ai-gene-review: Skill for Claude Code

AIGR PR Review Skill

Use this skill when reviewing AIGR pull requests or drafting review feedback about gene review YAML, GO annotation decisions, evidence support, or UniProt-backed summaries.

Use the repository's existing guidance and agents where appropriate, especially CLAUDE.md and .claude/agents/annotation-reviewer.md.

Trust Validation

Do not re-check what just validate already covers.

If validation passes, do not spend review effort on:

• YAML formatting or whitespace
• Empty or null optional keys
• Required-vs-optional field presence
• Enum spelling, structural schema shape, or other deterministic validation concerns

The reviewer's job is the non-deterministic part: biological judgment, GO ontology judgment, evidence quality, and whether the curation narrative is coherent.

Focus Areas

1. GO term specificity and aspect correctness

• Prefer the most accurate GO term supported by the evidence, not the nearest generic match.
• Flag terms that are too broad, too narrow, or placed in the wrong GO aspect.
• Be especially skeptical of vague terms like protein binding when a more informative MF term is available.
• If recommending MODIFY, provide the concrete replacement term(s) with GO IDs.

1. Evidence quality

• Each annotation review should be supported by accessible evidence.
• Check that cited PMIDs, GO references, file references, and supporting text actually justify the claimed action.
• Do not accept unsupported NEW annotations.
• If the relevant publication or evidence cannot be accessed, prefer UNDECIDED.

1. Core function identification

• core_functions should capture the gene's main conserved molecular/cellular role.
• Do not treat every phenotype, developmental consequence, or systems-level effect as core.
• Use the combination of review YAML, UniProt annotations, deep research, notes, and cited publications to infer what is core vs peripheral.

1. Description quality

• The top-level description should be a standalone biological summary for a biologist.
• Flag project or workflow framing in description, including phrases such as Proteostasis Network, PN, this review, curation, GOA correctly captures, or should be annotated.
• Project-specific observations, disagreements with a project source list, and annotation-propagation cautions belong in *-notes.md, review.reason, core_functions, or suggested_questions, not in description.