Task

Phage / pathogen reads

This task area covers microbial sequence-read classification. Identifying a phage and identifying a pathogen are distinct endpoints.

Sources

nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.

No reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.

0 evaluations · 0 results

Overview

Datasets

No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.

inapplicable

Metrics

Label-specific classification metrics and explicit false-positive/negative counts. State the unit scored and the treatment of unclassified reads.

Allowed inputs

Sequence reads or fragments with task-specific reference labels; reference database identity and version are part of the protocol.

Sources

nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.

Evaluation procedure diagram

How it worksConceptual evaluation workflow

Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.

Sources

nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.

Source 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

Choose a concrete label definition before evaluating read classifications. A phage-versus-non-phage benchmark does not establish clinical pathogenicity or organism abundance. Record reference-library coverage and the taxonomic or sequence separation between training and assessment. This guide describes evaluation scope and introduces no sequence-design procedure.

Sources

nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.

Task 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

nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.

Run 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

A defined label and held-out reference relationship make sequence-classification claims testable.
Sources
nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.

Limitations and conditions

Do not use a phage-detection score as evidence of pathogenicity, diagnostic accuracy or community abundance.
Sources
nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.

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-phage-pathogen-reads

Specifications

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.

Data, procedure and scoring
Property	Description and evidence
Entity type	Task guide; concrete protocol identities remain separate. Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.
Datasets	No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicable Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.
Organisms	No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicable Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.
Assays	No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicable Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.
Splits	No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicable Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.
Allowed inputs	Sequence reads or fragments with task-specific reference labels; reference database identity and version are part of the protocol. Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.
Adaptation	No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicable Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.
Metrics	Label-specific classification metrics and explicit false-positive/negative counts. State the unit scored and the treatment of unclassified reads. Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.
Baselines	Compare against the conventional classifier specified by the selected protocol using the same reference information; candidate tools alone are not evidence. Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.

Applicable tests and references

Applicability is distinct from a completed evaluation.

Kraken2 · proposed

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-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.

Paper or primary resource	Version	Reference
ProkBERT family: genomic language models for microbiome applications	PMC full-text XML snapshot PMC10810988 at retrieval; byte-pinned by SHA-256	Read source DOI: 10.3389/fmicb.2023.1331233

Historical gaps recorded on 2026-09-17

The broad guide has no single common test population. No sequence-design instructions or pathogen enhancement content is needed for detection benchmarking.
Full paired numerical figure data remain unextracted; no estimated graph heights.

Search and extraction details

broad task primary protocol linked

Searches

Open Problems single cell label projection benchmark v1.0.0 paper
CAPRI assessment rounds 46 54 protein docking results
GEARS predicting transcriptional outcomes multigene perturbations 2023
scVI scANVI reference mapping benchmark primary paper
Boltz-2 affinity benchmark paper
ESMFold monomer structure benchmark Science 2023
"ProkBERT" "paper" "2024"
"scPertEval"
ProkBERT family prokaryotic language models microbe paper
Probabilistic harmonization annotation single-cell transcriptomics scANVI Nature Methods 2021
Evolutionary-scale prediction atomic-level protein structure language model ESMFold Science Lin 2023
Towards Principled Evaluation Single-Cell Perturbation Prediction Models Schäfer 2026

Evidence locations

Sections 2.4 and 3.4
Phage classification comparison figure

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

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
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	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps Define the classification endpoint Document reference and holdout scope Classify held-out reads Report label-specific errors Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title Conceptual evaluation workflow Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Entity type Task guide; concrete protocol identities remain separate. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	inapplicable automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Organisms No shared organism population is defined at this guide level. Record it for each selected dataset. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	inapplicable automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Assays No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	inapplicable automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Splits No executable split is attached to this task identity. Use the selected protocol’s split manifest. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	inapplicable automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Allowed inputs Sequence reads or fragments with task-specific reference labels; reference database identity and version are part of the protocol. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Adaptation No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	inapplicable automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.6.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

Release 2026-09-29-06401fd5b220 · Record review: discovered

5 source records and release history

ProkBERT official resource · Original source · Not reported
METAGENE-1 official resource · Original source · Not reported
Kraken2 official resource · Original source · Not reported
ProkBERT family: genomic language models for microbiome applications · Original source · PMC full-text XML snapshot PMC10810988 at retrieval; byte-pinned by SHA-256
nbrg-ppcu/prokbert: README.md · Original source · 8670ae92b816cff158a0b85647a8dea122e251eb

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Technical metadata and extraction receipts

Stable ID: catalog-task-phage-pathogen-reads

areas: microbes-communities
entity level: task
version: Not reported
task: Phage / pathogen reads
scope note: Classify held-out phage or pathogen sequences and record taxonomic distance.
benchmark research: review date: 2026-09-17; status: broad_task_primary_protocol_linked; primary sources: expansion-p3-prokbert; inspected locators: Sections 2.4 and 3.4; Phage classification comparison figure; searched queries: Open Problems single cell label projection benchmark v1.0.0 paper; CAPRI assessment rounds 46 54 protein docking results; GEARS predicting transcriptional outcomes multigene perturbations 2023; scVI scANVI reference mapping benchmark primary paper; Boltz-2 affinity benchmark paper; ESMFold monomer structure benchmark Science 2023; "ProkBERT" "paper" "2024"; "scPertEval"; ProkBERT family prokaryotic language models microbe paper; Probabilistic harmonization annotation single-cell transcriptomics scANVI Nature Methods 2021; Evolutionary-scale prediction atomic-level protein structure language model ESMFold Science Lin 2023; Towards Principled Evaluation Single-Cell Perturbation Prediction Models Schäfer 2026; gaps: The broad guide has no single common test population. No sequence-design instructions or pathogen enhancement content is needed for detection benchmarking.; Full paired numerical figure data remain unextracted; no estimated graph heights.; claim scope: Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
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: evidence-official-2efbfaba5a1c09f4f7fa; source locator: ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity.; ambiguities: None recorded

Related records

applicable to: Kraken2

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