudo-mock communities' Experimental setup

Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Retrieved: 2026-10-12T20:50:20Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.split

Source artifact SHA-256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Version
'Mock - Species out of DB' as described in Peres da Silva et al. 2024
Context-only references
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes

Original source ↗

Results 'MetageNN is more sensitive ... at the community-level for ONT pseudo-mock communities' Experimental setup

Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Retrieved: 2026-10-12T20:50:20Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.version

Source artifact SHA-256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Description
Pseudo-mock communities built from the isolate reads of species out of the database, 20 to 34 species each, up to 100,000 reads log-distributed across species.
Context-only references
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes

Original source ↗

Results 'MetageNN is more sensitive ... at the community-level for ONT pseudo-mock communities' Experimental setup

Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Retrieved: 2026-10-12T20:50:20Z

not individually reviewed

No individual claim review recorded

Audit details

Field: description

Source artifact SHA-256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Name
30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
Context-only references
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes

Original source ↗

Results 'MetageNN is more sensitive ... at the community-level for ONT pseudo-mock communities' Experimental setup

Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Retrieved: 2026-10-12T20:50:20Z

not individually reviewed

No individual claim review recorded

Audit details

Field: name

Source artifact SHA-256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Sources and history

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

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261012-metagenn-data-mocks

areas
microbes-communities
contexts
research
version
'Mock - Species out of DB' as described in Peres da Silva et al. 2024
population
30 pseudo-mock communities
split
Test only
access
Not released; built from the listed SRA runs
source locator
Results 'MetageNN is more sensitive ... at the community-level for ONT pseudo-mock communities' Experimental setup
review
method: source-hash-verification; 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; note: Checked against the re-downloaded article XML (SHA-256 matches).
Related records

Suggest a correction