Ensembl MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Capabilities
Features and capabilities supported by this server
| 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 | |
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