Koskamo

Bioportal MCP

The Bioportal MCP server provides four tools to interact with NCBO's biomedical ontology repository. It allows agents to search ontologies for terms, list available ontologies, retrieve full class records by IRI, and find cross-ontology mappings for concepts.

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Package and access

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

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

What you can do with it

  • Search biomedical ontologies for terms and retrieve matching classes
  • List available biomedical ontologies to select the right vocabulary
  • Retrieve full class records including synonyms and definitions by IRI
  • Find cross-ontology mappings for equivalent concepts

Source and maintenance

Community listingRegistry 0.2.1
mcp-registry: io.github.pipeworx-io/bioportal@0.2.1Source repositoryProject website
Maintenance checked

Packages and installation

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

@pipeworx/mcp-bioportal 0.2.1

npm
@pipeworx/mcp-bioportal package definition
{
  "version": "0.2.1",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-bioportal",
  "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.

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": {
    "bioportal-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-bioportal@0.2.1"
      ],
      "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": {
    "bioportal-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-bioportal@0.2.1"
      ],
      "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": {
    "bioportal-mcp": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-bioportal@0.2.1"
      ],
      "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": {
    "bioportal-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-bioportal@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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