Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Task
Metagenomic taxonomic classification
Metagenomic classification compares reference-based tools and examines dependence on reference-genome quality.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results tableAt a glance
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | CAMI2 Toy Human Microbiome Project samples are among the benchmark collections.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table |
| Splits | This is evaluation of reference-database classifiers on CAMI2 samples and Zymo mock communities, rather than a supervised train/validation/test split. Reference-database versions are specified separately; the regenerated CAMI sample19 is a distinct condition. · Not applicableSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: CAMI2 reference databases, Recreating CAMI sample19, Zymo community standards, Running classifiers |
| Metrics | Precision, recall, F1, Jaccard distance and Bray–Curtis distance distinguish detection from abundance agreement.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table |
| Baselines | MetaPhlAn3, Kraken and GOTTCHA, using defaults where applicable.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table |
| Leakage controls | The source discusses reference assembly age and database coverage as factors affecting apparent accuracy.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table |
| Entity type | Paper-specific computational evaluation protocol.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table |
| Organisms | CAMI2 human-microbiome community taxa.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table |
| Assays | Metagenomic sequence mixtures with reference taxonomy.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table |
| Allowed inputs | Sequencing reads and model-specific reference databases.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table |
| Adaptation | Taxonomic classification with default comparator settings where applicable.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table |
How it works
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results tableEvaluation methodology
CAMI2 Toy Human Microbiome Project samples are among the benchmark collections. Precision, recall, F1, Jaccard distance and Bray–Curtis distance distinguish detection from abundance agreement. MetaPhlAn3, Kraken and GOTTCHA, using defaults where applicable. The source discusses reference assembly age and database coverage as factors affecting apparent accuracy. The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results tableRecorded evaluations
Each evaluation records what was tested and under which conditions.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| NABAS+: Metagenomic taxonomic classification Configuration: NABAS+Task: Metagenomic taxonomic classificationDataset: CAMI II Toy human gastrooral sample19-new Newly generated sample19 used for classifier comparison. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.719 F1 score Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Table 3, Sample19-new / NABAS+ row, F1 score column Source checking is not independent reproduction. |
| MetaPhlAn3: Metagenomic taxonomic classification Configuration: MetaPhlAn3Task: Metagenomic taxonomic classificationDataset: CAMI II Toy human gastrooral sample19-new Newly generated sample19 used for classifier comparison. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.753 F1 score Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Table 3, Sample19-new / MetaPhlAn3 row, F1 score column Source checking is not independent reproduction. |
Papers and result coverage
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Advancing metagenomic classification with NABAS+: a novel alignment-based approach | PMC12231603.1 | Read source DOI: 10.1093/nargab/lqaf092 |
What is still missing
- Complete raw tables acquired.19 new versusold reference experiments separate; Bray-Curtis lower-is-better unlike F1. Reference database state required before chart groups. Structured extraction pending.
Search and extraction details
source found structured extraction pending
Searches
- Advancing metagenomic classification with NABAS+: a novel alignment-based approach primary paper benchmark results
Evidence locations
- Tables3–4; new/old reference database and community datasets
Strengths and limitations
Limitations and conditions
- The regenerated synthetic sample using newer assemblies is a separate evaluation condition. Exact sample identity must remain attached to each reported result.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table
Profile review details
Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.
Stable record: reported-task-92137759a9e7b0Evidence 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.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: Sequencing reads and model-specific reference databases.","Evaluation: Taxonomic classification with default comparator settings where applicable.","Readout: Precision, recall, F1, Jaccard distance and Bray–Curtis distance distinguish detection from abundance agreement."] Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets CAMI2 Toy Human Microbiome Project samples are among the benchmark collections. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits This is evaluation of reference-database classifiers on CAMI2 samples and Zymo mock communities, rather than a supervised train/validation/test split. Reference-database versions are specified separately; the regenerated CAMI sample19 is a distinct condition. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Methods: CAMI2 reference databases, Recreating CAMI sample19, Zymo community standards, Running classifiers Version: PMC12231603.1 | inapplicable automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Taxonomic classification with default comparator settings where applicable. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Precision, recall, F1, Jaccard distance and Bray–Curtis distance distinguish detection from abundance agreement. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines MetaPhlAn3, Kraken and GOTTCHA, using defaults where applicable. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The source discusses reference assembly age and database coverage as factors affecting apparent accuracy. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table Version: PMC12231603.1 | unreported automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
2 source records and release history
- Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Original source · PMC12231603.1
- Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Original source · PMC12231603.1
Technical metadata and extraction receipts
Stable ID: reported-task-92137759a9e7b0
- areas
- microbes-communities
- tasks
- Metagenomic taxonomic classification
- entity level
- task
- version
- Not reported
- task
- Metagenomic taxonomic classification
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: source_found_structured_extraction_pending; primary sources: evidence-expansion-p2-nabas-plus-2025-49903e751beb; inspected locators: Tables3–4; new/old reference database and community datasets; searched queries: Advancing metagenomic classification with NABAS+: a novel alignment-based approach primary paper benchmark results; gaps: Complete raw tables acquired.19 new versusold reference experiments separate; Bray-Curtis lower-is-better unlike F1. Reference database state required before chart groups. Structured extraction pending.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- historical missing metadata
- protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: nabas-plus-2025; source locator: Methods: reference classifiers; Discussion: CAMI evaluation; cached text lines 13–15, 108–109; task metric definitions and corresponding results table; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.