WormBase MCP Server
OfficialServer 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 |
|---|---|
| searchA | Search WormBase for genes, proteins, phenotypes, strains, and other biological entities. Supports natural language queries like 'genes involved in longevity' or specific IDs like 'WBGene00006763'. |
| get_geneB | Get detailed information about a C. elegans gene including description, function, expression, phenotypes, and orthologs. |
| get_proteinB | Get detailed information about a protein including sequence, domains, motifs, and structure. |
| get_phenotypeC | Get detailed information about a phenotype including associated genes, RNAi experiments, and variations. |
| get_diseaseB | Get information about human diseases with C. elegans models, including associated genes and orthologs. |
| get_strainC | Get information about a C. elegans strain including genotype, available from, and associated phenotypes. |
| get_variationB | Get information about a genetic variation/allele including molecular details, phenotypes, and strains. |
| get_interactionsC | Get protein-protein, genetic, or regulatory interactions for a gene or protein. |
| get_expressionC | Get expression pattern information for a gene including tissue/cell expression, life stage expression, and expression images. |
| get_ontologyA | Get Gene Ontology (GO) terms for a gene including molecular function, biological process, and cellular component annotations. |
| get_entityA | Get information about any WormBase entity type. Use this for entity types not covered by specific tools. |
| get_paperC | Get information about a scientific paper/publication including authors, abstract, and associated genes. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
| entity-types |
TDQS
Scored across 12 tools
Every tool has a clearly distinct purpose targeting specific biological entities or functions, such as get_gene for genes, get_phenotype for phenotypes, and get_expression for expression patterns. The descriptions explicitly differentiate each tool's scope, with get_entity serving as a fallback for uncovered types, ensuring no ambiguity in tool selection.
All tool names follow a consistent verb_noun pattern using 'get_' or 'search' prefixes, such as get_disease, get_gene, and search. This uniformity makes the tool set predictable and easy to navigate, with no deviations in naming conventions across the 12 tools.
With 12 tools, the server is well-scoped for its biological data domain, covering key entities like genes, proteins, phenotypes, and diseases. Each tool earns its place by addressing specific aspects of WormBase data, avoiding both thin coverage and excessive complexity.
The tool set provides comprehensive coverage for accessing WormBase data, including CRUD-like retrieval for all major entity types (e.g., genes, proteins, phenotypes) and a search tool for flexible queries. No obvious gaps exist, as get_entity acts as a catch-all for any uncovered types, ensuring complete access to the database.