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.

Managed

13 tools

Agent guide included

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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?

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 MCP server groups tools behind an endpoint that many clients can use.