EMBL-EBI 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 |
|---|---|
| embl_dataA | Access EMBL-EBI bioinformatics APIs including InterPro, Pfam, UniProt protein features, and NCBI taxonomy. Use the "method" parameter to select an operation: search_interpro, get_interpro_entry, get_protein_domains, search_pfam, get_protein_features, search_taxonomy. |
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 1 tool
Only one tool exists, so there is no possibility of confusion between tools. The methods within the tool are clearly distinct and cover separate domains or operations.
The method names follow a consistent verb_noun pattern (e.g., search_interpro, get_protein_features), but the tool name 'embl_data' is a generic noun that does not convey an action or purpose, resulting in minor inconsistency.
With only a single tool for a wide range of bioinformatics APIs, the tool surface is too thin. The multiple methods effectively act as sub-tools, but consolidating them into one tool makes the server feel under-scoped and reduces usability.
The methods cover essential read operations (search and retrieval) for major EMBL-EBI resources like InterPro, Pfam, UniProt features, and NCBI taxonomy. Minor gaps exist (e.g., no direct method to fetch a Pfam entry by ID), but the core querying needs are addressed.