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_symbol | Look up a gene by its symbol (e.g., BRCA2) and get detailed information including ID, location, and description |
| lookup_gene_by_id | Look up a gene by its Ensembl stable ID (e.g., ENSG00000139618) |
| get_sequence | Get the DNA/RNA/protein sequence for a given region or feature |
| get_variants_for_region | Get genetic variants for a genomic region |
| get_homology | Get homologous genes/proteins across species |
| get_phenotype_by_gene | Get phenotype annotations associated with a gene |
| get_regulatory_features | Get regulatory features in a genomic region |
| overlap_region | Get features that overlap a given genomic region |
| get_xrefs_by_gene | Get external references (cross-references) for a gene |
| get_xrefs_by_symbol | Get cross-references for a gene symbol |
| get_xrefs_by_name | Search cross-references by name |
| map_assembly | Map coordinates between different genome assemblies |
| map_cdna_to_region | Map cDNA coordinates to genomic coordinates |
| map_cds_to_region | Map CDS coordinates to genomic coordinates |
| map_translation_to_region | Map protein coordinates to genomic coordinates |
| get_ontology_by_id | Get ontology term information by ID |
| get_ontology_ancestors | Get ancestor terms for an ontology term |
| get_ontology_descendants | Get descendant terms for an ontology term |
| search_ontology_by_name | Search for ontology terms by name |
| get_taxonomy_by_id | Get taxonomy information by ID |
| get_taxonomy_classification | Get taxonomic classification for a species |
| search_taxonomy_by_name | Search taxonomy by name |
| overlap_id | Get features that overlap a specific feature by ID |
| overlap_translation | Get features overlapping a translation (protein) |
| vep_region | 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 | |