diff --git a/.claude/.mcp.json b/.claude/.mcp.json
new file mode 100644
index 0000000..0e61620
--- /dev/null
+++ b/.claude/.mcp.json
@@ -0,0 +1,16 @@
+{
+  "mcpServers": {
+    "ols-mcp": {
+      "type": "stdio",
+      "command": "uvx",
+      "args": [
+        "ols-mcp"
+      ],
+      "env": {}
+    },
+    "pubmed": {
+      "type": "http",
+      "url": "https://pubmed.mcp.claude.com/mcp"
+    }
+  }
+}
diff --git a/.claude/settings.json b/.claude/settings.json
new file mode 100644
index 0000000..29f0ffc
--- /dev/null
+++ b/.claude/settings.json
@@ -0,0 +1,14 @@
+{
+  "permissions": {
+    "allow": [
+        "Bash(*)",
+        "Edit",
+        "MultiEdit",
+        "NotebookEdit",
+        "FileEdit",
+        "WebFetch",
+        "WebSearch",
+        "Write"
+    ]
+  }
+}
diff --git a/.github/actions/claude-code-action/action.yml b/.github/actions/claude-code-action/action.yml
new file mode 100644
index 0000000..7616989
--- /dev/null
+++ b/.github/actions/claude-code-action/action.yml
@@ -0,0 +1,180 @@
+name: "Claude Code Action"
+description: "Run Claude Code in GitHub Actions workflows"
+
+inputs:
+  github_token:
+    description: "GitHub token with repo and issues permissions"
+    required: true
+  anthropic_api_key:
+    description: "Anthropic API key"
+    required: false
+  cborg_api_key:
+    description: "CBORG API key"
+    required: false
+  claude_code_oauth_token:
+    description: "Claude Code OAuth token"
+    required: false
+  prompt:
+    description: "The prompt to send to Claude Code"
+    required: false
+    default: ""
+  prompt_file:
+    description: "Path to a file containing the prompt to send to Claude Code"
+    required: false
+    default: ""
+  allowed_tools:
+    description: "Comma-separated list of allowed tools for Claude Code to use"
+    required: false
+    default: ""
+  output_file:
+    description: "File to save Claude Code output to (optional)"
+    required: false
+    default: ""
+  timeout_minutes:
+    description: "Timeout in minutes for Claude Code execution"
+    required: false
+    default: "10"
+  install_github_mcp:
+    description: "Whether to install the GitHub MCP server"
+    required: false
+    default: "false"
+  install_artl_mcp:
+    description: "Whether to install the ARTL MCP server"
+    required: false
+    default: "false"
+
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install uvx
+      shell: bash
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+        source $HOME/.cargo/env
+        which uvx || echo "uvx not found in PATH, installing via pip"
+        pip install uv || true
+
+    - name: Install Claude Code
+      shell: bash
+      run: npm install -g @anthropic-ai/claude-code
+
+    - name: Install GitHub MCP Server
+      if: inputs.install_github_mcp == 'true'
+      shell: bash
+      run: |
+        claude mcp add-json github '{
+          "command": "docker",
+          "args": [
+            "run",
+            "-i",
+            "--rm",
+            "-e",
+            "GITHUB_PERSONAL_ACCESS_TOKEN",
+            "ghcr.io/github/github-mcp-server:sha-ff3036d"
+          ],
+          "env": {
+            "GITHUB_PERSONAL_ACCESS_TOKEN": "${{ inputs.GITHUB_TOKEN }}"
+          }
+        }'
+
+    - name: Install ARTL MCP Server
+      if: inputs.install_artl_mcp == 'true'
+      shell: bash
+      run: |
+        claude mcp add-json artl '{
+          "command": "uvx",
+          "args": [
+            "artl-mcp"
+          ]
+        }'
+
+    - name: Prepare Prompt File
+      shell: bash
+      id: prepare_prompt
+      run: |
+
+        # Check if either prompt or prompt_file is provided
+        if [ -z "${{ inputs.prompt }}" ] && [ -z "${{ inputs.prompt_file }}" ]; then
+          echo "::error::Neither 'prompt' nor 'prompt_file' was provided. At least one is required."
+          exit 1
+        fi
+
+        # Determine which prompt source to use
+        if [ ! -z "${{ inputs.prompt_file }}" ]; then
+          # Check if the prompt file exists
+          if [ ! -f "${{ inputs.prompt_file }}" ]; then
+            echo "::error::Prompt file '${{ inputs.prompt_file }}' does not exist."
+            exit 1
+          fi
+
+          # Use the provided prompt file
+          PROMPT_PATH="${{ inputs.prompt_file }}"
+        else
+          mkdir -p /tmp/claude-action
+          PROMPT_PATH="/tmp/claude-action/prompt.txt"
+          echo "${{ inputs.prompt }}" > "$PROMPT_PATH"
+        fi
+
+        # Verify the prompt file is not empty
+        if [ ! -s "$PROMPT_PATH" ]; then
+          echo "::error::Prompt is empty. Please provide a non-empty prompt."
+          exit 1
+        fi
+
+        # Save the prompt path for the next step
+        echo "PROMPT_PATH=$PROMPT_PATH" >> $GITHUB_ENV
+
+    - name: Run Claude Code
+      shell: bash
+      id: run_claude
+      run: |
+
+        if [ ! -z "${{ inputs.claude_code_oauth_token }}" ]; then
+          echo CLAUDE AUTH TOKEN IS NOT SET
+        else
+          echo CLAUDE AUTH TOKEN IS SET
+          export ANTHROPIC_API_KEY=
+        fi
+
+        ALLOWED_TOOLS_ARG=""
+        if [ ! -z "${{ inputs.allowed_tools }}" ]; then
+          ALLOWED_TOOLS_ARG="--allowedTools ${{ inputs.allowed_tools }}"
+        fi
+
+        # Set a timeout to ensure the command doesn't run indefinitely
+        timeout_seconds=$((${{ inputs.timeout_minutes }} * 60))
+
+        if [ -z "${{ inputs.output_file }}" ]; then
+          # Run Claude Code and output to console
+          claude \
+            -p \
+            --verbose \
+            --output-format stream-json \
+            "$(cat ${{ env.PROMPT_PATH }})" \
+            ${{ inputs.allowed_tools != '' && format('--allowedTools "{0}"', inputs.allowed_tools) || '' }}
+        else
+          # Run Claude Code and tee output to console and file
+          claude \
+            -p \
+            --verbose \
+            --output-format stream-json \
+            "$(cat ${{ env.PROMPT_PATH }})" \
+            ${{ inputs.allowed_tools != '' && format('--allowedTools "{0}"', inputs.allowed_tools) || '' }} | tee output.txt
+
+          # Process output.txt into JSON in a separate step
+          jq -s '.' output.txt > output.json
+
+          # Extract the result from the last item in the array (system message)
+          jq -r '.[-1].result' output.json > "${{ inputs.output_file }}"
+
+          echo "Complete output saved to output.json, final response saved to ${{ inputs.output_file }}"
+        fi
+      
+      env:
+        ANTHROPIC_API_KEY: ${{ inputs.anthropic_api_key }}
+        # ANTHROPIC_AUTH_TOKEN: ${{ inputs.cborg_api_key }}
+        CLAUDE_CODE_OAUTH_TOKEN: ${{ inputs.claude_code_oauth_token }}
+        GITHUB_TOKEN: ${{ inputs.github_token }}
+        # ANTHROPIC_BASE_URL: "https://api.cborg.lbl.gov"
+        # DISABLE_NON_ESSENTIAL_MODEL_CALLS: "1"
diff --git a/.github/actions/claude-issue-summarize-action/action.yml b/.github/actions/claude-issue-summarize-action/action.yml
new file mode 100644
index 0000000..896af91
--- /dev/null
+++ b/.github/actions/claude-issue-summarize-action/action.yml
@@ -0,0 +1,78 @@
+name: "Claude Issue summarize Action"
+description: "Automatically Summarize GitHub issues using Claude Code"
+
+inputs:
+  timeout_minutes:
+    description: "Timeout in minutes for execution"
+    required: false
+    default: "5"
+  anthropic_api_key:
+    description: "Anthropic API key"
+    required: false
+  cborg_api_key:
+    description: "CBORG API key"
+    required: false
+  claude_code_oauth_token:
+    description: "Claude Code OAuth token"
+    required: false
+  github_token:
+    description: "GitHub token with repo and issues permissions"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Checkout repository code
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ github.ref }}
+
+    - name: Create prompt file
+      shell: bash
+      run: |
+        mkdir -p /tmp/claude-prompts
+        cat > /tmp/claude-prompts/claude-issue-summarize-prompt.txt << 'EOF'
+        You're an Summarization assistant for GitHub issues. Your task is to analyze the issue, look up related issues, and summarize the issue.
+
+        Remember that this repo is primarily a note-taking and memory device for Chris Mungall, so anything you can do to enhance and enrich that would be helpful.
+
+        IMPORTANT: Don't make any PRs. You should ONLY post a response, IN THE SAME ISSUE.
+
+        Issue Information:
+        - REPO: ${{ github.repository }}
+        - ISSUE_NUMBER: ${{ github.event.issue.number }}
+
+        TASK OVERVIEW:
+
+        1. First, use your judgement to determine the course of action.
+            - If the issue is an epic or has links to other issues, read those issues, and summarize them. Summarize their status etc. Given an overall summary.
+            - If the issue is an idea or a vague high level description, run with the idea, do deep research, give heloful suggestions with links to relevant papers etc.
+            - If there are links in the issue to websites, database entities, etc, then look these up.
+            - If there are links or references to papers, then looks these up and summarize (don't guess content - if you can't access the paper, then say "I can't access the paper")
+            - Try using artl-mcp to get paper fulltext.
+            - If you want a more powerful AI agent to take on this one and make a PR, use this magic phrase: `@dragon-ai-agent please <INSTRUCTIONS>`
+
+        2. Next, use the GitHub tools to get context about the issue:
+           - You have access to these github tools:
+             - mcp__github__get_issue: Use this to retrieve the current issue's details including title, description, and existing labels
+             - mcp__github__get_issue_comments: Use this to read any discussion or additional context provided in the comments
+             - mcp__github__update_issue: Use this to apply labels to the issue (do not use this for commenting)
+             - mcp__github__search_issues: Use this to find similar issues that might provide context for proper categorization and to identify potential duplicate issues
+             - mcp__github__list_issues: Use this to understand patterns in how other issues are labeled
+           - You can also use web searching and fetching.
+
+        - It's okay to not add any information if the issue is not clear.
+        EOF
+
+    - name: Run Claude Code
+      uses: ./.github/actions/claude-code-action
+      with:
+        prompt_file: /tmp/claude-prompts/claude-issue-summarize-prompt.txt
+        allowed_tools: "Bash(gh label list),WebFetch,Fetch,LS,mcp__github__get_issue,mcp__github__get_issue_comments,mcp__github__update_issue,mcp__github__add_issue_comment,mcp__github__search_issues,mcp__github__list_issues"
+        install_github_mcp: "true"
+        install_artl_mcp: "true"
+        timeout_minutes: ${{ inputs.timeout_minutes }}
+        anthropic_api_key: ${{ inputs.anthropic_api_key }}
+        claude_code_oauth_token: ${{ inputs.claude_code_oauth_token }}
+        cborg_api_key: ${{ inputs.cborg_api_key }}
+        github_token: ${{ inputs.github_token }}
diff --git a/.github/actions/claude-issue-triage-action/action.yml b/.github/actions/claude-issue-triage-action/action.yml
new file mode 100644
index 0000000..caaad89
--- /dev/null
+++ b/.github/actions/claude-issue-triage-action/action.yml
@@ -0,0 +1,95 @@
+name: "Claude Issue Triage Action"
+description: "Automatically triage GitHub issues using Claude Code"
+
+inputs:
+  timeout_minutes:
+    description: "Timeout in minutes for execution"
+    required: false
+    default: "5"
+  anthropic_api_key:
+    description: "Anthropic API key"
+    required: false
+  claude_code_oauth_token:
+    description: "Claude Code OAuth token"
+    required: false
+  cborg_api_key:
+    description: "CBORG API key"
+    required: true
+  github_token:
+    description: "GitHub token with repo and issues permissions"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Checkout repository code
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ github.ref }}
+
+    - name: Create prompt file
+      shell: bash
+      run: |
+        mkdir -p /tmp/claude-prompts
+        cat > /tmp/claude-prompts/claude-issue-triage-prompt.txt << 'EOF'
+        You're an issue triage assistant for GitHub issues. Your task is to analyze the issue and select appropriate labels from the provided list.
+
+        IMPORTANT: Don't post any comments or messages to the issue. Your only action should be to apply labels.
+
+        Issue Information:
+        - REPO: ${{ github.repository }}
+        - ISSUE_NUMBER: ${{ github.event.issue.number }}
+
+        TASK OVERVIEW:
+
+        1. First, fetch the list of labels available in this repository by running: `gh label list`. Run exactly this command with nothing else.
+
+        2. Next, use the GitHub tools to get context about the issue:
+           - You have access to these tools:
+             - mcp__github__get_issue: Use this to retrieve the current issue's details including title, description, and existing labels
+             - mcp__github__get_issue_comments: Use this to read any discussion or additional context provided in the comments
+             - mcp__github__update_issue: Use this to apply labels to the issue (do not use this for commenting)
+             - mcp__github__search_issues: Use this to find similar issues that might provide context for proper categorization and to identify potential duplicate issues
+             - mcp__github__list_issues: Use this to understand patterns in how other issues are labeled
+           - Start by using mcp__github__get_issue to get the issue details
+
+        3. Analyze the issue content, considering:
+           - The issue title and description
+           - The type of issue (bug report, feature request, question, etc.)
+           - Technical areas mentioned
+           - Severity or priority indicators
+           - User impact
+           - Components affected
+
+        4. Select appropriate labels from the available labels list provided above:
+           - Choose labels that accurately reflect the issue's nature
+           - Be specific but comprehensive
+           - Select priority labels if you can determine urgency (high-priority, med-priority, or low-priority)
+           - Consider platform labels (android, ios) if applicable
+           - If you find similar issues using mcp__github__search_issues, consider using a "duplicate" label if appropriate. Only do so if the issue is a duplicate of another OPEN issue.
+
+        5. Apply the selected labels:
+           - Use mcp__github__update_issue to apply your selected labels
+           - DO NOT post any comments explaining your decision
+           - DO NOT communicate directly with users
+           - If no labels are clearly applicable, do not apply any labels
+
+        IMPORTANT GUIDELINES:
+        - Be thorough in your analysis
+        - Only select labels from the provided list above
+        - DO NOT post any comments to the issue
+        - Your ONLY action should be to apply labels using mcp__github__update_issue
+        - It's okay to not add any labels if none are clearly applicable
+        EOF
+
+    - name: Run Claude Code
+      uses: ./.github/actions/claude-code-action
+      with:
+        prompt_file: /tmp/claude-prompts/claude-issue-triage-prompt.txt
+        allowed_tools: "Bash(gh label list),mcp__github__get_issue,mcp__github__get_issue_comments,mcp__github__update_issue,mcp__github__search_issues,mcp__github__list_issues"
+        install_github_mcp: "true"
+        timeout_minutes: ${{ inputs.timeout_minutes }}
+        anthropic_api_key: ${{ inputs.anthropic_api_key }}
+        claude_code_oauth_token: ${{ inputs.claude_code_oauth_token }}
+        cborg_api_key: ${{ inputs.cborg_api_key }}
+        github_token: ${{ inputs.github_token }}
diff --git a/.github/ai-controllers.json b/.github/ai-controllers.json
new file mode 100644
index 0000000..e6a0c19
--- /dev/null
+++ b/.github/ai-controllers.json
@@ -0,0 +1 @@
+["cmungall"]
diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
new file mode 120000
index 0000000..be77ac8
--- /dev/null
+++ b/.github/copilot-instructions.md
@@ -0,0 +1 @@
+../AGENTS.md
\ No newline at end of file
diff --git a/.github/copilot-setup-steps.yml b/.github/copilot-setup-steps.yml
new file mode 100644
index 0000000..a33b310
--- /dev/null
+++ b/.github/copilot-setup-steps.yml
@@ -0,0 +1,40 @@
+name: "Copilot Setup Steps"
+
+
+# Automatically run the setup steps when they are changed to allow for easy validation, and
+# allow manual testing through the repository's "Actions" tab
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+
+    # Set the permissions to the lowest permissions possible needed for your steps.
+    # Copilot will be given its own token for its operations.
+    permissions:
+      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission. If you don't clone the repository in your setup steps, Copilot will do this for you automatically after the steps complete.
+      contents: read
+
+    # You can define any steps you want, and they will run before the agent starts.
+    # If you do not check out your code, Copilot will do this for you.
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+
+    - name: Install Python tools
+      run: |
+        uv sync
+        source .venv/bin/activate
+      shell: bash
+      
diff --git a/.github/workflows/claude-code-review.yml b/.github/workflows/claude-code-review.yml
new file mode 100644
index 0000000..5bf8ce5
--- /dev/null
+++ b/.github/workflows/claude-code-review.yml
@@ -0,0 +1,78 @@
+name: Claude Code Review
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+    # Optional: Only run on specific file changes
+    # paths:
+    #   - "src/**/*.ts"
+    #   - "src/**/*.tsx"
+    #   - "src/**/*.js"
+    #   - "src/**/*.jsx"
+
+jobs:
+  claude-review:
+    # Optional: Filter by PR author
+    # if: |
+    #   github.event.pull_request.user.login == 'external-contributor' ||
+    #   github.event.pull_request.user.login == 'new-developer' ||
+    #   github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
+    
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code Review
+        id: claude-review
+        uses: anthropics/claude-code-action@beta
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+
+          # Optional: Specify model (defaults to Claude Sonnet 4, uncomment for Claude Opus 4)
+          # model: "claude-opus-4-20250514"
+          
+          # Direct prompt for automated review (no @claude mention needed)
+          direct_prompt: |
+            Please review this pull request and provide feedback on:
+            - Code quality and best practices
+            - Potential bugs or issues
+            - Performance considerations
+            - Security concerns
+            - Test coverage
+            
+            Be constructive and helpful in your feedback.
+
+          # Optional: Use sticky comments to make Claude reuse the same comment on subsequent pushes to the same PR
+          # use_sticky_comment: true
+          
+          # Optional: Customize review based on file types
+          # direct_prompt: |
+          #   Review this PR focusing on:
+          #   - For TypeScript files: Type safety and proper interface usage
+          #   - For API endpoints: Security, input validation, and error handling
+          #   - For React components: Performance, accessibility, and best practices
+          #   - For tests: Coverage, edge cases, and test quality
+          
+          # Optional: Different prompts for different authors
+          # direct_prompt: |
+          #   ${{ github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR' && 
+          #   'Welcome! Please review this PR from a first-time contributor. Be encouraging and provide detailed explanations for any suggestions.' ||
+          #   'Please provide a thorough code review focusing on our coding standards and best practices.' }}
+          
+          # Optional: Add specific tools for running tests or linting
+          # allowed_tools: "Bash(npm run test),Bash(npm run lint),Bash(npm run typecheck)"
+          
+          # Optional: Skip review for certain conditions
+          # if: |
+          #   !contains(github.event.pull_request.title, '[skip-review]') &&
+          #   !contains(github.event.pull_request.title, '[WIP]')
+
diff --git a/.github/workflows/claude-issue-summarize.yml b/.github/workflows/claude-issue-summarize.yml
new file mode 100644
index 0000000..710195f
--- /dev/null
+++ b/.github/workflows/claude-issue-summarize.yml
@@ -0,0 +1,27 @@
+name: Claude Issue summarize
+description: "Automatically summarize GitHub issues using Claude Code"
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  summarize-issue:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    permissions:
+      contents: read
+      issues: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.ref }}
+
+      - name: Run Claude Issue summarize
+        uses: ./.github/actions/claude-issue-summarize-action
+        with:
+          anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          cborg_api_key: ${{ secrets.CBORG_API_KEY }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/claude-issue-triage.yml b/.github/workflows/claude-issue-triage.yml
new file mode 100644
index 0000000..ddec43e
--- /dev/null
+++ b/.github/workflows/claude-issue-triage.yml
@@ -0,0 +1,27 @@
+name: Claude Issue Triage
+description: "Automatically triage GitHub issues using Claude Code"
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  triage-issue:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    permissions:
+      contents: read
+      issues: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.ref }}
+          
+      - name: Run Claude Issue Triage
+        uses: ./.github/actions/claude-issue-triage-action
+        with:
+          anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          cborg_api_key: ${{ secrets.CBORG_API_KEY }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/claude-ontology-review.yml b/.github/workflows/claude-ontology-review.yml
new file mode 100644
index 0000000..1f847b0
--- /dev/null
+++ b/.github/workflows/claude-ontology-review.yml
@@ -0,0 +1,115 @@
+# This action invokes claude to review a PR.
+# This is a generic action - you can customize, or delete in favor of the ontology review PR.
+# --
+# This github action is from the copier template in https://github.com/ai4curation/github-ai-integrations, donated by the Monarch Initiative
+# For more documentation, see https://ai4curation.github.io/aidocs/how-tos/set-up-github-actions/
+# Author: Chris Mungall (@cmungall)
+name: Claude Code Ontology Review
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+    paths:
+      - "src/ontology"
+
+jobs:
+  claude-review:
+    # Optional: Filter by PR author
+    # if: |
+    #   github.event.pull_request.user.login == 'external-contributor' ||
+    #   github.event.pull_request.user.login == 'new-developer' ||
+    #   github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
+    
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code Ontology Review
+        id: claude-review
+        uses: anthropics/claude-code-action@beta
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+
+          # Optional: Specify model (commenting defaults to Claude Sonnet 4)
+          model: "claude-opus-4-1-20250805"
+
+          # Direct prompt for automated review (no @claude mention needed)
+          direct_prompt: |
+            REPO: ${{ github.repository }}
+            PR NUMBER: ${{ github.event.pull_request.number }}
+
+            This PR modifies critical ontology files.
+
+            Review this PR against our team checklist:
+
+            ## Issue alignment
+            - [ ] The PR aligns with the source issue, and only closes it if all components of the issue addressed
+            - [ ] The PR summary gives sufficient context for any decisions made, attributing them to issue authors where appropriate
+
+            ## Ontology Metadata
+            - [ ] PR is linked to source issue(s) via appropriate annotation property
+            - [ ] any added definitions have provenance
+
+            ## Identifiers and hallucinations
+            - [ ] all identifiers are CURIEs (or URLs), with standard prefixes
+            - [ ] I have looked up term identifiers and confirm that they denote what is intended
+            - [ ] all PMIDs and publication references resolve to the appropriate article/title
+
+            ## Design patterns (DPs)
+            - [ ] any new terms conform to documented DPs for this ontology
+            - [ ] if the term fits into a DP, then the label is constructed in a standard way (although scientific norms prevail)
+            - [ ] if the term is compositional in nature, then it should conform to a DP, and have a relevant logical definition
+
+            ## Definitions (if the PR adds or updates a definition)
+            - [ ] Definitions are present for any new term
+            - [ ] Definitions conform to the style guide for this ontology
+            - [ ] Definitions follows genus-differentia form (while prioritizing normal scientific phrasing over awkward ontology language)
+            - [ ] The genus of the definition is an ancestor of the term
+            - [ ] The differentia of the definition are necessary and sufficient for distinguishing from the genus
+            - [ ] The definition has appropriate provenance
+            - [ ] I have looked up the provenance, and it is correct and relevant
+            - [ ] The label, definition, and logical definition (when present) are largely consistent
+
+            ## Relationships and logical axioms
+            - [ ] If a logical definition is not present, then there should be at least one is_a (subClassOf) to the most precise parent term
+            - [ ] If a logical definition is present, then there is reasonable expectation the term should classify precisely
+            - [ ] Other relationships are present to a reasonable degree and as dictated by the general ontology stye (e.g part-ofs for anatomy)
+            - [ ] Additional logical axioms (such as disjointness) are added as appropriate, depending on ontology style, and design patterns
+            - [ ] Additional logical axioms make sense and do not over-constrain
+            
+            Be constructive and helpful in your feedback.
+
+          # Optional: Use sticky comments to make Claude reuse the same comment on subsequent pushes to the same PR
+          use_sticky_comment: true
+          
+          # Optional: Customize review based on file types
+          # direct_prompt: |
+          #   Review this PR focusing on:
+          #   - For TypeScript files: Type safety and proper interface usage
+          #   - For API endpoints: Security, input validation, and error handling
+          #   - For React components: Performance, accessibility, and best practices
+          #   - For tests: Coverage, edge cases, and test quality
+          
+          # Optional: Different prompts for different authors
+          # direct_prompt: |
+          #   ${{ github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR' && 
+          #   'Welcome! Please review this PR from a first-time contributor. Be encouraging and provide detailed explanations for any suggestions.' ||
+          #   'Please provide a thorough code review focusing on our coding standards and best practices.' }}
+          
+          # Optional: Add specific tools for running tests or linting
+          # allowed_tools: "Bash(npm run test),Bash(npm run lint),Bash(npm run typecheck)"
+          
+          # Optional: Skip review for certain conditions
+          # if: |
+          #   !contains(github.event.pull_request.title, '[skip-review]') &&
+          #   !contains(github.event.pull_request.title, '[WIP]')
+
diff --git a/.github/workflows/claude.yml b/.github/workflows/claude.yml
new file mode 100644
index 0000000..e1d4a43
--- /dev/null
+++ b/.github/workflows/claude.yml
@@ -0,0 +1,90 @@
+name: Claude Code
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  claude:
+    if: |
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
+      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+      issues: write
+      id-token: write
+      actions: read # Required for Claude to read CI results on PRs
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+            
+      - name: Install python tools
+        run: |
+          uv sync
+
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@beta
+        
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          mcp_config: |
+            {
+              "mcpServers": {
+                "ols": {
+                  "command": "uvx",
+                  "args": [
+                    "ols-mcp"
+                  ]
+                },
+                "sequential-thinking": {
+                  "command": "npx",
+                  "args": [
+                    "-y",
+                    "@modelcontextprotocol/server-sequential-thinking"
+                  ]
+                }
+              }
+            }
+
+          # This is an optional setting that allows Claude to read CI results on PRs
+          additional_permissions: |
+            actions: read
+          
+          # Optional: Specify model (defaults to Claude Sonnet 4, uncomment for Claude Opus 4.1)
+          # model: "claude-opus-4-1-20250805"
+          
+          # Optional: Customize the trigger phrase (default: @claude)
+          # trigger_phrase: "/claude"
+          
+          # Optional: Trigger when specific user is assigned to an issue
+          # assignee_trigger: "claude-bot"
+          
+          # Optional: Allow Claude to run specific commands
+          allowed_tools: "Bash(*),FileEdit,Edit,MultiEdit,WebSearch,WebFetch,mcp__ols_mcp__search_all_ontologies,mcp__ols_mcp__get_terms_from_ontology"
+          
+          # Optional: Add custom instructions for Claude to customize its behavior for your project
+          # custom_instructions: |
+          #   Follow our coding standards
+          #   Ensure all new code has tests
+          #   Use TypeScript for new files
+          
+          # Optional: Custom environment variables for Claude
+          # claude_env: |
+          #   NODE_ENV: test
+
diff --git a/.github/workflows/dragon-ai.yml b/.github/workflows/dragon-ai.yml
new file mode 100644
index 0000000..584bb43
--- /dev/null
+++ b/.github/workflows/dragon-ai.yml
@@ -0,0 +1,190 @@
+name: Dragon AI Agent GitHub Mentions
+
+env:
+  ROBOT_VERSION: v1.9.7
+  TOOLS_DIR: ${{ github.workspace }}/tools
+
+on:
+  issues:
+    types: [opened, edited]
+  issue_comment:
+    types: [created, edited]
+  pull_request:
+    types: [opened, edited]
+  pull_request_review_comment:
+    types: [created, edited]
+
+jobs:
+  check-mention:
+    runs-on: ubuntu-latest
+    outputs:
+      result: ${{ steps.check.outputs.result }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        # this seems to be necessary to ensure actions uses the latest; see
+        # https://github.com/actions/checkout/issues/439
+        with:
+          ref: ${{ github.ref }}
+        
+      - name: Check for qualifying mention
+        id: check
+        uses: actions/github-script@v6
+        with:
+          github-token: ${{ secrets.PAT_FOR_PR }}  # Use PAT instead of default token
+          script: |
+            // Load allowed users from config
+            const fs = require('fs');
+            let allowedUsers = [];
+            try {
+              const configContent = fs.readFileSync('.github/ai-controllers.json', 'utf8');
+              allowedUsers = JSON.parse(configContent);
+            } catch (error) {
+              console.log('Error loading allowed users:', error);
+              allowedUsers = ['cmungall']; // Fallback
+            }
+            
+            // Get content and user from event payload directly to avoid API calls when possible
+            let content = '';
+            let userLogin = '';
+            let itemType = '';
+            let itemNumber = 0;
+            
+            if (context.eventName === 'issues') {
+              content = context.payload.issue.body || '';
+              userLogin = context.payload.issue.user.login;
+              itemType = 'issue';
+              itemNumber = context.payload.issue.number;
+            } else if (context.eventName === 'pull_request') {
+              content = context.payload.pull_request.body || '';
+              userLogin = context.payload.pull_request.user.login;
+              itemType = 'pull_request';
+              itemNumber = context.payload.pull_request.number;
+            } else if (context.eventName === 'issue_comment') {
+              content = context.payload.comment.body || '';
+              userLogin = context.payload.comment.user.login;
+              itemType = 'issue';
+              itemNumber = context.payload.issue.number;
+            } else if (context.eventName === 'pull_request_review_comment') {
+              content = context.payload.comment.body || '';
+              userLogin = context.payload.comment.user.login;
+              itemType = 'pull_request';
+              itemNumber = context.payload.pull_request.number;
+            }
+            
+            // Check if user is allowed and mention exists
+            const isAllowed = allowedUsers.includes(userLogin);
+            const mentionRegex = /@dragon-ai-agent\s+please\s+(.*)/i;
+            const mentionMatch = content.match(mentionRegex);
+            
+            const qualifiedMention = isAllowed && mentionMatch !== null;
+            const prompt = qualifiedMention ? mentionMatch[1].trim() : '';
+            
+            console.log(`User: ${userLogin}, Allowed: ${isAllowed}, Has mention: ${mentionMatch !== null}`);
+            
+            return {
+              qualifiedMention,
+              itemType,
+              itemNumber,
+              prompt,
+              user: userLogin,
+              controllers: allowedUsers.map(u => '@' + u).join(', ')
+            };
+
+  respond-to-mention:
+    needs: check-mention
+    if: fromJSON(needs.check-mention.outputs.result).qualifiedMention == true
+    permissions:
+      contents: write
+      pull-requests: write
+      issues: write
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.ref }}
+          token: ${{ secrets.PAT_FOR_PR }}  # Use PAT for checkout to allow committing later
+
+      - name: Configure Git
+        run: |
+          git config --global user.name "Dragon-AI Agent"
+          git config --global user.email "dragon-ai-agent[bot]@users.noreply.github.com"
+      
+      - name: Create tools directory
+        run: mkdir -p ${{ env.TOOLS_DIR }}
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v3
+        with:
+          node-version: '18'
+
+      - name: install claude
+        run: |
+          npm install -g @anthropic-ai/claude-code
+
+      
+      - name: Add tools to PATH
+        run: |
+          echo "${{ env.TOOLS_DIR }}" >> $GITHUB_PATH
+          ls -alt ${{ github.workspace }}
+          ls -alt ${{ env.TOOLS_DIR }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+          
+      - name: Install python tools
+        run: |
+          uv venv
+          source .venv/bin/activate
+
+      - name: Set up environment
+        run: |
+          # Safely write prompt to file
+          mkdir -p /tmp/claude-input
+          echo "${{ fromJSON(needs.check-mention.outputs.result).prompt }}" > /tmp/claude-input/prompt.txt
+
+      - name: Create structured Claude prompt
+        env:
+          CLAUDE_CODE_OAUTH_TOKEN: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
+          GH_TOKEN: ${{ secrets.PAT_FOR_PR }} 
+        run: |
+          cat > /tmp/claude-input/claude_prompt.txt << EOL
+          You are @dragon-ai-agent.
+          You're responding to a request from or relayed by @${{ fromJSON(needs.check-mention.outputs.result).user }} on GitHub ${{ fromJSON(needs.check-mention.outputs.result).itemType }} #${{ fromJSON(needs.check-mention.outputs.result).itemNumber }}.
+          You only respond to requests from the following authorized controllers: ${{ fromJSON(needs.check-mention.outputs.result).controllers }}.
+
+          You should use \`gh\` to communicate with the user via the GitHub issue/ticket.
+          If instructed to modify files, you should make changes on a branch and submit a PR, communicating clearly and in
+          detail on the PR.
+
+          Always end by informing the user what you did (or were not able to do) with a message, either on an issue or a PR,
+          as appropriate.
+          
+          The request is below, enclosed in triple backticks:
+          \`\`\`
+          $(cat /tmp/claude-input/prompt.txt)
+          \`\`\`
+
+          However, you should use `gh` to read the complete context of the request, and look at any linked issues or PRs
+          that provide additional context.
+
+          EOL
+      
+      
+      - name: Run Claude Code in headless mode
+        id: claude-response
+        env:
+          CLAUDE_CODE_OAUTH_TOKEN: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+
+          export PATH="${{ env.TOOLS_DIR }}:$PATH"
+
+          # Run Claude with proper permissions
+          claude -p "$(cat /tmp/claude-input/claude_prompt.txt)" \
+            --permission-mode bypassPermissions \
+            --output-format stream-json \
+            --verbose 
+          
diff --git a/.goosehints b/.goosehints
new file mode 120000
index 0000000..47dc3e3
--- /dev/null
+++ b/.goosehints
@@ -0,0 +1 @@
+AGENTS.md
\ No newline at end of file
diff --git a/AGENTS.md b/AGENTS.md
new file mode 100644
index 0000000..e1ffe42
--- /dev/null
+++ b/AGENTS.md
@@ -0,0 +1,77 @@
+# AGENTS.md for semantic-sql
+
+SQL and SQLite builds of common OWL ontologies, including all of OBO
+
+TODO: fill in extra description here
+
+## Repo management
+
+This repo uses `uv` for managing dependencies. Never use commands like `pip` to add or manage dependencies.
+`uv run` is the best way to run things, unless you are using `justfile` or `makefile` target
+
+`mkdocs` is used for documentation.## This is a LinkML Schema repository
+
+Layout:
+
+ * `src/semantic_sql/schema/semantic_sql.yaml` - LinkML source schema (edit this)
+ * `project` - derived files (do not edit these directly, they are derived from the LinkML)
+ * `src/docs` - source markdown for documentation
+ * `docs` - derived docs - do not edit these directly
+ * `src/data/examples/{valid,invalid}` - example data files
+    * always include positive examples of each class in the `valid` subfolder
+    * include negative examples for unit tests and to help illustrate pitfalls
+    * format is `ClassName-{SOMENAME}.yaml`
+ * `examples` - derived examples. Do not edit these directly
+
+Building and testing:
+
+* `just --list` to see all commands
+* `just gen-project` to generate `project` files
+* `just test` to test schema and pos/neg examples
+* `just lint` analogous to ruff for python
+
+These are wrappers on top of existing linkml commands such as `gen-project`, `linkml-convert`, `linkml-run-examples`.
+You can run the underlying commands (with `uv run ...`) but in general justfile targets should be favored.
+
+Best practice:
+
+* For full documentation, see https://linkml.io/linkml/
+* Follow LinkML naming conventions (CamelCase for classes, snake_case for slots/attributes)
+* For schemas with polymorphism, consider using field `type` marked as a `type_designator: true`
+* Include meaningful descriptions of each element
+* map to standards where appropriate (e.g. dcterms)
+* Never guess OBO term IDs. Always use the OLS MCP to look for relevant ontology terms
+* be proactive in using due diligence to do deep research on the domain, and look at existing standards## This is a Python repository
+
+Layout:
+
+ * `src/semantic_sql/` - Code goes here
+ * `docs` - mkdocs docs
+ * `mkdocs.yml` - index of docs
+ * `tests/input` - example files
+
+Building and testing:
+
+* `just --list` to see all commands
+* `just test` performs unit tests, doctests, ruff/liniting
+* `just test-full` as above plus integration tests
+
+You can run the underlying commands (with `uv run ...`) but in general justfile targets should be favored.
+
+Best practice:
+
+* Use doctests liberally - these serve as both explanatory examples for humans and as unit tests
+* For longer examples, write pytest tests
+* always write pytest functional style rather than unittest OO style
+* use modern pytest idioms, including `@pytest.mark.parametrize` to test for combinations of inputs
+* NEVER write mock tests unless requested. I need to rely on tests to know if something breaks
+* For tests that have external dependencies, you can do `@pytest.mark.integration`
+* Do not "fix" issues by changing or weakening test conditions. Try harder, or ask questions if a test fails.
+* Avoid try/except blocks, these can mask bugs
+* Fail fast is a good principle
+* Follow the DRY principle
+* Avoid repeating chunks of code, but also avoid premature over-abstraction
+* Pydantic or LinkML is favored for data objects
+* For state in engine-style OO classes, dataclasses is favored
+* Declarative principles are favored
+* Always use type hints, always document methods and classes
\ No newline at end of file
diff --git a/CLAUDE.md b/CLAUDE.md
new file mode 120000
index 0000000..47dc3e3
--- /dev/null
+++ b/CLAUDE.md
@@ -0,0 +1 @@
+AGENTS.md
\ No newline at end of file