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cyanheads

pubmed-mcp-server

by cyanheads

Pubmed Europepmc Fetch

pubmed_europepmc_fetch
Read-only

Retrieve full abstracts and complete Europe PMC records for search hits with truncated abstracts, including preprints, patents, and Agricola records without PMID or DOI.

Instructions

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
noticeNoGuidance when one or more requested records could not be resolved. Absent when every record came back.
recordsYesResolved records, in the order Europe PMC returned them
notFoundNoRequested `source` + `epmcId` pairs Europe PMC returned no record for
Behavior5/5

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

Adds behavioral context beyond annotations: full abstract retrieval, handling of truncation, and support for non-PubMed records. No contradiction with readOnlyHint or openWorldHint.

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?

Each sentence serves a distinct role: purpose, linkage to search, sibling exclusion, limit. No fluff. Front-loaded with the core action.

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?

Given the tool's complexity (array parameter, output schema exists), the description covers retrieval path, truncation handling, source-specific quirks, and alternatives. Leaves no obvious gaps for the intended use case.

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 coverage is 100%, but description adds crucial nuance: instructs to copy epmcId from search results, explains source enum meanings (e.g., PMC returns canonical MED record with pmcId), and clarifies the need for both params. This goes beyond schema definitions.

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?

Clearly states the action (fetch records including full abstract) and the resource (Europe PMC records addressed by source and epmcId). Distinguishes from sibling tools like pubmed_europepmc_search and mentions specific record types (PPR, PAT, AGR).

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?

Explicitly explains when to use this tool (after pubmed_europepmc_search returns truncated abstracts) and when not to (for records with PMID/DOI, use other tools). Provides batch limit of 25 records per call.

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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