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Pubmed

science__pubmed
Read-onlyIdempotent

Search PubMed for biomedical literature to find relevant research articles and clinical studies using structured queries.

Instructions

[Science & Research Agent] Search PubMed for biomedical literature. Returns PubMed IDs matching the query. Source: PubMed / NCBI (Public Domain), updates daily. Returns the Katzilla envelope { data, quality, citation } — quality scores freshness/uptime/confidence; citation carries the source URL, license, and a SHA-256 data hash for audit.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesSearch query for biomedical literature
limitNoNumber of results to return

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
dataYesStructured payload from the upstream source.
textNoPre-rendered text representation, when applicable.
qualityYesQuality scorecard: freshness, uptime, completeness, confidence, certainty.
citationYesProvenance block — source, license, retrieval timestamp, SHA-256 data hash, pre-formatted citation text.
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, idempotentHint=true, and openWorldHint=true. The description adds valuable context beyond this: it specifies the source (PubMed/NCBI), update frequency (daily), and details about the return format (Katzilla envelope with quality scores and citation data). This enriches the agent's understanding without contradicting 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 efficiently structured in two sentences: the first states the purpose and return type, the second adds source, update frequency, and output format details. Every sentence provides essential information without redundancy, making it front-loaded and zero waste.

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 (search with parameters), rich annotations covering safety and behavior, and the presence of an output schema (implied by mention of Katzilla envelope), the description is complete. It covers purpose, source, update frequency, and return format adequately, leaving detailed output structure to the schema.

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%, with clear descriptions for both parameters (query and limit). The description does not add any additional meaning or syntax details beyond what the schema provides, such as query formatting examples or result ordering. Baseline 3 is appropriate when the schema does the heavy lifting.

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 purpose with specific verbs ('Search PubMed for biomedical literature') and resource ('PubMed / NCBI'), and distinguishes it from siblings by specifying it returns PubMed IDs and the Katzilla envelope format. It explicitly mentions the source and update frequency, making it distinct from other science tools like arXiv or Semantic Scholar.

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 provides clear context for when to use this tool ('Search PubMed for biomedical literature'), but does not explicitly state when not to use it or name alternatives among siblings. It implies usage for biomedical queries but lacks explicit exclusions or comparisons to other literature search tools.

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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