ai-gene-review

Curate, review, or repair ai-gene-review ModuleReview YAML documents under modules/, including pathway/module boundary setting, parts and variant modeling, annoton-level molecular functions, representative UniProt/PTN grounding, module deep-research provenance, validation, rendering, and project batch updates.

Work with BioReason-Pro predictions and reasoning traces for protein function. Use when: comparing BioReason outputs against curated reviews, converting web exports to YAML, reviewing reasoning trace quality, or running the SFT/RL comparison. Triggers: "bioreason", "GO-GPT predictions", "reasoning trace review", "bioreason comparison", "SFT vs RL".

Review computational protein or gene function predictions and fill PredictionReview YAML files using the COR/CNN/LSP/UNC/PLI/NPI/REP biological-validity taxonomy. Use for DeepECTF, BioReason/GO-GPT, InterPro2GO, PANTHER/IBA, CLEAN, GloEC, MAPred, ProteinInfer, or other predicted EC/GO annotations.

Use when running or wiring OpenScientist for AI Gene Review gene-function hypotheses, especially blinded comparisons against local bioinformatics analyses.

Evaluate and review GO-CAM (Gene Ontology Causal Activity Model) activities / annotons — molecular-function typing, has-input, causal relations, complexes, evidence — and check their consistency with gene annotation reviews. Use when reviewing cached GO-CAMs under gocams/, filling a GoCamReview YAML (gocams/<id>/<id>-review.yaml), or grounding a module in GO-CAM models.

Use this agent when you need to synthesize and distill the core functions of a gene from multiple information sources (textual summaries, reviewed annotations, bioinformatics analysis) and populate the `core_functions` section of a gene review YAML file. This agent should be called after completing the gene research, annotation review, and bioinformatics analysis phases of a gene review project.

Use this agent when you need to systematically review existing GO annotations for a gene and make curation decisions based on literature evidence and functional analysis. This agent should be called after seeding the SPECIES/GENE/GENE-ai-review.yaml file, which seeds each annotation with `action: PENDING`; these should all be manually reviewed.

Use ONLY when the user explicitly asks to orchestrate parallel external agents (Codex or Claude Code) in tmux sessions via tp (tmux-pilot). Or when a user tells you that you're the boss or orchestrator. You can also use this if you are an operclaw agent. NEVER auto-invoke for a generic "do this in parallel" request. For in-process subagents, use superpowers:dispatching-parallel-agents instead.

Manage and drive forward an ongoing project, tracked in projects/ dir

Use this agent when you need to extract and summarize key findings from scientific references that are relevant to a gene's function. This agent should be used after references have been identified in a gene review to provide detailed supporting evidence from the literature. The agent will look up cached publications and extract only the most relevant findings related to the gene's direct function, excluding irrelevant experimental details unless they directly inform gene function.

Review, either de-novo, or augment the review of an existing one. A list of deep research providers may be specified.

Review AI Gene Review pull requests and curation changes for GO term quality, evidence support, core function identification, and annotation action justification. Use for PR review comments, review follow-up automation, and QA of gene review YAML.

Use this agent when you need to perform custom bioinformatics analyses on genes or proteins that go beyond standard database lookups. This includes situations where existing domain/family annotations from UniProt are insufficient, when you need to verify dubious annotations, or when you need to perform comparative analyses across gene sets. The agent creates reproducible analysis pipelines with proper dependency management and documentation.

Use this agent when you need to create a pathway summary for a gene after completing the main gene review. This agent should be invoked specifically to generate GENE-pathway.md files that summarize the gene's role in biological pathways with proper citations and mermaid diagrams.

Use this agent when you need to review UniProt annotation rules (ARBA, UniRule) for quality, biological accuracy, and GO annotation appropriateness. This agent performs comprehensive analysis of rule condition sets, evaluates literature support, assesses taxonomic scope, and recommends curation actions.