ensembl_lookup_gene
ActiveTool of io.github.cyanheads/ensembl-mcp-server
Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location (chr:start-end:strand), biotype, description, and transcript list. Entry point for most workflows — the stable ID and coordinates returned here are inputs to other tools. Accepts both symbol lookup (BRCA2 + homo_sapiens) and direct ID lookup (ENSG00000139618). Supports batch lookup of up to 20 IDs or symbols in one call via the ids or symbols field. Provide exactly one of symbol, id, ids, or symbols. For symbol lookups species defaults to homo_sapiens (override for other organisms); for ID lookups species is not needed. Use ensembl_list_species to discover valid species names.
Parameters schema
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"properties": {
"id": {
"type": "string",
"description": "Ensembl stable gene ID (e.g. ENSG00000139618 or ENSG00000139618.7 with version). Species is not required for ID lookup."
},
"ids": {
"type": "array",
"items": {
"type": "string",
"description": "An Ensembl stable gene or transcript ID to resolve in this batch."
},
"maxItems": 20,
"description": "Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols."
},
"symbol": {
"type": "string",
"description": "Gene symbol to look up (e.g. BRCA2, TP53, EGFR). Species defaults to homo_sapiens; set species for other organisms. Case-insensitive in most species."
},
"species": {
"type": "string",
"description": "Species in Ensembl internal format: lowercase scientific name with underscores (e.g. homo_sapiens, mus_musculus, danio_rerio). Optional for symbol lookups — defaults to homo_sapiens; set it for other organisms. Use ensembl_list_species to discover valid values."
},
"symbols": {
"type": "array",
"items": {
"type": "string",
"description": "A gene symbol to resolve in this batch (e.g. BRCA2, TP53)."
},
"maxItems": 20,
"description": "Batch lookup: up to 20 gene symbols. Species defaults to homo_sapiens; set species for other organisms. Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols."
},
"expand_transcripts": {
"type": "boolean",
"default": false,
"description": "When true, include the full transcript list in the response. Each transcript has its ID, biotype, canonical flag, and coordinates. Default is false to keep responses compact."
}
}
}Parent server
io.github.cyanheads/ensembl-mcp-server
https://github.com/cyanheads/ensembl-mcp-server
1/7 registries