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Pubmed Fetch Fulltext

pubmed_fetch_fulltext
Read-only

Fetch full-text articles from PubMed Central with structured sections and references. Falls back to Europe PMC and Unpaywall for articles not in 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), then to Unpaywall — publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text. Provide exactly one of pmcids (PMC IDs directly), pmids (PubMed IDs, auto-resolved), or dois (preprints and EPMC-only OA records that lack PMID/PMCID).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmcidsNoPMC IDs to fetch (e.g. ["PMC9575052"]). Provide exactly one of `pmcids`, `pmids`, or `dois`.
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.
doisNoDOIs to resolve (e.g. ["10.21203/rs.3.rs-9010375/v1"]). Provide exactly one of `pmcids`, `pmids`, or `dois`. Covers preprints and EPMC-only OA records that lack PMID/PMCID. Chain: Europe PMC search-by-DOI → fullTextXML → Unpaywall.
includeReferencesNoInclude reference list. Applies to `source=pmc` results only.
maxSectionsNoMaximum top-level body sections. Applies to `source=pmc` results only.
sectionsNoFilter to specific sections by title, case-insensitive (e.g. ["Introduction", "Methods", "Results", "Discussion"]). Applies to `source=pmc` results only.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
articlesYesFull-text articles
totalReturnedYesNumber of articles returned
unavailableNoPer-identifier explanations for any requested PMIDs, PMCIDs, or DOIs with no returnable full text. `idType` discriminates which branch the id came from.
Behavior5/5

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

With annotations readOnlyHint=true and openWorldHint=true, the description adds substantial behavioral context: transparent fallback, output formats (structured JATS, HTML-as-Markdown, PDF-as-text), and dependency on UNPAYWALL_EMAIL for Unpaywall fallback. 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.

Conciseness5/5

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

The description is concise (four sentences) and front-loaded with the primary purpose. Every sentence adds value, with no redundant information.

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 complexity (6 parameters, multi-source fallback), the description covers key behaviors: input options, fallback logic, and output types. The presence of an output schema reduces the need to explain return values.

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

Parameters4/5

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

Parameter schema descriptions are detailed (100% coverage), but the main description provides a concise overview and clarifies the overall fallback chain, adding value 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 clearly states the tool's primary function: 'Fetch full-text articles from PubMed Central with structured sections and references.' It also explains the fallback mechanism to Europe PMC and Unpaywall. This distinguishes it from sibling tools like pubmed_fetch_articles, which likely fetch abstracts or metadata.

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

Usage Guidelines4/5

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

The description mandates providing exactly one of pmcids, pmids, or dois, and explains the fallback chain for each. It does not explicitly compare to siblings like pubmed_fetch_articles, but the context of full-text fetching is clear.

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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