Case studies
Every page in this section describes one repository that runs agents on real curation work. Each page points at the files and folders you can open and copy.
We do not centralize the material here. The repositories are the source of truth. If a page disagrees with the repository, trust the repository and open an issue.
Block A: ontologies
These are established OBO ontologies that added agents to an existing editor workflow. The ontology file stays the product. Agents work through issues and pull requests.
| Repository | Best known for | Read this first |
|---|---|---|
| GO | The largest skill library of any ontology repository | .claude/skills/ |
| Uberon | Subagents for specialist jobs | .claude/agents/ |
| Mondo | A Goose-based agent alongside Claude Code subagents | .github/workflows/ai-agent.yml |
| Cell Ontology | Live agent traffic with almost no supporting structure | CLAUDE.md |
| EFO | An orchestrator that routes work to specialists | CLAUDE.md |
Block B: the mechs
These are newer knowledge bases built for agents from the start. The record is a YAML file. Validation is strict. Most edits come from agents.
| Repository | What it curates | Read this first |
|---|---|---|
| DisMech | Disease mechanisms | CONTRIBUTING.md |
| AI Gene Review | Gene Ontology annotations | .claude/skills/ |
| CommunityMech | Microbial communities | src/communitymech/schema/ |
| HabitatMech | Microbial habitats | data/habitats/ |
Four more repositories in the CultureBot family follow the same shape: CultureMech (culture media), MediaIngredientMech (media ingredients), TraitMech (microbial traits), and proteintraitsmech (protein traits). See CommunityMech for how the family fits together.
How to read a case study
Each page has the same four sections:
- What to look at lists paths in the repository.
- What works describes practices worth copying.
- What to copy first is the shortest useful step.
- Gaps records what the repository has not solved. These sections are honest, not critical. Every setup here has gaps.
Where the observations come from
Counts of skills, subagents, and workflows come from agent-watcher, which scans these repositories on a schedule and publishes dated reports. See Evidence.