bioretrieval-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| NCBI_API_KEY | No | NCBI API key; raises the rate limit from 3 to 10 req/s | |
| BIORETRIEVAL_DEVICE | No | Device to run local models on: cuda / mps / cpu | auto |
| BIORETRIEVAL_CACHE_DIR | No | HTTP response cache (SQLite) and ESM embedding cache directory | ~/.cache/bioretrieval-mcp |
| BIORETRIEVAL_MAP_INDEX | No | Map index .npz; enables retrieve_maps | |
| BIORETRIEVAL_NCBI_EMAIL | No | Email used for NCBI identification | |
| BIORETRIEVAL_HTTP_TIMEOUT_S | No | Per-request timeout in seconds | 20 |
| BIORETRIEVAL_CPGPT_EMBEDDINGS | No | CpGPT embedding store; enables cpgpt_embed | |
| BIORETRIEVAL_HTTP_CACHE_TTL_S | No | Response cache TTL in seconds | 86400 |
| BIORETRIEVAL_HTTP_MAX_RETRIES | No | Retries on timeouts, connection errors, 408/425/429/5xx | 3 |
| BIORETRIEVAL_RETRIEVAL_CHECKPOINT | No | Two-tower checkpoint (sequence tower) |
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 | {
"listChanged": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_emdbA | Search the Electron Microscopy Data Bank for cryo-EM entries. Returns per-entry metadata: title, resolution (Å), method, source organisms, fitted PDB models, UniProt cross-references, Pfam names, microscope, release date and primary citation. Results are relevance-ranked by EMDB. |
| get_uniprotA | Fetch a UniProtKB entry: amino-acid sequence, curated function, Pfam families, gene names, organism, review status, and EMDB cross-references. |
| search_geo_methylationA | Search NCBI GEO for DNA-methylation series (GSE) run on a given Illumina array. Returns total hit count plus, per series: accession, title, summary (truncated), platforms, sample count, organisms, submission date and linked PubMed IDs. |
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 3 tools
Each tool targets a clearly different resource and action: EMDB search, UniProt entry retrieval, and GEO methylation series search. There is no realistic overlap in selection, even though EMDB results may contain UniProt cross-references.
All tools use consistent snake_case verb_noun naming: search_emdb, get_uniprot, search_geo_methylation. The mix of search and get reflects the intended action rather than inconsistent conventions.
Three tools is well within a focused retrieval server’s scope, and each covers a distinct biological data source. None appears redundant or gratuitous.
Coverage is uneven: UniProt has fetch but no search, while EMDB and GEO methylation have search but no dedicated full-entry retrieval beyond returned metadata. These are notable gaps for common retrieval workflows, though partial workarounds exist via cross-references and search metadata.