Koskamo

NCBI Datasets MCP

The NCBI Datasets MCP server provides tools to access the US National Library of Medicine's genome, gene, and taxonomy reference data. It allows agents to list genome assemblies for organisms, look up genes by symbol, and resolve organisms in the NCBI Taxonomy tree, returning authoritative records such as assembly levels, gene descriptions, and lineage information.

Visit Pipeworx

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

NCBI Datasets MCP logo, by PipeworxCommunity listingLocal stdioSource reviewed; not executedPublished by Pipeworx
Vendor documentation

What you can do with it

  • List genome assemblies for a specific organism
  • Look up gene details by symbol
  • Resolve organism taxonomy lineage

Source and maintenance

Community listingRegistry 0.2.0MIT
mcp-registry: io.github.pipeworx-io/ncbi-datasets@0.2.0Source repositoryProject website
Last repository push
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

@pipeworx/mcp-ncbi-datasets 0.2.0

npm
@pipeworx/mcp-ncbi-datasets package definition
{
  "version": "0.2.0",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-ncbi-datasets",
  "registryType": "npm",
  "environmentVariables": [
    {
      "name": "PIPEWORX_API_KEY",
      "description": "Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Maintenance history

Public check and source-refresh events. Editorial and ownership records remain private.

  • · repository · passed · metadata changed · updated
  • · backfill · recorded · Pre-expansion baseline; unobserved rich metadata remains unknown

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "ncbi-datasets-mcp-pipeworx-mcp-ncbi-datasets": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ncbi-datasets@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "ncbi-datasets-mcp-pipeworx-mcp-ncbi-datasets": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ncbi-datasets@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "ncbi-datasets-mcp-pipeworx-mcp-ncbi-datasets": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ncbi-datasets@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "ncbi-datasets-mcp-pipeworx-mcp-ncbi-datasets": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ncbi-datasets@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Let your agent find its tools

Find servers like NCBI Datasets MCP from your agent. Add Koskamo once to search the index for endpoints, access requirements, and client setup. Public discovery needs no key.

Connect Koskamo Explore workflows
See all 4,469