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
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| lookup_gene_by_symbolC | Look up a gene by its symbol (e.g., BRCA2) and get detailed information including ID, location, and description |
| lookup_gene_by_idB | Look up a gene by its Ensembl stable ID (e.g., ENSG00000139618) |
| get_sequenceB | Get the DNA/RNA/protein sequence for a given region or feature |
| get_variants_for_regionC | Get genetic variants for a genomic region |
| get_homologyB | Get homologous genes/proteins across species |
| get_phenotype_by_geneC | Get phenotype annotations associated with a gene |
| get_regulatory_featuresC | Get regulatory features in a genomic region |
| overlap_regionC | Get features that overlap a given genomic region |
| get_xrefs_by_geneC | Get external references (cross-references) for a gene |
| get_xrefs_by_symbolB | Get cross-references for a gene symbol |
| get_xrefs_by_nameC | Search cross-references by name |
| map_assemblyC | Map coordinates between different genome assemblies |
| map_cdna_to_regionC | Map cDNA coordinates to genomic coordinates |
| map_cds_to_regionC | Map CDS coordinates to genomic coordinates |
| map_translation_to_regionC | Map protein coordinates to genomic coordinates |
| get_ontology_by_idB | Get ontology term information by ID |
| get_ontology_ancestorsB | Get ancestor terms for an ontology term |
| get_ontology_descendantsC | Get descendant terms for an ontology term |
| search_ontology_by_nameC | Search for ontology terms by name |
| get_taxonomy_by_idC | Get taxonomy information by ID |
| get_taxonomy_classificationC | Get taxonomic classification for a species |
| search_taxonomy_by_nameD | Search taxonomy by name |
| overlap_idB | Get features that overlap a specific feature by ID |
| overlap_translationC | Get features overlapping a translation (protein) |
| vep_regionB | Predict variant consequences for a genomic region using the Variant Effect Predictor (VEP). Returns detailed consequence predictions including transcript effects, protein changes, and regulatory impacts. |
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 25 tools
Most tools have distinct purposes, such as get_sequence for sequences and get_homology for homologous genes, but some overlap exists: get_xrefs_by_gene, get_xrefs_by_symbol, and get_xrefs_by_name all handle cross-references with slight variations, which could cause minor confusion. Overall, descriptions clarify boundaries, but the xrefs tools are somewhat redundant.
All tool names follow a consistent verb_noun pattern, primarily using 'get_', 'lookup_', 'map_', 'overlap_', 'search_', and 'vep_' prefixes, with snake_case throughout. This predictability makes it easy for agents to understand and navigate the tool set without naming conflicts.
With 25 tools, the count is borderline high for a genomic data server, feeling slightly heavy but not excessive. It covers various aspects like sequences, variants, and mappings, but could potentially be streamlined by consolidating overlapping tools (e.g., the xrefs group).
The tool set provides comprehensive coverage for genomic and bioinformatics tasks, including data retrieval (e.g., genes, sequences, variants), mapping between coordinates, ontology and taxonomy lookups, and variant prediction with VEP. There are no obvious gaps; it supports full lifecycle operations from search to analysis.