Ensembl REST API
Ensembl REST API for retrieving comparative genomics, gene, transcript, variation, sequence, and genomic region data across Ensembl species.
Connect this API to an AI agent Browse all specs
What you can do with Ensembl REST API via MCP
Every endpoint below becomes a governed tool your AI agent (Claude, ChatGPT, or a customer-facing VX agent) can call — with scoped permissions, sandbox testing, and audit logs.
| Method | Path | Operation | Description |
|---|---|---|---|
| GET | /lookup/id/{id} |
get_lookup_id_id | Look up an Ensembl identifier Method: GET Path: /lookup/id/{id} IMPORTANT: This function has 1 REQUIRED parameter(s) and 2 OPTIONAL parameter(s) REQUIRED parameters MUST be provided OPTIONAL parameters can be omitted if not needed Parameters: Path Parameters: REQUIRED: - id: Ensembl gene, transcript, or variation ID Query Parameters: OPTIONAL: - expand: Expand child features - content-type: Requested representation |
| GET | /sequence/id/{id} |
get_sequence_id_id | Retrieve a sequence by identifier Method: GET Path: /sequence/id/{id} IMPORTANT: This function has 1 REQUIRED parameter(s) and 2 OPTIONAL parameter(s) REQUIRED parameters MUST be provided OPTIONAL parameters can be omitted if not needed Parameters: Path Parameters: REQUIRED: - id: Ensembl sequence identifier Query Parameters: OPTIONAL: - type: Sequence type - content-type: Requested representation |
| GET | /overlap/region/{species}/{region} |
get_overlap_region_species_region | Find features overlapping a genomic region Method: GET Path: /overlap/region/{species}/{region} IMPORTANT: This function has 2 REQUIRED parameter(s) and 1 OPTIONAL parameter(s) REQUIRED parameters MUST be provided OPTIONAL parameters can be omitted if not needed Parameters: Path Parameters: REQUIRED: - species: Ensembl species name - region: Region such as 1:100000-101000 Query Parameters: OPTIONAL: - feature: Feature type |
| GET | /xrefs/symbol/{species}/{symbol} |
get_xrefs_symbol_species_symbol | Resolve a gene symbol to cross-references Method: GET Path: /xrefs/symbol/{species}/{symbol} IMPORTANT: This function has 2 REQUIRED parameter(s) and 0 OPTIONAL parameter(s) REQUIRED parameters MUST be provided OPTIONAL parameters can be omitted if not needed Parameters: Path Parameters: REQUIRED: - species: Ensembl species name - symbol: Gene symbol |
Usage guide
Ensembl REST endpoints are publicly readable without an API key. Send the documented `Content-Type` and `Accept` headers, include the species and identifier parameters required by each route, and respect the service rate limits. Official documentation: https://rest.ensembl.org/
How to use this spec
- Create a free VX Agents account (sandbox tools included).
- Open the marketplace and connect “Ensembl REST API” to an agent.
- Expose it as an MCP server for Claude/ChatGPT, or chat with it directly.