Mondo
The Mondo Disease Ontology. Mondo is the clearest example of a repository whose automated agent and whose subagent library are on different tracks.
Repository: monarch-initiative/mondo
Product: src/ontology/mondo-edit.obo
Agent surface: GitHub mention through dragon-ai-agent, local Claude Code sessions
What to look at
| Path | What it is |
|---|---|
.github/workflows/ai-agent.yml |
The automated agent, built on dragon-ai-agent and Goose |
.claude/agents/ |
Six subagents for Claude Code |
.config/goose/ |
Goose configuration used by the workflow |
CLAUDE.md |
Repository instructions |
The subagents are deep-research-specialist, design-pattern-advisor,
identifier-validator, metadata-checker, ontology-reasoner, and
task-coordinator. Four of these names also appear in
Uberon.
What works
Mondo has run agent-assisted curation longer than most of the repositories on this site. Its issue tracker is a good place to read real agent pull requests from end to end, including the ones that went wrong: issues involving dragon-ai-agent.
The subagents are a working library. If you want a starting set for an OBO ontology, read Mondo's and Uberon's together and take the four they share.
What to copy first
Read the merged agent pull requests before you copy any configuration. Mondo has enough history to show you what agent output looks like after review, which is more useful than any template.
Gaps
The only automated agent workflow runs dragon-ai-agent and Goose. The six
subagents under .claude/agents/ are Claude Code features. An agent triggered
by ai-agent.yml therefore cannot reach them. They are available in local
Claude Code sessions only.
Mondo is also the last repository we track that still runs the
dragon-ai-agent machine account. It authenticates with a personal access token
held in the PAT_FOR_PR secret. DisMech has moved the same job to a GitHub App
with a token minted per run. See Bots.
This is not necessarily wrong, but it is undocumented. If you have both, say in
CLAUDE.md which surface each one serves. If you want the subagents reachable
from GitHub, add a workflow that runs Claude Code the way
GO and Uberon do.
Goose is no longer a tool we recommend for new setups. See Harnesses.