PubMed MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| PUBMED_EMAIL | No | Your email address (optional, recommended for better API access) | |
| ABSTRACT_MODE | No | Abstract mode: 'quick' (1500 chars) or 'deep' (6000 chars) | quick |
| FULLTEXT_MODE | No | Fulltext mode: 'disabled', 'enabled', or 'auto' | disabled |
| PUBMED_API_KEY | No | Your NCBI API key (optional, for higher rate limits) |
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 |
|---|---|
| pubmed_searchA | Search PubMed biomedical literature database. Returns articles matching your query with metadata, abstracts, and citations. Supports Boolean operators (AND, OR, NOT), MeSH terms, and field tags like [Title], [Author]. Use format="compact" for quick overviews when browsing, "detailed" for in-depth analysis. Use days_back to limit to recent publications. |
| pubmed_get_detailsA | Retrieve complete metadata for specific PubMed articles by PMID. Accepts a single PMID or array of PMIDs (up to 20). Returns full article records including abstract, authors, journal, DOI, MeSH terms. Use when you have specific PMIDs from a previous search or citation and need the full record. |
| pubmed_extract_infoA | Extract specific structured sections from a PubMed article. Use when you need only certain aspects (author details, structured abstract, keywords, DOI) rather than the full record. More token-efficient than get_details for targeted extraction. |
| pubmed_find_relatedA | Find articles related to a given PubMed article. Discovers similar papers or review articles to build a comprehensive literature picture. Use after identifying a key paper to expand your search in relevant directions. |
| pubmed_manage_cacheA | View cache statistics or perform maintenance. Use action="stats" to check hit rates and storage usage. Use action="clean" to remove expired entries, or action="clear" to wipe a specific cache layer. |
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 5 tools
Each tool has a clear primary purpose: search, fetch full records, extract specific fields, find related articles, and manage cache. However, pubmed_get_details and pubmed_extract_info could be confused by an agent, as both retrieve article information, though the descriptions differentiate full records from targeted extraction.
All tool names follow a consistent pattern: 'pubmed_' prefix followed by a verb or verb_noun phrase (search, get_details, extract_info, find_related, manage_cache). The naming is uniform, snake_case, and clearly indicates the operation performed.
Five tools is a well-scoped set for a PubMed MCP server, covering core literature search and retrieval without redundancy. The count feels appropriately moderate, not overwhelming or thin.
The toolset covers the full typical workflow: search for articles, retrieve full details, extract specific sections, discover related articles, and manage cache for efficiency. No obvious critical gaps exist for a literature search domain.