Add Examples gallery documenting AI4Curation implementations

docs/examples.md

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+# Example Repositories Using AI4Curation Setup
+
+This page showcases repositories that have implemented AI agent integration for knowledge base curation, providing real-world examples for learning and reference.
+
+## Ontology Repositories
+
+These repositories demonstrate AI agent integration for ontology curation workflows:
+
+### Mondo Disease Ontology
+**Repository**: [monarch-initiative/mondo](https://github.com/monarch-initiative/mondo)
+
+The Mondo Disease Ontology is an exemplar implementation of the dragon-ai-agent GitHub Actions setup using Goose as the agent platform.
+
+**Key Files to Explore**:
+- [ai-agent.yml](https://github.com/monarch-initiative/mondo/blob/master/.github/workflows/ai-agent.yml) - GitHub Actions workflow configuration
+- [CLAUDE.md](https://github.com/monarch-initiative/mondo/blob/master/CLAUDE.md) - Agent instructions
+- [.config/goose/config.yaml](https://github.com/monarch-initiative/mondo/tree/master/.config/goose) - Goose configuration with MCP extensions
+
+**Agent Platform**: Goose (via dragon-ai-agent)
+
+**Notable Features**:
+- Uses dragon-ai-agent/github-mention-detector for detecting @mentions
+- Configured with dragon-ai-agent/run-goose-obo for ontology-specific tasks
+- Includes MCP extensions for developer tools, memory, and PDF reading
+- LiteLLM proxy integration for cost management
+
+### Cell Ontology (CL)
+**Repository**: [obophenotype/cell-ontology](https://github.com/obophenotype/cell-ontology)
+
+Cell Ontology provides structured knowledge about cell types and has integrated AI agents into its curation workflow.
+
+**Key Files to Explore**:
+- CLAUDE.md - Agent instructions for cell ontology curation
+
+**Agent Platform**: Part of the unified ontology pipeline effort
+
+**Domain Focus**: Cell type classification and relationships
+
+### Uberon Anatomy Ontology
+**Repository**: [obophenotype/uberon](https://github.com/obophenotype/uberon)
+
+Uberon provides cross-species anatomy ontology and has explored multiple AI agent platforms.
+
+**Key Files to Explore**:
+- [PR #3580](https://github.com/obophenotype/uberon/pull/3580) - GitHub Copilot integration for reviews and PRs
+
+**Agent Platform**: GitHub Copilot (in addition to other setups)
+
+**Notable Features**:
+- Demonstrates GitHub Copilot setup for automated reviews
+- Part of the OBO Phenotype ontology ecosystem
+
+## Documentation Repositories
+
+### AI4Curators Documentation
+**Repository**: [ai4curation/aidocs](https://github.com/ai4curation/aidocs) (this repository)
+
+This documentation repository serves as both a guide and example of AI agent integration.
+
+**Key Files to Explore**:
+- `.github/workflows/` - GitHub Actions for AI agent integration
+- `CLAUDE.md` - Repository-specific instructions
+- Documentation in `docs/` demonstrating best practices
+
+**Agent Platform**: Multiple (Claude Code, Goose)
+
+**Notable Features**:
+- Comprehensive documentation on AI integration patterns
+- Examples and how-to guides
+- Reference implementations
+
+## Additional Known Implementations
+
+These repositories are confirmed to use AI agent setups, though detailed configuration may vary:
+
+- **EFO (Experimental Factor Ontology)** - Part of the unified ontology pipeline effort
+- **NAMO** - Mentioned in pipeline unification discussions
+
+## Learning from These Examples
+
+When exploring these repositories, look for:
+
+1. **Workflow Configuration**: `.github/workflows/` files showing how agents are triggered
+2. **Agent Instructions**: `CLAUDE.md`, `.goosehints`, or similar instruction files
+3. **MCP Configuration**: `.config/goose/config.yaml` or `.claude/settings.json` for tool integrations
+4. **Access Control**: `.github/ai-controllers.json` for authorized users
+5. **Example PRs**: Search for PRs created by the agent to see real interactions
+
+## Comparison of Agent Platforms
+
+### Goose (via dragon-ai-agent)
+- **Used by**: Mondo, Cell Ontology, many OBO ontologies
+- **Strengths**: Open source, MCP support, self-hosted options
+- **Setup**: Requires `.config/goose/` configuration
+- **API**: Anthropic Claude (typically via LiteLLM proxy)
+
+### Claude Code
+- **Used by**: Various repositories, simplified setup
+- **Strengths**: Streamlined installation via `claude install-github-app`
+- **Setup**: Automated GitHub Actions configuration
+- **API**: Anthropic Claude (direct)
+
+### GitHub Copilot
+- **Used by**: Uberon (for reviews)
+- **Strengths**: Native GitHub integration
+- **Setup**: Simple file changes for review automation
+- **API**: GitHub/OpenAI
+
+## Related Resources
+
+- [How to set up GitHub Actions](how-tos/set-up-github-actions.md) - Step-by-step setup guide
+- [How to instruct the GitHub agent](how-tos/instruct-github-agent.md) - Writing effective agent instructions
+- [Issue #40: Unify ontology pipelines](https://github.com/ai4curation/aidocs/issues/40) - Ongoing standardization effort
+
+## Contributing to This Gallery
+
+If you have implemented AI agent integration in your repository and would like to be included in this gallery, please:
+
+1. Open an issue with the repository URL and description
+2. Submit a pull request adding your repository to this page
+3. Contact the AI4Curation team
+
+We're particularly interested in examples that demonstrate:
+- Novel use cases or workflows
+- Different agent platforms or configurations
+- Domain-specific adaptations
+- Advanced features or integrations
+
+## Future Directions
+
+The AI4Curation community is working toward:
+
+- **Pipeline unification**: Standardizing AI agent patterns across repositories (see [Issue #40](https://github.com/ai4curation/aidocs/issues/40))
+- **Best practices**: Documenting proven patterns and anti-patterns
+- **Tooling**: Developing shared tools and actions
+- **Community**: Building a network of practitioners and knowledge sharing

mkdocs.yml

@@ -37,6 +37,7 @@ plugins:
 nav:
   - Home: index.md
   - FAQ: faq.md
+  - Examples: examples.md
   - Curator how-tos:
      - Instruct the GitHub agent: how-tos/instruct-github-agent.md
      - Make identifiers hallucination-resistant: how-tos/make-ids-hallucination-resistant.md