Open Data

BridgeDB MCP Server

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BridgeDB is a biological identifier mapping service that helps researchers convert between different gene, protein, and metabolite database identifiers. Map identifiers across multiple biological databases and retrieve cross-references for bioinformatics research.

13 tools
Agent guide included
No auth required
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AI Skill
SKILL.md

Domain knowledge for BridgeDB — workflow patterns, data models, and gotchas for your AI agent.

BridgeDB

BridgeDB maps biological identifiers across gene, protein, and metabolite databases. No auth.

Data Model

  • Organisms use short codes (e.g. Hs = Homo sapiens). All operations require organism.
  • Data sources: Source and target systems. system_code from list. Required for mappings.
  • Mappings: Check supported mappings; get cross-references. Need system_code and identifier.
  • Search: By query. Returns identifier for use in attribute and xref operations.
  • Hierarchy: organism → system_code (from sourceDataSources) → identifier (from search) → xrefs/attributes.

Tools in this Server (13)

Get Organism Attributesearch Query

Returns a list of xrefs and associated attributes that contain the query string for a given organism. Results are not restricted to exact matches. Opt...

Get Organism Attributeset

Returns the supported attributes to the given Organism.

Get Organism Attributes Systemcode Identifier

Returns the attributes for a given identifier, data source, organism. Optionally display only a specified attribute

Get Organism Isfreesearchsupported

Returns `true` or `false` based on whether or not /{organism}/search/{query} is supported for a given organism.

Get Organism Mapping Supported

Returns `true` or `false` based on whether or not /{organism}/xrefs/{systemCode}/{identifier} would possibly return a {targetSystemCode} result given ...

Get Organism Properties

Returns the list of properties available for a given organism

Get Organism Search Query

Returns a list of xrefs with identifiers that contain the query string for a given organism. Results are not restricted to exact matches. Optionally l...

Get Organism Sourcedatasources

Returns a list of data sources available as xref sources for a given organism.

Get Organism Targetdatasources

Returns a list of data sources available as xref targets for a given organism.

Get Organism Xrefexists Systemcode Identifier

Returns `true` or `false` based on whether or not an xref exists in the database given an identifier, data source, and organism.

Get Organism Xrefs Systemcode Identifier

Returns a list of xrefs that map to a given identifier, data source, and organism.

Post Organism Xrefsbatch

Returns a list of xrefs, per identifier, that maps to a given list of identifiers an data source given an organism.

Post Organism Xrefsbatch Systemcode

Returns a list of xrefs, that maps to a given list of identifiers to a given data source and organism.

Frequently Asked Questions

What is the BridgeDB MCP server?

BridgeDB is a biological identifier mapping service that helps researchers convert between different gene, protein, and metabolite database identifiers. Map identifiers across multiple biological databases and retrieve cross-references for bioinformatics research. It provides 13 tools that AI agents can use through the Model Context Protocol (MCP).

How do I connect BridgeDB to my AI agent?

Add the MCPBundles server URL to your MCP client configuration (Claude Desktop, Cursor, VS Code, etc.). The URL format is: https://mcp.mcpbundles.com/bundle/bridgedb-org. Authentication is handled automatically.

How many tools does BridgeDB provide?

BridgeDB provides 13 tools that can be called by AI agents, along with a SKILL.md that gives your AI agent domain knowledge about when and how to use them.

What authentication does BridgeDB require?

BridgeDB uses open data APIs — no authentication required.

Setup Instructions

Connect BridgeDB to any MCP client in minutes

https://mcp.mcpbundles.com/bundle/bridgedb-org

What is MCP?

Model Context Protocol lets AI tools call external capabilities securely through a single URL. This bundle groups tools behind an MCP endpoint that many clients can use.

Use this bundle in 3 steps

  1. Copy the MCP URL above
  2. Open your AI tool and add a new MCP/connector
  3. Paste the URL and follow any auth prompts

Claude Desktop Users

Skip the manual setup! Use the .mcpb file format for one-click installation. Check the Claude Desktop tab for setup instructions.

Pick your tool tab for exact steps

Select ChatGPT, Cursor, Claude Code, or another tab for copy-paste config.

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BridgeDB MCP Server & Skill — 13 Tools