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Pubmed Search Articles

pubmed_search_articles
Read-only

Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), and pagination via offset for paging through large result sets.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sortNoSort order: relevance (default), pub_date (newest first), author, or journalrelevance
queryYesPubMed search query (supports full NCBI syntax)
authorNoFilter by author name (e.g. "Smith J")
offsetNoResult offset for pagination (0-based). PubMed serves at most the first 9999 records of a result set, so this caps at 9998; narrow the query or add filters to reach anything beyond it.
journalNoFilter by journal name
speciesNoFilter by species
languageNoFilter by language (e.g. "english")
dateRangeNoFilter by date range. The filter is applied only when both `minDate` and `maxDate` are non-empty; either one empty disables the entire date range.
meshTermsNoFilter by MeSH terms. Multiple terms are AND'd — all must match.
maxResultsNoMaximum results to return
hasAbstractNoOnly include articles with abstracts
freeFullTextNoOnly include free full text articles
summaryCountNoFetch brief summaries for top N results (0 = PMIDs only). Above the 50 cap, pass the remaining PMIDs to pubmed_fetch_articles.
publicationTypesNoFilter by publication type (e.g. "Review", "Clinical Trial", "Meta-Analysis"). Multiple values are OR'd — any match qualifies.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
pmidsNoPubMed IDs
queryNoOriginal query
noticeNoOptional guidance when the result set does not reflect what was asked for — a field tag PubMed ignored, a phrase it matched nothing for, a dateRange dropped for having one bound, no matches at all, or paging past the end. Absent when nothing applies.
offsetNoResult offset used
searchUrlNoPubMed search URL
summariesNoBrief summaries (empty array when summaryCount is 0)
totalCountNoTotal matching articles
appliedFiltersNoNormalized filter values that were applied to the PubMed query
effectiveQueryNoSanitized query sent to PubMed after applying all active filters

TDQS

A4.3/5.0
Behavior4/5

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

Annotations include readOnlyHint=true and openWorldHint=true. The description adds behavioral context: it mentions PubMed's limit of 9999 records (offset cap at 9998) and the note about summarizing with a cap of 50, directing to pubmed_fetch_articles for remaining PMIDs. It also clarifies date range behavior (only applied when both minDate and maxDate are non-empty) which is in the schema but the description sets expectations. These are useful beyond annotations. Not a contradiction.

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 a single paragraph that is relatively concise given the tool's complexity (14 parameters). It front-loads the main purpose and return type, then lists key capabilities. It doesn't repeat schema details, so it's efficient. Could be slightly more structured (e.g., bullet points) but overall good.

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?

The tool is complex with 14 parameters, but the schema covers all parameter details and the output schema exists. The description adds important context about pagination limits, summarization limits, and the hint to use another tool. It does not explain the output schema, but that is not required when output schema is provided. Overall, complete for an agent to call it correctly.

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?

Schema description coverage is 100%, so parameters are well-documented in the schema. The description adds a few semantic details beyond the schema: it explicitly mentions that offset is 0-based and that PubMed serves at most 9999 records, and that summaryCount above 50 requires passing PMIDs to a sibling. These are minor clarifications, but since the schema already covers parameters, a high score is appropriate. The description doesn't fully compensate for anything missing, but adds a little value.

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 states a specific verb ('Search') and resource ('PubMed') with explicit scope: 'full query syntax, filters, and date ranges'. It also indicates return type ('PMIDs and optional brief summaries') and supports pagination. This clearly distinguishes it from siblings like pubmed_fetch_articles or pubmed_convert_ids.

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 clearly states what the tool does, including filters and pagination, but does not explicitly mention when not to use it or direct to alternatives. It implies usage for searching PubMed, and mentions 'pagination via offset' which is a usage pattern. However, it doesn't name specific sibling tools or conditions for when to choose them instead (e.g., when to use pubmed_fetch_articles for full text). Thus, it's clear context but lacks explicit exclusions.

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.