EBI BioStudies

FreeNot checked

Biological studies metadata and cross-database links from the EMBL-EBI BioStudies repository.

by pipeworx-io

GitHub Embed

About

Biological studies metadata and cross-database links from the EMBL-EBI BioStudies repository.

README

EBI BioStudies MCP.

Part of Pipeworx — an MCP gateway connecting AI agents to 1394+ live data sources.

Tools

Tool	Description
`search_studies`	Search EBI BioStudies — a keyless database of biological study descriptions that links across EBI archives (ArrayExpress, PRIDE, etc.). Find studies by keyword and get accession, title, authors, type, release date, and link/file counts.
`get_study`	Get the metadata for a single EBI BioStudies study by accession (e.g. "S-EPMC6010251"). Returns the title, flattened attributes (abstract, release date, data source, etc.), and counts of links and subsections. EBI BioStudies links across EBI archives. Keyless.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "biostudies": {
      "url": "https://gateway.pipeworx.io/biostudies/mcp"
    }
  }
}

Or connect to the full Pipeworx gateway for access to all 1394+ data sources:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English:

ask_pipeworx({ question: "your question about Biostudies data" })

The gateway picks the right tool and fills the arguments automatically.

License

MIT

from github.com/pipeworx-io/mcp-biostudies

Install EBI BioStudies in Claude Desktop, Claude Code & Cursor

Recommended · one command, every IDE

unyly install ebi-biostudies

Installs into Claude Desktop, Claude Code, Cursor & VS Code — handles npx, uvx and build-from-source repos for you.

First time? Get the CLI: curl -fsSL https://unyly.org/install | sh

Or configure manually

Run in your terminal:

claude mcp add ebi-biostudies -- npx -y @pipeworx/mcp-biostudies

Step-by-step: how to install EBI BioStudies

Install EBI BioStudies in Claude Desktop Install EBI BioStudies in Claude Code Install EBI BioStudies in Cursor Install EBI BioStudies in VS Code

FAQ

Is EBI BioStudies MCP free?

Yes, EBI BioStudies MCP is free — one-click install via Unyly at no cost.

Does EBI BioStudies need an API key?

No, EBI BioStudies runs without API keys or environment variables.

Is EBI BioStudies hosted or self-hosted?

Self-hosted: the server runs locally on your machine via the install command above.

How do I install EBI BioStudies in Claude Desktop, Claude Code or Cursor?

Open EBI BioStudies on unyly.org, pick your client tab (Claude Desktop, Claude Code, Cursor) and press Install — the config is generated automatically, no JSON editing.

Related MCPs

wenb1n-dev/SmartDB_MCP

A universal database MCP server supporting simultaneous connections to multiple databases. It provides tools for database operations, health analysis, SQL optim

by wenb1n-dev

Postgres Server

This server enables interaction with PostgreSQL databases through the Model Context Protocol, optimized for the AWS Bedrock AgentCore Runtime. It provides tools

by madhurprash

Postgres

Query your database in natural language

by Anthropic

PostgreSQL

Read-only database access with schema inspection.

by modelcontextprotocol

Compare EBI BioStudies with

EBI BioStudiesvswenb1n-dev/SmartDB_MCP EBI BioStudiesvsPostgres Server EBI BioStudiesvsPostgres EBI BioStudiesvsPostgreSQL

Not sure what to pick?

Find your stack in 60 seconds

Author?

Embed badge for your README

Browse similar

All data MCPs