review

name	review
description	Review, either de-novo, or augment the review of an existing one. A list of deep research providers may be specified.
argument-hint	[ORGANISM] [GENE_SYMBOL] (using [DEEP_RESEARCH_PROVIDER])

Review the gene specified in $ARGUMENTS.

• ORGANISM should typically be a uniprot species code (in a few cases we use lowercase GO names)
• GENE_SYMBOL should be the human readable gene symbol for that org

IMPORTANT: you MUST consult the annotation-reviewer.md subagent for this task.

Step 1: Ensure gene data is fetched

Run just fetch-gene ORGANISM GENE_SYMBOL if the gene directory doesn't exist yet.

Step 2: Run deep research AND publication caching in parallel

Publication caching only needs the GOA file (created by fetch-gene), so it can run concurrently with deep research. Launch both at the same time:

• Deep research: If the user specifies a deep research provider(s), use that provider(s), otherwise default to falcon. Use --fallback perplexity-lite so that if the primary provider times out, it automatically retries with perplexity-lite. E.g. just deep-research-falcon ORGANISM GENE_SYMBOL --fallback perplexity-lite
• Publication caching: just fetch-gene-pmids ORGANISM GENE_SYMBOL

Run these two steps in parallel (e.g. as concurrent background agents or shell jobs). Do NOT wait for deep research to finish before starting publication caching.

Step 3: Fetch additional data (bacterial organisms)

For bacterial organisms (e.g. PSEPK, ECOLI, SALTY, or any prokaryote), after deep research, also fetch FEBA/RB-TnSeq fitness data if available:

just fetch-fitness ORGANISM GENE_SYMBOL

This creates a GENE-fitness.md file with mutant fitness phenotypes and cofitness partners. The annotation-reviewer agent will use this data as additional evidence when reviewing annotations.

Step 4: Run annotation review

Invoke the annotation-reviewer subagent to systematically review all annotations.