From 9abc05dbb777c2aaf4cf14bd346a92a0ccf7c373 Mon Sep 17 00:00:00 2001 From: Dragon-AI Agent Date: Tue, 18 Nov 2025 03:42:13 +0000 Subject: [PATCH 1/2] Add Examples gallery page documenting AI4Curation implementations MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit addresses issue #47 by creating a new examples documentation page that showcases repositories using AI agent integration for knowledge base curation. Key additions: - New docs/examples.md with gallery of example repositories - Documented Mondo, Cell Ontology, Uberon, and other implementations - Comparison of agent platforms (Goose, Claude Code, GitHub Copilot) - Learning resources and contribution guidelines - Added Examples page to mkdocs.yml navigation The gallery includes: - Ontology repositories (Mondo, CL, Uberon, EFO, NAMO) - Documentation repositories (this repo as self-example) - Key configuration files to explore in each repo - Platform comparisons and use cases - Links to related how-to guides This provides users with real-world examples to learn from and helps support the pipeline unification effort discussed in issue #40. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude --- docs/examples.md | 136 +++++++++++++++++++++++++++++++++++++++++++++++ mkdocs.yml | 1 + 2 files changed, 137 insertions(+) create mode 100644 docs/examples.md diff --git a/docs/examples.md b/docs/examples.md new file mode 100644 index 0000000..3245457 --- /dev/null +++ b/docs/examples.md @@ -0,0 +1,136 @@ +# 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 diff --git a/mkdocs.yml b/mkdocs.yml index 159af61..cc59b82 100644 --- a/mkdocs.yml +++ b/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 From 653f50880231f398f68401bbd2bb00448e52cafb Mon Sep 17 00:00:00 2001 From: Dragon-AI Agent Date: Sat, 22 Nov 2025 02:30:29 +0000 Subject: [PATCH 2/2] Streamline examples page per issue #47 feedback MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Remove content after Documentation Repositories section - Add EFO (Experimental Factor Ontology) with GitHub Copilot - Add search links for agent activity in each repository - Remove generic verbiage, keeping only specific factual information 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude --- docs/examples.md | 115 +++++++---------------------------------------- 1 file changed, 17 insertions(+), 98 deletions(-) diff --git a/docs/examples.md b/docs/examples.md index 3245457..1b8ad59 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -1,136 +1,55 @@ # 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 +- [.config/goose/config.yaml](https://github.com/monarch-initiative/mondo/tree/master/.config/goose) - Goose configuration **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 +**Agent Activity**: [Search for @dragon-ai-agent mentions and PRs](https://github.com/monarch-initiative/mondo/issues?q=involves%3Adragon-ai-agent) ### 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 +- CLAUDE.md - Agent instructions -**Agent Platform**: Part of the unified ontology pipeline effort +**Agent Platform**: Goose (via dragon-ai-agent) -**Domain Focus**: Cell type classification and relationships +**Agent Activity**: [Search for @dragon-ai-agent mentions and PRs](https://github.com/obophenotype/cell-ontology/issues?q=involves%3Adragon-ai-agent) ### 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 +- [PR #3580](https://github.com/obophenotype/uberon/pull/3580) - GitHub Copilot integration + +**Agent Platform**: GitHub Copilot, Goose + +**Agent Activity**: [Search for @dragon-ai-agent mentions and PRs](https://github.com/obophenotype/uberon/issues?q=involves%3Adragon-ai-agent) -**Agent Platform**: GitHub Copilot (in addition to other setups) +### EFO (Experimental Factor Ontology) +**Repository**: [EBISPOT/efo](https://github.com/EBISPOT/efo) -**Notable Features**: -- Demonstrates GitHub Copilot setup for automated reviews -- Part of the OBO Phenotype ontology ecosystem +**Agent Platform**: GitHub Copilot + +**Agent Activity**: [Search for Copilot activity](https://github.com/EBISPOT/efo/issues?q=author%3Aapp%2Fcopilot) ## 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: +**Agent Platform**: Claude Code, Goose -- **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 +**Agent Activity**: [Search for @dragon-ai-agent mentions and PRs](https://github.com/ai4curation/aidocs/issues?q=involves%3Adragon-ai-agent)