MCP Server Proto-OKN

## Installation ### Prerequisites The MCP Proto-OKN server requires the `uv` package manager to be installed on your system. If you don't have it installed run: ```bash # macOS/Linux curl -LsSf https://astral.sh/uv/install.sh | sh ``` ``` # Windows powershell -c "irm https://astral.sh/uv/install.ps1 | iex" ``` > **Note**: Once `uv` is installed, the `uvx` command in the configuration below will automatically download and run the latest version from PyPI when needed. ### Claude Desktop Setup **Recommended for most users** 1. **Download and Install Claude Desktop** Visit [https://claude.ai/download](https://claude.ai/download) and install Claude Desktop for your operating system. > **Requirements**: Claude Pro or Max subscription is required for MCP server functionality. 2. **Configure MCP Server** **Option A: Download Pre-configured File (Recommended)** Download the pre-configured `claude_desktop_config.json` file with FRINK endpoints from the repository and copy it to the appropriate location: **macOS**: ```bash # Download the config file curl -o /tmp/claude_desktop_config.json https://raw.githubusercontent.com/sbl-sdsc/mcp-proto-okn/main/config/claude_desktop_config.json # Copy to Claude Desktop configuration directory cp /tmp/claude_desktop_config.json "$HOME/Library/Application Support/Claude/" ``` **Windows PowerShell**: ```powershell # Download the config file Invoke-WebRequest -Uri "https://raw.githubusercontent.com/sbl-sdsc/mcp-proto-okn/main/config/claude_desktop_config.json" -OutFile "$env:TEMP\claude_desktop_config.json" # Copy to Claude Desktop configuration directory Copy-Item "$env:TEMP\claude_desktop_config.json" "$env:APPDATA\Claude\" ``` **Option B: Manual Configuration** Alternatively, you can manually edit the configuration file in Claude Desktop. Navigate to `Claude->Settings->Developer->Edit Config` to edit it. Below is an example of how to configure FRINK endpoints. Third-party SPARQL endpoints with a custom description can be added (see uniprot-sparql example below). ```json { "mcpServers": { "spoke-okn": { "command": "uvx", "args": [ "mcp-proto-okn", "--endpoint", "https://frink.apps.renci.org/spoke-okn/sparql" ] }, "biobricks-ice": { "command": "uvx", "args": [ "mcp-proto-okn", "--endpoint", "https://frink.apps.renci.org/biobricks-ice/sparql" ] }, "uniprot": { "command": "uvx", "args": [ "mcp-proto-okn", "--endpoint", "https://sparql.uniprot.org/sparql", "--description", "Resource for protein sequence and function information. For details: https://purl.uniprot.org/html/index-en.htm" ] } } } ``` > **Important**: If you have existing MCP server configurations, do not use Option A as it will overwrite your existing configuration. Instead, use Option B and manually merge the Proto-OKN endpoints with your existing `mcpServers` configuration. 3. **Restart Claude Desktop** After saving the configuration file, quit Claude Desktop completely and restart it. The application needs to restart to load the new configuration and start the MCP servers. 4. **Verify Installation** 1. Launch Claude Desktop 2. Navigate to `Claude->Settings->Connectors` 3. Verify that the configured Proto-OKN endpoints appear in the connector list 4. You can configure each service to always ask for permission or to run it unsupervised (recommended) ### VS Code Setup **For advanced users and developers** 1. **Install VS Code Insiders** Download and install VS Code Insiders from [https://code.visualstudio.com/insiders/](https://code.visualstudio.com/insiders/) > **Note**: VS Code Insiders is required as it includes the latest MCP (Model Context Protocol) features. 2. **Install GitHub Copilot Extension** - Open VS Code Insiders - Sign in with your GitHub account - Install the GitHub Copilot extension > **Requirements**: GitHub Copilot subscription is required for MCP integration. 3. **Configure MCP Server** **Option A: Download Pre-configured File (Recommended)** Download the pre-configured `mcp.json` file with FRINK endpoints from the repository and copy it to the appropriate location. **macOS**: ```bash # Download the config file curl -o /tmp/mcp.json https://raw.githubusercontent.com/sbl-sdsc/mcp-proto-okn/main/config/mcp.json # Copy to VS Code Insiders configuration directory cp /tmp/mcp.json "$HOME/Library/Application Support/Code - Insiders/User/mcp.json" ``` > **Note**: VS Code Insiders mcp.json file is identical to the claude_desktop_config.json file, except "mcpServer" is replace by "server". 4. **Use the MCP Server** 1. Open a new chat window in VS Code 2. Select **Agent** mode 3. Choose **Claude Sonnet 4.5 or later** model for optimal performance 4. The MCP servers will automatically connect and provide knowledge graph access