This task area covers microbial sequence-read classification. Identifying a phage and identifying a pathogen are distinct endpoints.
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.Sourcesnbrg-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 applicableSourcesnbrg-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 applicableSourcesnbrg-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 applicableSourcesnbrg-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 applicableSourcesnbrg-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.Sourcesnbrg-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 applicableSourcesnbrg-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.Sourcesnbrg-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.Sourcesnbrg-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. |
Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.
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.
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.
Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.
No evaluations linked in this release.
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 |
broad task primary protocol linked
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-readsApplicability is distinct from a completed evaluation.
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 | 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. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | 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: SHA-256 of retrieved original artifact bytes Format: original_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 ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | 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: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title Conceptual evaluation workflow Individual claims | 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. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | 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: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | 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. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | 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: SHA-256 of retrieved original artifact bytes Format: original_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 ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | 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: SHA-256 of retrieved original artifact bytes Format: original_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 ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | 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: SHA-256 of retrieved original artifact bytes Format: original_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 ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | 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: SHA-256 of retrieved original artifact bytes Format: original_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 ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | 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: SHA-256 of retrieved original artifact bytes Format: original_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 ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | 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: SHA-256 of retrieved original artifact bytes Format: original_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 ProkBERT README: phage identification and downstream tasks. The combined task label is catalogue scope, not a claim that phage identity establishes pathogenicity. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | 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: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Release 2026-09-17-d277315f7d76 · Record review: discovered
Stable ID: catalog-task-phage-pathogen-reads