Ensembl MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Server capabilities have not been inspected yet.
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| ensembl_feature_overlapB | Find genomic features (genes, transcripts, regulatory elements) that overlap with a genomic region or specific feature. Automatically handles assembly-specific format variations (GRCh38/hg38, chromosome naming conventions, coordinate systems). Covers /overlap/region and /overlap/id endpoints. |
| ensembl_regulatoryC | Get regulatory features, binding matrices, and regulatory annotations. Covers regulatory overlap endpoints and binding matrix data. |
| ensembl_protein_featuresC | Get protein-level features, domains, and annotations for proteins and translations. |
| ensembl_metaA | Get server metadata, data releases, species info, and system status. Covers /info/* endpoints and /archive/id for version tracking. |
| ensembl_lookupB | Look up genes, transcripts, variants by ID or symbol. Get cross-references and perform ID translation. Covers /lookup/* and /xrefs/* endpoints plus variant_recoder. |
| ensembl_sequenceC | Retrieve DNA, RNA, or protein sequences for genes, transcripts, regions. Covers /sequence/id and /sequence/region endpoints. |
| ensembl_mappingC | Map coordinates between different coordinate systems (genomic ↔ cDNA/CDS/protein) and between genome assemblies. Covers /map/* endpoints. |
| ensembl_comparaC | Comparative genomics: gene trees, homology, species alignments, and evolutionary analysis. Covers /genetree/, /homology/, /alignment/* endpoints. |
| ensembl_variationC | Variant analysis: VEP consequence prediction, variant lookup, LD analysis, phenotype mapping, haplotypes. Covers /variation/, /vep/, /ld/, /phenotype/ endpoints. |
| ensembl_ontotaxC | Ontology term search and NCBI taxonomy traversal. Search GO terms, phenotype ontologies, and taxonomic classifications. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 10 tools
Each tool has a clearly distinct purpose targeting specific genomic data types or operations, such as comparative genomics, feature overlap, sequence retrieval, or variant analysis. The descriptions explicitly differentiate their scopes (e.g., 'ensembl_compara' for evolutionary analysis vs. 'ensembl_sequence' for sequence retrieval), with no apparent overlap that could cause agent misselection.
All tool names follow a consistent 'ensembl_' prefix with descriptive suffixes (e.g., 'compara', 'lookup', 'mapping'), using snake_case uniformly throughout. This predictable pattern enhances readability and helps agents quickly identify the tool's domain without confusion.
With 10 tools, the server is well-scoped for genomic data access and analysis, covering key areas like sequence retrieval, variant analysis, and metadata. Each tool earns its place by addressing distinct aspects of the Ensembl database, avoiding bloat while providing comprehensive coverage for typical bioinformatics workflows.
The tool set offers complete coverage for genomic data operations, including lookup, mapping, sequence retrieval, variation analysis, and metadata access. It supports full CRUD-like workflows (e.g., from data query to analysis) with no obvious gaps, ensuring agents can handle end-to-end tasks without dead ends.