Connect your AI Agents to PubMed in minutes
Available tools
match_citations
Match partial citation information to PubMed IDs. Provide journal name, year, and optionally volume, first page, and author name. Useful for finding PMIDs when you have bibliographic information but not the PMID.
fetch_articles
Fetch full article data (title, abstract, authors, journal, DOI) by PMIDs. Use search_pubmed first to get PMIDs. Returns structured article data including abstracts and author information. Max 200 IDs per request.
get_database_info
Get information about NCBI databases. Without db parameter, returns list of all available databases. With db parameter, returns details including searchable fields, record counts, and available links to other databases.
find_related_articles
Find articles related to given PMIDs using PubMed's similarity algorithm. Can also find links between databases (e.g., PubMed to PMC, PubMed to Gene). Returns scored results by relevance.
search_pubmed
Search PubMed for biomedical articles by keywords, authors, dates, or MeSH terms. Returns PMIDs which can be used with fetch_articles to get full article data. Supports date filtering and field-specific searches.
get_article_summaries
Get quick document summaries for multiple PMIDs. Faster than fetch_articles but with less detail. Returns title, authors, journal, publication date, and identifiers. Max 500 IDs per request.
How to set up Merge Agent Handler
In an mcp.json file, add the configuration below, and restart Cursor.
Learn more in the official documentation ↗
1{
2 "mcpServers": {
3 "agent-handler": {
4 "url": "https://ah-api-develop.merge.dev/api/v1/tool-packs/{TOOL_PACK_ID}/registered-users/{REGISTERED_USER_ID}/mcp",
5 "headers": {
6 "Authorization": "Bearer yMt*****"
7 }
8 }
9 }
10}
11Open your Claude Desktop configuration file and add the server configuration below. You'll also need to restart the application for the changes to take effect.
Make sure Claude is using the Node v20+.
Learn more in the official documentation ↗
1{
2 "mcpServers": {
3 "agent-handler": {
4 "command": "npx",
5 "args": [
6 "-y",
7 "mcp-remote@latest",
8 "https://ah-api-develop.merge.dev/api/v1/tool-packs/{TOOL_PACK_ID}/registered-users/{REGISTERED_USER_ID}/mcp",
9 "--header",
10 "Authorization: Bearer ${AUTH_TOKEN}"
11 ],
12 "env": {
13 "AUTH_TOKEN": "yMt*****"
14 }
15 }
16 }
17}Open your Windsurf MCP configuration file and add the server configuration below.
Click on the refresh button in the top right of the Manage MCP server page or in the top right of the chat box in the box icon.
Learn more in the official documentation ↗
1{
2 "mcpServers": {
3 "agent-handler": {
4 "command": "npx",
5 "args": [
6 "-y",
7 "mcp-remote@latest",
8 "https://ah-api.merge.dev/api/v1/tool-packs/<tool-pack-id>/registered-users/<registered-user-id>/mcp",
9 "--header",
10 "Authorization: Bearer ${AUTH_TOKEN}"
11 ],
12 "env": {
13 "AUTH_TOKEN": "<ah-production-access-key>"
14 }
15 }
16 }
17 }In Command Palette (Cmd+Shift+P on macOS, Ctrl+Shift+P on Windows), run "MCP: Open User Configuration".
You can then add the configuration below and press "start" right under servers. Enter the auth token when prompted.
Learn more in the official documentation ↗
1{
2 "inputs": [
3 {
4 "type": "promptString",
5 "id": "agent-handler-auth",
6 "description": "Agent Handler AUTH_TOKEN", // "yMt*****" when prompt
7 "password": true
8 }
9 ],
10 "servers": {
11 "agent-handler": {
12 "type": "stdio",
13 "command": "npx",
14 "args": [
15 "-y",
16 "mcp-remote@latest",
17 "https://ah-api-develop.merge.dev/api/v1/tool-packs/{TOOL_PACK_ID}/registered-users/{REGISTERED_USER_ID}/mcp",
18 "--header",
19 "Authorization: Bearer ${input:agent-handler-auth}"
20 ]
21 }
22 }
23}FAQs on using Merge's PubMed MCP server
FAQs on using Merge's PubMed MCP server
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