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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.
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Domain knowledge for BridgeDB — workflow patterns, data models, and gotchas for your AI agent.
BridgeDB maps biological identifiers across gene, protein, and metabolite databases. No auth.
Get Organism Attribute Search 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. Optionally limit results to a specified number per data source, or by the type of attribute. See possible attribute types via /{organism}/attributeSet.
Get Organism Attribute Set
Returns the supported attributes to the given Organism.
Get Organism Attributes System Code Identifier
Returns the attributes for a given identifier, data source, organism. Optionally display only a specified attribute
Connect BridgeDB to any MCP client in minutes
Opens ChatGPT on the web or desktop and asks it to use the WebMCP tools available here.
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https://mcp.mcpbundles.com/bundle/bridgedb-orgSign in once, then chat here with saved access — one connection to many servers, with a history of what your AI ran.
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Browse all toolsGet Organism Is Free Search Supported
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 a {sourceSystemCode} query. This function basically combines the results of /{organism}/sourceDataSources and /{organism}/targetDataSources into a single boolean result.
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 limit results to a specified number per data source.
Get Organism Source Data Sources
Returns a list of data sources available as xref sources for a given organism.
Get Organism Target Data Sources
Returns a list of data sources available as xref targets for a given organism.
Get Organism Xref Exists System Code 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 System Code Identifier
Returns a list of xrefs that map to a given identifier, data source, and organism.
Post Organism Xrefs Batch
Returns a list of xrefs, per identifier, that maps to a given list of identifiers an data source given an organism.
Post Organism Xrefs Batch System Code
Returns a list of xrefs, that maps to a given list of identifiers to a given data source and organism.
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).
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.
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.
BridgeDB uses open data APIs — no authentication required.
© 2026 ThinkChain Inc. All rights reserved.
MCPBundles is an independent platform built on the open Model Context Protocol standard. Not affiliated with Anthropic PBC or Claude.
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