Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@BridgeDb MCP Server Map ENSG00000139618 to HGNC symbol"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
A Model Context Protocol server that exposes the BridgeDb identifier-mapping webservice as a small set of curated tools, so an LLM client (Claude Desktop, Claude Code, or any MCP-compatible client) can perform biological identifier mapping directly.
It is a thin, stateless proxy over https://webservice.bridgedb.org — it does
not reimplement any mapping logic. The value it adds over the raw REST API is
LLM-friendly tool descriptions, name→system-code guidance, and clean JSON output
instead of tab-delimited text.
Tool | Purpose |
| Translate data-source names to system codes (En, L, S, Ch, …) |
| Organisms loaded in the deployment |
| Valid source/target data sources for an organism |
| Check a source→target mapping is available before requesting it |
| Check an identifier exists |
| Map one identifier to equivalents (optionally to one target) |
| Map many identifiers (same source) in one call |
| Free-text identifier search |
| Annotation attributes (Symbol, Description, …) for an xref |
Resource bridgedb://system-codes returns the full system-code table.
BridgeDb works in xref pairs: an identifier plus the system code of the
data source that issued it. Always pass the code (En), never the name
(Ensembl). Use list_system_codes to translate.
Related MCP server: BioMCP
cd bridgedb-mcp
python -m venv .venv && source .venv/bin/activate
pip install -e .
# stdio transport (for Claude Desktop / Claude Code)
bridgedb-mcp
# or serve over HTTP
BRIDGEDB_MCP_TRANSPORT=streamable-http bridgedb-mcpEnv var | Default | Meaning |
|
| Webservice base URL (point at a local docker container if desired) |
|
|
|
|
| HTTP timeout in seconds |
{
"mcpServers": {
"bridgedb": {
"command": "bridgedb-mcp"
}
}
}Point BRIDGEDB_BASE_URL at your own deployment (e.g. the VHP4Safety
bridgedb.cloud.vhp4safety.nl service or a local docker container) via an env
block if you don't want to use the public endpoint.
"Map the human Ensembl gene ENSG00000139618 to its HGNC symbol and UniProt ID."
The client calls map_identifier(identifier="ENSG00000139618", source="En", target="H") and map_identifier(..., target="S"), returning BRCA2 and
P51587.
This server is a companion to the BridgeDb webservice, whose OpenAPI spec
(/swagger.yaml) and /llms.txt guide describe the same endpoints. Those docs
are the machine-readable contract; this MCP server is the runtime tool interface
built on top of them.
This server cannot be deployed
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