Datasets
No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.
inapplicable
Task
Community profiling
Community profiling estimates which microorganisms are present in a sample and their relative abundances.
Sources
CAMI-challenge/OPAL official source · README: Overview, Computed metrics and InputsNo reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.
Overview
Metrics
OPAL reports precision, recall, F1, abundance errors such as L1 and Bray–Curtis, and diversity measures. These are distinct endpoints.
Allowed inputs
Predicted and reference taxonomic profiles with consistent taxon identifiers and abundance definitions.
Sources
CAMI-challenge/OPAL official source · README: Overview, Computed metrics and InputsEvaluation procedure diagram
How it worksConceptual evaluation workflow
Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.
Sources
CAMI-challenge/OPAL official source · README: Overview, Computed metrics and InputsSource reviewed · Automated source review, 2026-09-16. All specifications and missing details
Results
All evaluations
0 evaluations · 0 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
No evaluations linked in this release.
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Choosing an evaluation
Compare a predicted taxonomic profile with a specified reference profile at declared taxonomic ranks. OPAL separates detection errors from abundance errors and diversity summaries. The reference taxonomy, filtering and abundance normalisation must accompany a result; changing these can change what is scored.
Sources
CAMI-challenge/OPAL official source · README: Overview, Computed metrics and InputsTask scope
This is a task guide, not a single versioned benchmark protocol. The connected resources provide examples or concrete procedures. A candidate method or proposed control is not evidence that an evaluation has been completed.
Sources
CAMI-challenge/OPAL official source · README: Overview, Computed metrics and InputsRun instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Strengths and limitations
Strengths supported by sources
- Separate presence and abundance metrics reveal different failure modes instead of hiding them behind a single accuracy number.
Sources
CAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs
Limitations and conditions
- A profile-level result is not a read-binning result. Reference coverage and taxonomic rank affect interpretation.
Sources
CAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs
Profile review details
Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol.
Stable record: catalog-task-community-profilingSpecifications
Inputs, training, access and other details
Explanatory profile: source reviewed · 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 |
|---|---|
| Entity type | Task guide; concrete protocol identities remain separate.SourcesCAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs |
| Datasets | No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicableSourcesCAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs |
| Organisms | No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicableSourcesCAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs |
| Assays | No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicableSourcesCAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs |
| Splits | No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicableSourcesCAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs |
| Allowed inputs | Predicted and reference taxonomic profiles with consistent taxon identifiers and abundance definitions.SourcesCAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs |
| Adaptation | No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicableSourcesCAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs |
| Metrics | OPAL reports precision, recall, F1, abundance errors such as L1 and Bray–Curtis, and diversity measures. These are distinct endpoints.SourcesCAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs |
| Baselines | Compare profilers against the same reference profile and taxonomic ranks; OPAL is an evaluator, not a predictive baseline.SourcesCAMI-challenge/OPAL official source · README: Overview, Computed metrics and Inputs |
Evidence
Source checking verifies the cited claim or transcription. It does not establish 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 |
|---|---|---|
| Critical Assessment of Metagenome Interpretation: the second round of challenges | PMC9007738 | Read source DOI: 10.1038/s41592-022-01431-4 |
| Assessing taxonomic metagenome profilers with OPAL | PMC6398228 | Read source DOI: 10.1186/s13059-019-1646-y |
Historical gaps recorded on 2026-09-17
- OPAL is an evaluator rather than a single dataset. Numerical comparisons require selected community dataset, taxonomic rank and profiling output version. No complete main-text score matrix; source data remains pending.
Search and extraction details
broad task requires concrete protocol links
Searches
- Community profiling primary paper benchmark results
Evidence locations
- Table1 rankings; main figures and linked supplementary material
- Methods and benchmark Results; figure captions and source availability
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.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims | CAMI-challenge/OPAL official source README: Overview, Computed metrics and Inputs Version: 98120c326eef08e391899e4bd3a362e0e6558b4a | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| CAMI-challenge/OPAL official source README: Overview, Computed metrics and Inputs Version: 98120c326eef08e391899e4bd3a362e0e6558b4a | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Conceptual evaluation workflow Individual claims | CAMI-challenge/OPAL official source README: Overview, Computed metrics and Inputs Version: 98120c326eef08e391899e4bd3a362e0e6558b4a | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | CAMI-challenge/OPAL official source README: Overview, Computed metrics and Inputs Version: 98120c326eef08e391899e4bd3a362e0e6558b4a | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims | CAMI-challenge/OPAL official source README: Overview, Computed metrics and Inputs Version: 98120c326eef08e391899e4bd3a362e0e6558b4a | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Organisms No shared organism population is defined at this guide level. Record it for each selected dataset. Individual claims | CAMI-challenge/OPAL official source README: Overview, Computed metrics and Inputs Version: 98120c326eef08e391899e4bd3a362e0e6558b4a | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Assays No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. Individual claims | CAMI-challenge/OPAL official source README: Overview, Computed metrics and Inputs Version: 98120c326eef08e391899e4bd3a362e0e6558b4a | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits No executable split is attached to this task identity. Use the selected protocol’s split manifest. Individual claims | CAMI-challenge/OPAL official source README: Overview, Computed metrics and Inputs Version: 98120c326eef08e391899e4bd3a362e0e6558b4a | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Allowed inputs Predicted and reference taxonomic profiles with consistent taxon identifiers and abundance definitions. Individual claims | CAMI-challenge/OPAL official source README: Overview, Computed metrics and Inputs Version: 98120c326eef08e391899e4bd3a362e0e6558b4a | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. Individual claims | CAMI-challenge/OPAL official source README: Overview, Computed metrics and Inputs Version: 98120c326eef08e391899e4bd3a362e0e6558b4a | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: discovered
4 source records and release history
- MetaPhlAn official resource · Original source · Not reported
- Critical Assessment of Metagenome Interpretation: the second round of challenges · Original source · PMC9007738
- Assessing taxonomic metagenome profilers with OPAL · Original source · PMC6398228
- CAMI-challenge/OPAL official source · Original source · 98120c326eef08e391899e4bd3a362e0e6558b4a
Technical metadata and extraction receipts
Stable ID: catalog-task-community-profiling
- areas
- microbes-communities
- entity level
- task
- version
- Not reported
- task
- Community profiling
- scope note
- Estimate taxon abundances in metagenomic samples.
- benchmark research
- review date: 2026-09-17; status: broad_task_requires_concrete_protocol_links; primary sources: evidence-expansion-p2-evidence-discovery-final-cami2-da932c1cde8b; evidence-expansion-p2-evidence-discovery-final-opal-a4503ef32e99; inspected locators: Table1 rankings; main figures and linked supplementary material; Methods and benchmark Results; figure captions and source availability; searched queries: Community profiling primary paper benchmark results; gaps: OPAL is an evaluator rather than a single dataset. Numerical comparisons require selected community dataset, taxonomic rank and profiling output version. No complete main-text score matrix; source data remains 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_yet_extracted
- 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 record identifies the biological prediction question or a suite-specific task, rather than a uniquely fixed evaluated procedure. Preserve its task identity and leave split, model adaptation and scoring details on linked protocols/evaluations.; source ids: src-discovery-cami-challenge-opal; source locator: README: Overview, Computed metrics and Inputs; ambiguities: None recorded