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.
• For generic protein binding, follow the action policy in the annotation-reviewer skill.
• 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.
• For a NEW process term, check participation, not just evidence: does the gene product do any of the work — catalyse a step, or contribute the structure or cofactor activity a step depends on — or is it merely required for the process, consumed by it, or the thing it acts on? Knockout/rescue and human loss-of-function data establish necessity, which is what being a substrate means, and do not settle this. A substrate that scaffolds or catalyses part of its own conversion can legitimately carry the term (CLAUDE.md works thyroglobulin, fibrinogen and C3 through the three cases).
• Treat "every other participant carries this term and this gene does not" as a red flag rather than a justification. Ask for the comparator check — two or three other gene products in the same role relative to the same kind of process — and check the term's parents (a process under GO:0006508 proteolysis names whatever does the cleaving, which is the substrate itself in the autoprocessing case, GO:0016540, and otherwise is not) and the cached GO-CAMs, which often already contain the gene in the role GO intends for it.
• Flag a proposed term that is an ancestor or descendant of another proposed term, or of one the gene already carries, as redundant rather than additional.
• If the relevant publication or evidence cannot be accessed, prefer UNDECIDED.