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pubmed-mcp-server

by io.github.cyanheads

Pubmed Europepmc Fetch

pubmed_europepmc_fetch
Read-only

Fetch complete Europe PMC records — including the full, untruncated abstract — for records addressed by source plus epmcId. Pairs with pubmed_europepmc_search, which returns bounded abstractSnippet values and flags cut ones with abstractTruncated: true; pass those hits' source and epmcId here to read the whole abstract. This is the retrieval path for preprint (PPR), patent (PAT), and Agricola (AGR) records, which frequently carry no PMID and no DOI, so pubmed_fetch_articles and pubmed_fetch_fulltext cannot address them. Up to 25 records per call.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
recordsYesRecords to retrieve, each addressed by the `source` and `epmcId` of a `pubmed_europepmc_search` hit. The whole batch resolves in one Europe PMC request.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
noticeNoGuidance when one or more requested records could not be resolved. Absent when every record came back.
recordsNoResolved records, in the order Europe PMC returned them
notFoundNoRequested `source` + `epmcId` pairs Europe PMC returned no record for

TDQS

A4.8/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true. The description adds batch limit (up to 25), confirms the return includes full abstracts, and notes the truncation flag from the sibling search. It doesn't describe the exact response shape or error/side-effect behavior, but for a read-only fetch with annotations covering safety, the added context is valuable and not redundant.

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?

The description packs high-density information (purpose, sibling routing, use-case scope, batch limit, parameter sourcing) into four compact sentences with clear logical flow: what it does → when to use it → constraints. No filler or repetition of schema details beyond what adds value.

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?

The description fully covers when to use this tool over siblings, how to obtain the required parameters (from search hit), the batch limit, and what data it returns. Given readOnly annotations and an output schema, nothing missing that an agent needs to select and invoke it correctly.

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

Parameters5/5

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

Schema provides 100% coverage with descriptions for both parameters. The description goes further by explaining the relationship: epmcId is copied from the search hit, and for MED records it equals the PMID. This directly helps an agent know how to obtain and populate the parameters correctly, which the schema alone doesn't convey.

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 specifies the verb (fetch), resource (Europe PMC records), and key output (full abstracts). It explicitly differentiates from sibling tools by naming the retrieval path for PPR, PAT, and AGR records that pubmed_fetch_articles and pubmed_fetch_fulltext cannot address. This is a precise, non-tautological statement.

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

Usage Guidelines5/5

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

It clearly states when to use this tool: to read full abstracts for records flagged as abstractTruncated by pubmed_europepmc_search, and for preprint/patent/Agricola records lacking PMID/DOI. It also explicitly mentions alternatives (pubmed_fetch_articles, pubmed_fetch_fulltext) and why they'd fail. Explicit when-to-use and when-not guidance.

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.

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