ensembl_lookup
Query genomic data by ID or symbol to retrieve genes, transcripts, variants, and cross-references. Translate IDs and access additional details like exons or UTRs. Supports species-specific lookup via the Ensembl MCP Server.
Instructions
Look up genes, transcripts, variants by ID or symbol. Get cross-references and perform ID translation. Covers /lookup/* and /xrefs/* endpoints plus variant_recoder.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| expand | No | Additional data to include (e.g., ['Transcript', 'Exon'], ['Translation'], ['UTR']) | |
| external_db | No | External database name for xrefs lookup (e.g., 'HGNC', 'UniProtKB/Swiss-Prot', 'RefSeq_mRNA') | |
| identifier | Yes | ID or symbol to look up (gene, transcript, variant, etc.) (e.g., 'ENSG00000141510', 'BRCA1', 'rs699', 'ENST00000288602') | |
| lookup_type | No | Type of lookup to perform | id |
| species | No | Species name (e.g., 'homo_sapiens', 'mus_musculus') | homo_sapiens |
Input Schema (JSON Schema)
{
"properties": {
"expand": {
"description": "Additional data to include (e.g., ['Transcript', 'Exon'], ['Translation'], ['UTR'])",
"items": {
"type": "string"
},
"type": "array"
},
"external_db": {
"description": "External database name for xrefs lookup (e.g., 'HGNC', 'UniProtKB/Swiss-Prot', 'RefSeq_mRNA')",
"type": "string"
},
"identifier": {
"description": "ID or symbol to look up (gene, transcript, variant, etc.) (e.g., 'ENSG00000141510', 'BRCA1', 'rs699', 'ENST00000288602')",
"type": "string"
},
"lookup_type": {
"default": "id",
"description": "Type of lookup to perform",
"enum": [
"id",
"symbol",
"xrefs",
"variant_recoder"
],
"type": "string"
},
"species": {
"default": "homo_sapiens",
"description": "Species name (e.g., 'homo_sapiens', 'mus_musculus')",
"type": "string"
}
},
"required": [
"identifier"
],
"type": "object"
}