name

efo-pr-review

description

Use when asked to review an EFO pull request or the current branch's changes. Dispatches the read-only efo-pr-reviewer subagent, which reviews src/ontology/efo-edit.owl against the canonical EFO checklist (hierarchy, definitions, xrefs/PMIDs, synonym typing, obsoletion safety, temporary EFO_099xxxx ID handling), returns a structured report, and can optionally publish it as a PR comment on explicit request.

Review EFO PR

On-demand, local PR/branch review for the Experimental Factor Ontology. It never runs automatically and never posts to GitHub unless the user explicitly asks. The edit file is always src/ontology/efo-edit.owl.

The heavy diff + ontology analysis runs in an isolated, read-only subagent (efo-pr-reviewer) so it does not clutter the main conversation and cannot accidentally modify or push anything. All review substance lives in the canonical checklist docs/agents-documentation/efo-pr-review-checklist.md, which the subagent reads.

Step 1 — Determine the target

Argument given (a PR number): target that PR. Confirm the repo with gh repo view --json nameWithOwner -q .nameWithOwner.
No argument: review the current branch against the default branch (works even with no open PR):
- default branch: git symbolic-ref --quiet refs/remotes/origin/HEAD (strip to the name), else master.
- target = git diff <base>...HEAD.
If there is no PR and the branch has no diff vs. base, tell the user there's nothing to review and stop.

Step 2 — Dispatch the read-only reviewer

Dispatch the efo-pr-reviewer subagent (Agent tool, subagent_type: "efo-pr-reviewer"). Hand it the concrete target, e.g.:

Review PR #1234 in repo EBISPOT/efo. Get the diff with gh pr diff 1234 and context with gh pr view 1234 --json title,body,files,baseRefName,headRefName. Read the canonical checklist at docs/agents-documentation/efo-pr-review-checklist.md and return your structured report.

or, for a local branch:

Review the local branch issue-123 against base master in EBISPOT/efo. Get the diff with git diff master...HEAD. Read the canonical checklist at docs/agents-documentation/efo-pr-review-checklist.md and return your structured report.

The subagent is read-only: it produces a report and returns it — it does not edit, commit, push, or post.

Step 3 — Relay the report

Show the subagent's returned report to the user (it is already formatted as a markdown review). Add a one-line note that nothing was posted to GitHub and that you can publish it on request.

Step 4 — Publish only if the user asks

This is an outward-facing action — do it only on an explicit request, and confirm the PR number + repo first.

Write the report to a temp file and post it as a non-blocking comment: gh pr comment <N> --repo EBISPOT/efo --body-file <file>
Do not submit a formal gh pr review --approve/--request-changes unless the user explicitly asks — this is a local advisory review, not the CI review gate.
If there is no PR yet (local-branch review), there is nothing to comment on; tell the user to open the PR first.

Notes

Read-only by construction: the reviewer has no Edit/Write tools and is instructed never to push or post. The only GitHub-writing step is Step 4, which lives here in the main thread under explicit user control.
EFO-specialized and repo-checked-in: this skill and the efo-pr-reviewer subagent ship with the repo, so any contributor with Claude Code gets EFO PR review out of the box. Copilot and Codex have equivalent wrappers (.github/agents/EFO-pr-reviewer.md, docs/agents-documentation/efo-pr-review-codex.md) that reference the same canonical checklist.

Review EFO PR

Step 1 — Determine the target

Argument given (a PR number): target that PR. Confirm the repo with gh repo view --json nameWithOwner -q .nameWithOwner.

No argument: review the current branch against the default branch (works even with no open PR):

default branch: git symbolic-ref --quiet refs/remotes/origin/HEAD (strip to the name), else master.
target = git diff <base>...HEAD.

If there is no PR and the branch has no diff vs. base, tell the user there's nothing to review and stop.

Step 2 — Dispatch the read-only reviewer

Dispatch the efo-pr-reviewer subagent (Agent tool, subagent_type: "efo-pr-reviewer"). Hand it the concrete target, e.g.:

Review PR #1234 in repo EBISPOT/efo. Get the diff with gh pr diff 1234 and context with gh pr view 1234 --json title,body,files,baseRefName,headRefName. Read the canonical checklist at docs/agents-documentation/efo-pr-review-checklist.md and return your structured report.

or, for a local branch:

Review the local branch issue-123 against base master in EBISPOT/efo. Get the diff with git diff master...HEAD. Read the canonical checklist at docs/agents-documentation/efo-pr-review-checklist.md and return your structured report.

The subagent is read-only: it produces a report and returns it — it does not edit, commit, push, or post.

Step 3 — Relay the report

Show the subagent's returned report to the user (it is already formatted as a markdown review). Add a one-line note that nothing was posted to GitHub and that you can publish it on request.

Step 4 — Publish only if the user asks

This is an outward-facing action — do it only on an explicit request, and confirm the PR number + repo first.

Write the report to a temp file and post it as a non-blocking comment: gh pr comment <N> --repo EBISPOT/efo --body-file <file>

Do not submit a formal gh pr review --approve/--request-changes unless the user explicitly asks — this is a local advisory review, not the CI review gate.

If there is no PR yet (local-branch review), there is nothing to comment on; tell the user to open the PR first.

Notes

Read-only by construction: the reviewer has no Edit/Write tools and is instructed never to push or post. The only GitHub-writing step is Step 4, which lives here in the main thread under explicit user control.

EFO-specialized and repo-checked-in: this skill and the efo-pr-reviewer subagent ship with the repo, so any contributor with Claude Code gets EFO PR review out of the box. Copilot and Codex have equivalent wrappers (.github/agents/EFO-pr-reviewer.md, docs/agents-documentation/efo-pr-review-codex.md) that reference the same canonical checklist.