Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Schema
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| ensembl_feature_overlap | 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_regulatory | Get regulatory features, binding matrices, and regulatory annotations. Covers regulatory overlap endpoints and binding matrix data. |
| ensembl_protein_features | Get protein-level features, domains, and annotations for proteins and translations. |
| ensembl_meta | Get server metadata, data releases, species info, and system status. Covers /info/* endpoints and /archive/id for version tracking. |
| ensembl_lookup | 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_sequence | Retrieve DNA, RNA, or protein sequences for genes, transcripts, regions. Covers /sequence/id and /sequence/region endpoints. |
| ensembl_mapping | Map coordinates between different coordinate systems (genomic ↔ cDNA/CDS/protein) and between genome assemblies. Covers /map/* endpoints. |
| ensembl_compara | Comparative genomics: gene trees, homology, species alignments, and evolutionary analysis. Covers /genetree/, /homology/, /alignment/* endpoints. |
| ensembl_variation | Variant analysis: VEP consequence prediction, variant lookup, LD analysis, phenotype mapping, haplotypes. Covers /variation/, /vep/, /ld/, /phenotype/ endpoints. |
| ensembl_ontotax | Ontology term search and NCBI taxonomy traversal. Search GO terms, phenotype ontologies, and taxonomic classifications. |