BioMapper for VS Code
io.github.trentleslie/biomapper
Resolve metabolite, lipid, protein, gene and lab names to knowledge-graph IDs.
client:VS Code
transport:stdio
runtime:pypi
Install BioMapper in VS Code
.vscode/mcp.json
{
"inputs": [
{
"type": "promptString",
"id": "biomapper-mcp-roots",
"description": "BIOMAPPER_MCP_ROOTS",
"password": true
},
{
"type": "promptString",
"id": "biomapper-api-key",
"description": "BIOMAPPER_API_KEY",
"password": true
},
{
"type": "promptString",
"id": "biomapper-base-url",
"description": "BIOMAPPER_BASE_URL",
"password": true
},
{
"type": "promptString",
"id": "biomapper-mcp-home",
"description": "BIOMAPPER_MCP_HOME",
"password": true
}
],
"servers": {
"biomapper": {
"type": "stdio",
"command": "uvx",
"args": [
"biomapper"
],
"env": {
"BIOMAPPER_MCP_ROOTS": "${input:biomapper-mcp-roots}",
"BIOMAPPER_API_KEY": "${input:biomapper-api-key}",
"BIOMAPPER_BASE_URL": "${input:biomapper-base-url}",
"BIOMAPPER_MCP_HOME": "${input:biomapper-mcp-home}"
}
}
}
}VS Code prompts for each input the first time the server starts, so no secret is written to the file. VS Code docs