ryogena-pubmed-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| NCBI_EMAIL | No | Optional email address recommended by NCBI for better service. | |
| NCBI_API_KEY | No | Optional API key to raise rate limit from 3 to 10 requests per second. |
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
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_pubmedA | Search PubMed and return slim metadata for each hit. Two-step under the hood: |
| fetch_articleA | Fetch one article with full abstract text. Returns title, abstract (with section labels preserved if structured),
authors, journal, pubdate, DOI, and a clickable PubMed URL. Returns
|
| find_relatedA | Walk the PubMed citation neighbor graph from one PMID. NCBI's "related articles" use a probabilistic topic-similarity model over title/abstract/MeSH. Returns slim metadata for each neighbor. Useful for "what else should I read about this paper?" follow-ups. |
| search_by_authorA | Find an author's PubMed-indexed publications. Wraps |
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 purpose: fetch_article gets full text for a PMID, find_related walks citation neighbors, search_by_author targets author queries, and search_pubmed does general search. No overlap in functionality.
All tool names follow a consistent verb_noun pattern with underscores: fetch_article, find_related, search_by_author, search_pubmed. Verbs are descriptive and nouns are specific.
Four tools cover the core PubMed operations (search, fetch, related articles) without unnecessary duplication. The number is within the recommended 3-15 range and well-scoped for the purpose.
The tool set covers the main workflows: searching (general and by author), fetching full articles, and exploring related papers. Minor gaps exist, such as search by topic/MeSH or filtering by date, but agents can accomplish common tasks without dead ends.