PubTator 3 MCP — biomedical entity search, literature search with entity
Setup
Choose your client, copy the config, then fill in any required environment variables.
claude mcp add --transport http pubtator https://gateway.pipeworx.io/pubtator/mcp~/.codex/config.toml
[mcp_servers.pubtator]
url = "https://gateway.pipeworx.io/pubtator/mcp"
# codex mcp add pubtator --url https://gateway.pipeworx.io/pubtator/mcp~/.cursor/mcp.json
{
"mcpServers": {
"pubtator": {
"url": "https://gateway.pipeworx.io/pubtator/mcp"
}
}
}.vscode/mcp.json
{
"servers": {
"pubtator": {
"type": "http",
"url": "https://gateway.pipeworx.io/pubtator/mcp"
}
}
}~/.gemini/settings.json
{
"mcpServers": {
"pubtator": {
"httpUrl": "https://gateway.pipeworx.io/pubtator/mcp"
}
}
}claude_desktop_config.json · Customize › Connectors › Add custom connector
{
"mcpServers": {
"pubtator": {
"command": "npx",
"args": [
"-y",
"mcp-remote",
"https://gateway.pipeworx.io/pubtator/mcp"
]
}
}
}.trae/mcp.json
{
"mcpServers": {
"pubtator": {
"url": "https://gateway.pipeworx.io/pubtator/mcp"
}
}
}