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pubmed_paper_search_by_query

Search PubMed via keyword query and retrieve normalized article records including title, abstract, authors, journal, DOI, and PMID through NCBI Entrez.

Instructions

Search PubMed by keyword via NCBI Entrez (ESearch to get PMIDs, then EFetch to retrieve and parse the article XML). Returns normalized records (title, abstract, authors, journal, doi, pmid, pmcid, keywords, date).

query is passed to NCBI verbatim, so PubMed field tags and MeSH terms work. To pin down one known paper, use the title tag WITHOUT quotes, e.g. Genome engineering using the CRISPR-Cas9 system[Title] — wrapping the title in quotes together with the tag ("..."[Title]) makes NCBI return 0 results.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
max_resultsNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv3.5.0

TDQS

A4.2/5.0
Behavior4/5

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

No annotations are provided, so the description carries the disclosure burden. It transparently explains that the tool queries NCBI Entrez, retrieves XML, and normalizes records, and it exposes the surprising behavior where quoted title tags cause zero results. It does not mention rate limits, authentication needs, or failure modes, but for a read-only search tool the disclosed behavior is substantial.

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 well-structured: the first sentence states the core purpose and pipeline, the second lists output fields, and a focused final paragraph gives a practical query-formatting caveat with an example. Every sentence adds useful information with no filler.

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?

Given there is no output schema and no annotations, the description is largely self-sufficient: it explains the workflow, return fields, query syntax, and a key pitfall. The main omission is the effect/limits of `max_results`, and it does not discuss error conditions, but the essential information for calling the tool correctly is present.

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?

With 0% schema description coverage, the description must compensate for both parameters. It thoroughly explains `query`: verbatim passing, field tags, MeSH terms, and the title-tag warning. However, `max_results` is never mentioned in the description; only its default value appears in the schema, so the description only partially compensates for the schema's lack of parameter documentation.

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 opens with a specific action and resource: 'Search PubMed by keyword via NCBI Entrez'. It also clarifies the internal pipeline (ESearch then EFetch) and the normalized output fields, which clearly distinguishes it from sibling tools that retrieve by ID or look up related articles.

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 gives concrete usage guidance for a common case: how to pin down a known paper using the `[Title]` tag without quotes, and warns against a quoting pitfall that returns zero results. However, it does not explicitly contrast this tool with sibling PubMed tools (e.g., summary lookup or related-article search) or state when not to use it.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.