How do I use Sage MCP?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type `@` followed by the MCP server name and your instructions, e.g., "`@Sage MCP` Find recent research papers about machine learning interpretability" That's it! The server will respond to your query, and you can continue using it as needed. Here is a [step-by-step guide with screenshots](https://glama.ai/blog/2025-07-08-how-to-install-and-use-mcp-servers).

Sage MCP - Academic Research Server

An MCP (Model Context Protocol) server that provides LLMs with access to academic papers and periodicals for research-grounded responses.

Features

Full-text search across papers using SQLite FTS5
Topic/publication filtering for targeted research
Paper retrieval with full content for detailed analysis
Extensible database - add your own papers programmatically

Tools Available

Tool	Description
`search_papers`	Semantic/keyword search across all papers
`get_paper`	Retrieve full paper content by ID
`list_topics`	Browse available research topics
`list_publications`	Browse available journals/sources
`get_papers_by_topic`	Filter papers by topic
`get_papers_by_publication`	Filter papers by journal
`add_paper`	Add new papers to the database

Quick Start (Local Setup)

Prerequisites

Node.js 18+ (recommended: 20 LTS)
npm 9+

1. Clone/Download and Install

cd C:\AIapps\SageMCP # or your chosen directory npm install npm run build

2. Seed the Database

# Option A: Sample papers (10 ML/AI papers) npm run seed # Option B: Import from XML (if you have papers_database.xml) npm run import-xml

3. Verify Installation

npm start # Should output: "Sage MCP Server running on stdio" # Press Ctrl+C to stop

Connecting to MCP Clients

Claude Desktop (Windows)

Locate config file:
%APPDATA%\Claude\claude_desktop_config.json
Usually: C:\Users\<YourName>\AppData\Roaming\Claude\claude_desktop_config.json
Edit the config (create if doesn't exist):
{ "mcpServers": { "sage": { "command": "node", "args": ["C:/AIapps/SageMCP/dist/index.js"] } } }
Restart Claude Desktop completely (quit from system tray, reopen)
Verify connection: Look for the hammer 🔨 icon in Claude's chat input - click it to see available tools

Claude Desktop (macOS)

Config location:
~/Library/Application Support/Claude/claude_desktop_config.json
Config content:
{ "mcpServers": { "sage": { "command": "node", "args": ["/Users/<you>/path/to/SageMCP/dist/index.js"] } } }

Windsurf / Cascade

Add to your MCP settings (Settings → MCP Servers):

{ "sage": { "command": "node", "args": ["C:/AIapps/SageMCP/dist/index.js"] } }

Cline (VS Code Extension)

Open VS Code settings
Search for "Cline MCP"
Add server configuration:
{ "sage": { "command": "node", "args": ["C:/AIapps/SageMCP/dist/index.js"] } }

Custom MCP Client (Programmatic)

import { Client } from '@modelcontextprotocol/sdk/client/index.js'; import { StdioClientTransport } from '@modelcontextprotocol/sdk/client/stdio.js'; const transport = new StdioClientTransport({ command: 'node', args: ['C:/AIapps/SageMCP/dist/index.js'], }); const client = new Client({ name: 'my-client', version: '1.0.0' }, {}); await client.connect(transport); // List available tools const tools = await client.listTools(); console.log(tools); // Call a tool const result = await client.callTool({ name: 'search_papers', arguments: { query: '神學', limit: 5 } }); console.log(result);

Configuration

Environment Variables

Variable	Description	Default
`SAGE_DB_PATH`	Custom database file path	`./data/sage.db`

Example with custom DB path:

{ "mcpServers": { "sage": { "command": "node", "args": ["C:/AIapps/SageMCP/dist/index.js"], "env": { "SAGE_DB_PATH": "D:/Research/my_papers.db" } } } }

Adding Your Own Papers

Via the MCP Tool

LLMs can use the add_paper tool directly to add papers.

Via XML Import

Place your XML file in data/ and run:

npm run import-xml -- ./data/your_papers.xml

Programmatically

import { initDb, addPaper } from './dist/db.js'; await initDb(); addPaper({ title: 'Your Paper Title', authors: 'Author One, Author Two', abstract: 'Paper abstract...', content: 'Full paper content...', publication: 'Journal Name', publication_date: '2024-01-15', doi: '10.1234/example', url: 'https://example.com/paper', topics: 'Topic1, Topic2', keywords: 'keyword1, keyword2, keyword3' });

Database Schema

Papers are stored in SQLite with full-text search indexing:

Field	Type	Description
`id`	INTEGER	Auto-incrementing primary key
`title`	TEXT	Paper title
`authors`	TEXT	Comma-separated author list
`abstract`	TEXT	Paper abstract
`content`	TEXT	Full paper text
`publication`	TEXT	Journal/conference name
`publication_date`	TEXT	Publication date (YYYY-MM-DD)
`doi`	TEXT	DOI identifier (optional)
`url`	TEXT	URL to paper (optional)
`topics`	TEXT	Comma-separated topics
`keywords`	TEXT	Comma-separated keywords

VPS Deployment

Single command deploys everything (from your local machine):

# Windows PowerShell .\deploy\deploy.ps1 -VpsHost "user@your-vps.com" # Linux/macOS ./deploy/deploy.sh user@your-vps.com

This automatically:

Installs Node.js and dependencies on VPS
Creates sage user and directories
Copies source files and database
Builds the project
Sets up and starts systemd service

Uninstall:

# Windows .\deploy\uninstall.ps1 -VpsHost "user@your-vps.com" # Linux/macOS (or directly on VPS) ./deploy/uninstall.sh

See deploy/README.md for detailed options and troubleshooting.

Troubleshooting

"Cannot find module" errors

npm run build # Rebuild TypeScript

Claude Desktop doesn't show tools

Check config JSON syntax (use a JSON validator)
Ensure path uses forward slashes: C:/path/to/file not C:\path\to\file
Restart Claude Desktop completely (quit from system tray)
Check Claude's logs: %APPDATA%\Claude\logs\

Database errors

# Reset database rm -rf data/sage.db npm run seed # or npm run import-xml

Test MCP server manually

echo '{"jsonrpc":"2.0","id":1,"method":"tools/list"}' | node dist/index.js

License

MIT

Sage MCP