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open-data-mcp

open-data-mcp

by markatdataandbeyond
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Hybrid

dataandbeyond--pubmed-search

Read-only

Search PubMed articles, DOI, PMCID, and author details via NCBI E-utilities. Query with PubMed syntax and optionally add an NCBI API key for higher rate limits.

Instructions

PubMed search with articles, DOI, PMCID and authors via NCBI E-utilities. Optional NCBI_API_KEY for higher rate limits.

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "dataandbeyond--pubmed-search"
  }
}

Input Schema

NameRequiredDescriptionDefault
sortNoRelevance or newest first. Example values: "relevance"relevance
queriesNoPubMed syntax, e.g. "crispr[Title] AND 2024[dp]". Example values: ["semaglutide[tiab] AND 2024[dp]"]
waitSecsNoMax seconds (0–45, default 30) to cap the wait for the Actor run to reach terminal state. For long-running Actors the response returns at the cap with the current run status; follow `nextStep` to poll via get-actor-run. Set to 0 to fire-and-forget.
ncbiApiKeyNoFree key raises rate limit to 10 req/s.
maxResultsPerQueryNoUp to 1000. Example values: 20

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv1.1.0

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, openWorldHint and destructiveHint=false, so safety is covered. The description adds the useful operational fact that the tool proxies NCBI E-utilities and that an API key raises throughput to higher rate limits, but says nothing about pagination caps, result completeness, or failure modes.

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?

Two short sentences, front-loaded with the purpose before the optional configuration note. Nothing is wasted, though the brevity leaves little room for routing guidance.

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?

For a read-only search wrapper with full schema coverage and no output schema, the description covers what is returned and the rate-limit lever. It is still missing the key disambiguation against scholar-search and any hint about result volume or paging, which matters for an agent picking among research siblings.

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 all five parameters (including PubMed query syntax, sort, maxResultsPerQuery and waitSecs) are documented in the schema itself. The description only echoes the API-key rate-limit benefit and adds no syntax or format detail beyond the schema, so the baseline 3 applies.

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?

Names a specific verb and resource ("PubMed search") and states the returned fields (articles, DOI, PMCID, authors) plus the backing source (NCBI E-utilities). It is clear what the tool does and implicitly distinct from the sibling scholar-search, but it never says so 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?

No guidance on when to choose this over the sibling scholar-search, no mention of query-count limits, and no note about long-running behavior beyond the API key remark. The only usage-adjacent statement is that an NCBI_API_KEY raises rate limits.

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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