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masa061580
by masa061580

Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault
NCBI_API_KEYNoOptional NCBI API key to increase rate limit from 3 req/s to 10 req/s. Obtain from NCBI account settings.

Capabilities

Features and capabilities supported by this server

CapabilityDetails
tools
{
  "listChanged": true
}

Tools

Functions exposed to the LLM to take actions

NameDescription
searchA

Search PubMed with MeSH support, structured filters, pagination, and selectable output verbosity. output_mode=minimal returns id/title/url/full_text_available only (legacy-compatible); compact (default) adds authors/journal/year/doi/pmcid; full additionally includes abstract/mesh_terms/publication_types.

fetchA

Retrieve abstract for a single PMID (OpenAI MCP compliant). Accepts exactly one PMID. For multiple PMIDs, use fetch_batch.

fetch_batchA

Retrieve abstracts for multiple PMIDs in a single batch request. Returns structured data per PMID. Set include_abstract=false to omit the abstract field (e.g., when you only need full author lists).

get_full_textA

Retrieve full text of articles from PubMed Central (PMC) by PMC ID. Supports section filtering to reduce token usage.

countA

Get only the count of search results for query adjustment and optimization. Fast — retrieves no actual data. Useful for refining search strategies.

find_similar_articlesA

Find similar articles for a given PMID using MeSH terms and title-based similarity. Useful for literature review and related research discovery.

export_to_risA

Export PubMed articles to RIS format for citation managers (EndNote/Zotero/Mendeley). Returns compact RIS with minimal metadata — citation managers auto-fetch the rest via PMID.

get_citation_countsA

Get citation counts for PMIDs. Default source is iCite (counts only, includes citations from outside PubMed). Set citing_source='pubmed' for elink-based PubMed-internal citations and to retrieve citing PMIDs (useful for backward snowballing).

convert_idsA

Convert between PMID, PMCID, and DOI identifiers using NCBI ID Converter API.

batch_processA

Run multiple operations against the same set of PMIDs in one call. Helpful for systematic-review style workflows. operations is an array drawn from: 'abstract', 'citations', 'similar', 'ris_export', 'full_text'. Respects NCBI rate limits via max_concurrency (default 3).

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

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