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pubmed-mcp-server

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Pubmed Fetch Fulltext

pubmed_fetch_fulltext
Read-only

Fetch full-text articles from PubMed Central with structured sections and references, using PMC IDs, PubMed IDs, or DOIs, with fallback to Europe PMC.

Instructions

Fetch full-text articles from PubMed Central with structured sections and references. When PMC misses, transparently falls back to Europe PMC fullTextXML (structured JATS for records with a PMC counterpart). Provide exactly one of pmcids (PMC IDs directly), pmids (PubMed IDs, auto-resolved), or dois (DOIs, auto-resolved to PMC via the ID Converter; preprints with a PMC counterpart recover via Europe PMC).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
doisNoDOIs to resolve (e.g. ["10.21203/rs.3.rs-9010375/v1"]). Provide exactly one of `pmcids`, `pmids`, or `dois`. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled.
pmidsNoPubMed IDs. Provide exactly one of `pmcids`, `pmids`, or `dois`. Articles in PMC are returned as structured JATS; articles not in PMC fall through to Europe PMC (when EPMC has a `fullTextXML`), then to Unpaywall when `UNPAYWALL_EMAIL` is set and a DOI is available.
pmcidsNoPMC IDs to fetch (e.g. ["PMC9575052"]). Provide exactly one of `pmcids`, `pmids`, or `dois`.
sectionsNoFilter to specific sections by title, case-insensitive (e.g. ["Introduction", "Methods", "Results", "Discussion"]). Applies to `source=pmc` results only.
maxSectionsNoMaximum top-level body sections. Applies to `source=pmc` results only.
includeReferencesNoInclude reference list. Applies to `source=pmc` results only.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
noticeNoOptional guidance when a `sections` filter removed every body section — names the requested section terms and the affected article id(s), and suggests retrying without `sections` or using broader headings. Absent when no section filter was applied or sections matched.
articlesYesFull-text articles
unavailableNoPer-identifier explanations for any requested PMIDs, PMCIDs, or DOIs with no returnable full text. `idType` discriminates which branch the id came from.
totalReturnedYesNumber of articles returned

Tool Definition Quality

A4.9/5.0
Behavior5/5

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

Annotations already declare readOnlyHint and openWorldHint. The description adds valuable transparency about the fallback chain (Europe PMC, Unpaywall), the JATS format, and the resolution logic for DOIs and PMIDs. There is no contradiction with annotations.

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

Conciseness4/5

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

The description is well-structured with the main purpose first, followed by parameter details. However, it is slightly verbose with repeated phrases like 'Provide exactly one...' and 'Applies to source=pmc results only.' Could be tightened without losing clarity.

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 (6 parameters, fallback logic, multiple sources), the description covers all necessary aspects: input constraints, fallback behavior, source-specific options, and the nature of the output. No gaps remain.

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?

Although schema coverage is 100%, the description goes beyond by explaining the mutual exclusivity of the three identifier parameters, the fallback behavior tied to each, and which parameters are source-specific. This adds significant meaning beyond the schema descriptions.

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?

Description starts with a clear action ('Fetch full-text articles...') and resource ('PubMed Central') and specifies the return format ('structured sections and references'). It distinguishes from siblings like pubmed_fetch_articles by emphasizing full-text and fallback behavior, making the tool's unique purpose unmistakable.

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 states 'Provide exactly one of pmcids, pmids, or dois' and explains fallback logic for when PMC misses. Also indicates which parameters (sections, maxSections, includeReferences) apply only to 'source=pmc' results, giving clear context for parameter choice.

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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