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PubMed MCP Server

PubMed MCP Server

by Augmented-Nature
OverviewSchemaSourceRelated ServersDiscussionsAdmin
TypeScript
Remote

search_articles

Find biomedical articles from PubMed using keywords, authors, journals, dates, or MeSH terms. Retrieve PMIDs and basic metadata for each result.

Instructions

Search PubMed for articles by keywords, authors, journals, dates, or MeSH terms. Returns PMIDs and basic metadata.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "query": "<query>"
    },
    "name": "search_articles"
  }
}

Input Schema

NameRequiredDescriptionDefault
queryYesSearch query (e.g., "cancer treatment", "Smith J[Author]", "Nature[Journal]")
max_resultsNoMaximum number of results to return (1-1000, default: 20)
startNoStarting position for pagination (default: 0)
sortNoSort order
date_fromNoStart date for date range (YYYY/MM/DD format)
date_toNoEnd date for date range (YYYY/MM/DD format)

Implementation Reference

  • src/index.ts:62-98 (registration)
    Tool registration with input schema for search_articles in the ListToolsRequestSchema handler
      name: 'search_articles',
  description: 'Search PubMed for articles by keywords, authors, journals, dates, or MeSH terms. Returns PMIDs and basic metadata.',
  inputSchema: {
    type: 'object',
    properties: {
      query: {
        type: 'string',
        description: 'Search query (e.g., "cancer treatment", "Smith J[Author]", "Nature[Journal]")'
      },
      max_results: {
        type: 'number',
        description: 'Maximum number of results to return (1-1000, default: 20)',
        minimum: 1,
        maximum: 1000
      },
      start: {
        type: 'number',
        description: 'Starting position for pagination (default: 0)',
        minimum: 0
      },
      sort: {
        type: 'string',
        description: 'Sort order',
        enum: ['relevance', 'pub_date', 'author', 'journal']
      },
      date_from: {
        type: 'string',
        description: 'Start date for date range (YYYY/MM/DD format)'
      },
      date_to: {
        type: 'string',
        description: 'End date for date range (YYYY/MM/DD format)'
      }
    },
    required: ['query']
  }
},

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv1.0.0

TDQS

B3.1/5.0
Behavior2/5

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

With no annotations, the description must carry the full burden. It states the return type (PMIDs and basic metadata) but lacks disclosure on important behaviors like pagination limits, whether it's read-only, or any authentication requirements.

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?

Two sentences, direct and efficient. Every word adds value, no redundancy.

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

Completeness3/5

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

Given 6 parameters and no output schema or annotations, the description is adequate but incomplete. It doesn't cover pagination behavior, error handling, or detailed output format. The schema helps, but the description could be richer.

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 baseline is 3. The description adds minimal value beyond the schema, merely listing searchable fields without explaining query syntax or parameter interactions. It does not compensate for any gaps since there are none.

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 clearly states the tool searches PubMed for articles by various criteria and returns PMIDs and basic metadata. It implies a general-purpose search capability, distinguishing it from specialized siblings like search_by_author or search_by_journal, though not explicitly.

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 description provides no guidance on when to use this tool versus alternatives like advanced_search or search_by_mesh_terms. There is no mention of when not to use it or which sibling to choose for specific needs.

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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