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u9401066

pubmed-search-mcp

by u9401066
OverviewSchemaRelated ServersScoreDiscussions
Python
Remote

prepare_export

Export PubMed citations to reference manager formats like RIS, BibTeX, and CSL-JSON for use in EndNote, Zotero, or LaTeX documents.

Instructions

Export citations to reference manager formats.

╔═══════════════════════════════════════════════════════════════════╗ ║ RECOMMENDED: Use source="official" (default) for best quality ║ ╚═══════════════════════════════════════════════════════════════════╝

When to Use

  • Exporting references to EndNote, Zotero, Mendeley

  • Creating BibTeX for LaTeX documents

  • Generating citation lists for manuscripts

Source Options

Source

Formats

Quality

Speed

official

ris, medline, csl

★★★★★

Fast

local

ris, bibtex, csv, medline, json

★★★★

Fast

Format Selection Guide

  • ris: EndNote, Zotero, Mendeley (official recommended)

  • medline: NBIB format for PubMed tools

  • csl: JSON for programmatic citation styling

  • bibtex: LaTeX documents (local only)

  • csv: Data analysis, Excel (local only)

Args: pmids: Articles to export. Accepts: - "last" → results from previous search - "12345678,87654321" → comma-separated PMIDs - ["12345678", "87654321"] → list of PMIDs - "PMID:12345678" → with prefix format: Export format (default: "ris") - official API: ris, medline, csl - local only: bibtex, csv, json include_abstract: Include abstracts in output (default: True) source: Citation source (default: "official") - "official": NCBI Citation API (recommended, best quality) - "local": Local formatting (more formats, offline capable)

Returns: JSON with status and export_text containing formatted citations.

Examples: # Export last search results (recommended) prepare_export(pmids="last", format="ris")

# Export specific PMIDs to BibTeX
prepare_export(pmids="12345678,87654321", format="bibtex", source="local")

# Get CSL-JSON for programmatic use
prepare_export(pmids="last", format="csl", source="official")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmidsYes
formatNoris
include_abstractNo
sourceNoofficial

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes

Tool Definition Quality

A4.6/5.0
Behavior4/5

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

No annotations are provided, so the description takes full responsibility. It explains source options (official vs local), format availability, and output format. However, it omits details about error handling, rate limits, or idempotency, which would enhance transparency.

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 with sections, tables, and examples. It is front-loaded with the purpose and recommended source. Every sentence adds value, and the length is justified by the tool's complexity.

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 presence of an output schema, the description doesn't need to detail return values. It fully covers input parameters, format selection, source options, and provides examples. The description is complete for the tool's complexity.

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

Parameters5/5

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

With 0% schema description coverage, the description compensates thoroughly. It explains pmids with multiple accepted formats, format with per-source options, include_abstract default, and source with two options. Examples further clarify usage.

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 'Export citations to reference manager formats.' and lists specific formats (EndNote, Zotero, Mendeley, BibTeX). It distinguishes itself from sibling citation tools by focusing on exporting, with detailed format and source guidance.

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 'When to Use' section explicitly lists use cases, and the format selection guide provides context. However, it doesn't explicitly state when not to use or how it differs from alternatives like fetch_article_details or get_article_references, missing clear exclusion criteria.

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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