BioLit MCP
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| NCBI_EMAIL | No | Optional contact email sent to NCBI, as NCBI recommends. | |
| NCBI_API_KEY | No | Optional NCBI API key for a higher rate limit (10 req/s instead of 3). |
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_pubmedA | Search PubMed. Returns PMIDs, titles, journals, years and publication types (no abstracts). |
| get_abstractsA | Fetch abstracts and metadata for PMIDs. PMIDs that do not exist are returned in not_found. Use this to read papers before citing them and to verify citations. |
| lookup_geneA | Look up a gene in NCBI Gene: full name, chromosome, cytogenetic location, aliases and summary. |
| lookup_proteinA | Look up the reviewed (Swiss-Prot) UniProt entry for a gene: accession, protein name, length, function. |
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 4 tools
Each tool has a clearly distinct role: search_pubmed finds PMIDs, get_abstracts retrieves full text by PMID, lookup_gene and lookup_protein target different NCBI/UniProt resources. The search-then-fetch pipeline is explicit and no two tools could be confused.
All four names follow a clean verb_noun snake_case pattern (search_pubmed, get_abstracts, lookup_gene, lookup_protein). The verbs vary (search/get/lookup) but each is accurate for its action, and the convention is uniform throughout.
Four tools is on the lean side but each earns its place and matches the narrow literature-lookup scope. A slightly richer surface (e.g. full-text or citation helpers) would round it out.
Core workflow of searching literature, reading abstracts, and resolving gene/protein metadata is covered, including not_found handling. Gaps remain around full-text retrieval, citation formatting, and sequence/variant detail, but agents can work around them.