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Pubmed Fetch Articles

pubmed_fetch_articles
Read-only

Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmidsYesPubMed IDs to fetch
includeMeshNoInclude MeSH terms
includeGrantsNoInclude grant information

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
noticeNoOptional guidance when no articles were returned — points to discovery tools. Absent on successful fetches.
articlesNoParsed articles
totalReturnedNoNumber of articles returned
unavailablePmidsNoPMIDs that returned no article data

TDQS

B3.4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, and the description's 'Fetch' is consistent with those hints. The description adds useful context about return fields (abstract, authors, journal, MeSH terms), but it does not disclose behavior for invalid/missing IDs, errors, or rate limits, though the schema caps batch size at 200.

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 two sentences with zero waste. The core action and input mode are front-loaded, and the second sentence adds value by summarizing the return payload without unnecessary detail.

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

Completeness4/5

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

For a straightforward fetch-by-ID tool, the description together with the full schema, output schema, and read-only annotations covers the essential invocation requirements. The main gap is the absence of explicit routing to sibling tools for search or full-text retrieval, but this does not prevent correct invocation.

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 three parameters. The description adds marginal value by mentioning MeSH terms, which aligns with includeMesh, but does not explain includeGrants behavior or parameter semantics beyond what the schema provides.

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

Purpose4/5

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

The description states a specific action ('Fetch'), resource ('full article metadata'), and input mode ('by PubMed IDs'), and enumerates key return fields (abstract, authors, journal, MeSH terms). This makes it clear what the tool does and broadly distinguishes it from sibling tools like pubmed_search_articles and pubmed_fetch_fulltext, though it does not explicitly name those alternatives.

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

Usage Guidelines2/5

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

The phrase 'by PubMed IDs' implies a prerequisite, but the description gives no explicit guidance about when to use this tool versus alternatives. It does not direct agents to pubmed_search_articles when IDs are unknown or to pubmed_fetch_fulltext when full text is needed, leaving usage inference to the agent.

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.