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pubmed-mcp-server

by io.github.cyanheads

Pubmed Lookup Mesh

pubmed_lookup_mesh
Read-only

Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms, plus pagination via offset for paging past the maxResults cap.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesMeSH descriptor name or free-text term to look up
offsetNoResult offset for pagination (0-based). Pass the `nextOffset` from the previous response to get the following page; the exact-descriptor match is pinned to the first page only.
maxResultsNoMaximum results
includeDetailsNoFetch full MeSH records (scope notes, tree numbers, entry terms)

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
queryNoOriginal search query
noticeNoOptional guidance when no descriptors matched or the offset overshot the result set — suggests spell-check, free-text search, or resetting the offset. Absent on successful result pages.
offsetNoResult offset this page was read from
resultsNoMatching MeSH records
nextOffsetNoOffset to request for the next page. Omitted when this is the last page, so its absence is the end-of-results signal.
totalCountNoTotal MeSH descriptors matching the query upstream, before the maxResults cap

TDQS

A4.1/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already mark it read-only and open-world; the description adds useful behavioral detail by disclosing the returned record fields and the offset-based pagination mechanism for paging past maxResults. It does not contradict the annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

A single sentence that front-loads the purpose, then states the output contents and pagination behavior. There is no filler or repetition of schema details.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a read-only search tool with a full output schema and well-documented parameters, the description covers the essential behavior: what is returned and how pagination works. Nothing needed for correct invocation is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the schema already documents all four parameters. The description adds some context about return contents and pagination, but it does not materially expand parameter meaning beyond the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description names a specific resource (MeSH controlled vocabulary) and a clear action (search and explore), and specifies the return contents (descriptor records with tree numbers, scope notes, entry terms). This distinguishes it from the sibling PubMed article/citation tools, none of which target MeSH.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies the tool is for MeSH vocabulary lookups, which gives an agent a clear context, but it does not explicitly state when to prefer this over sibling tools or mention exclusions. There is no direct comparison to alternatives like pubmed_search_articles.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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TDQS

A4.2/5.0
Disambiguation4/5

The tools constitute a well-designed set targeting distinct workflow steps: searching (pubmed_search_articles, pubmed_europepmc_search), fetching (pubmed_fetch_articles, pubmed_fetch_fulltext, pubmed_europepmc_fetch), ID conversion (pubmed_convert_ids), related articles (pubmed_find_related), citations (pubmed_format_citations, pubmed_lookup_citation), MeSH lookup (pubmed_lookup_mesh), and spelling (pubmed_spell_check). While search and fetch tools in PubMed vs Europe PMC overlap somewhat, the descriptions explicitly differentiate them (local PubMed vs broader Europe PMC with preprints/patents), so ambiguity is minor.

Naming Consistency5/5

All tools follow a consistent `pubmed_` prefix followed by verb_noun pattern: `search_articles`, `fetch_articles`, `lookup_citation`, `format_citations`, `convert_ids`, `find_related`, etc. The verbs are all lowercase snake_case, and the pattern is uniform across the entire set, even for the Europe PMC variants (`pubmed_europepmc_search`, `pubmed_europepmc_fetch`).

Tool Count5/5

11 tools makes for a well-scoped server. Each tool serves a clearly distinct purpose within the biomedical literature retrieval domain: searching, fetching metadata/full-text, ID conversion, citation formatting/lookup, MeSH exploration, related-articles, and spell-check. No tool feels redundant or trivial; the count is appropriate for the domain's complexity.

Completeness5/5

The tool set provides comprehensive coverage of the core PubMed/PMC workflow: search with full query syntax, fetch metadata and full text, convert identifiers across DOI/PMID/PMCID, find related articles, format citations, and explore MeSH vocabulary. Notable gaps like more advanced search history management or batch operations exist but are not essential to the domain's core purpose. The fallback logic (e.g., europepmc_fetch for non-PMC records, fulltext fallback chain) fills potential dead ends.

Resources