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eutils-mcp-server

by iwinoid
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TypeScript
Remote

Entrez Database Info

eutils_einfo
Read-onlyIdempotent

List all Entrez databases or describe a single database's searchable fields, record counts, and links to other databases. Use to discover what you can query in NCBI Entrez.

Instructions

List Entrez databases, or describe one database's searchable fields and links.

Call with no arguments to list all Entrez databases. Call with db to get that database's record count, last update time, searchable field names, and the links available to other databases.

Args:

  • db (string, optional): database to describe, for example "pubmed". Omit to list all.

  • response_format ('markdown' | 'json'): output format. Default 'markdown'.

Returns: Without db: { count, databases: string[] } With db: { database, menu_name, description, record_count, last_update, build, field_count, fields: [{ name, fullname, description, termcount? }], link_count, links: [{ name, dbto, menu }] }

Examples:

  • Use when: "what fields can I search in PubMed?" -> db="pubmed"

  • Use when: "which Entrez databases exist?" -> no arguments

  • Use when: "what databases link from a gene record?" -> db="gene"

  • Don't use when: you want record counts for a query (use eutils_egquery instead)

Error Handling:

  • Rejects a database name that is not one of the known Entrez databases, and lists samples

  • Returns a parse error if NCBI changes the response shape

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
dbNoEntrez database to describe, for example "pubmed" or "protein". Omit to list all databases.
response_formatNoOutput format: 'markdown' for human-readable text, or 'json' for machine-readable data. Default: 'markdown'.markdown

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countNoNumber of Entrez databases, when no db was given.
linksNo
fieldsNo
databaseNoDatabase name, when db was given.
databasesNoDatabase names, when no db was given.
link_countNo
field_countNo
record_countNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.6/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, idempotentHint, openWorldHint and destructiveHint=false, so safety is covered. The description goes further by disclosing error behavior (unknown db names are rejected with samples; parse errors if NCBI changes the response shape) and by enumerating exactly what data each mode returns, including last_update and record_count.

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?

The core behavior is front-loaded in the first paragraph, followed by clearly labeled Args, Returns, Examples, and Error Handling sections. The Returns block partly duplicates the output schema, but the Examples and Error Handling sections earn their space.

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?

For a two-parameter, zero-required tool with a full output schema and rich annotations, the description covers both modes, the argument semantics, worked examples, sibling routing, and failure modes. An agent has everything needed to select and invoke it correctly; return-value detail is a bonus given the output schema exists.

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

Parameters4/5

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 genuine meaning beyond the schema by explaining the consequence of each choice: omitting db yields the full list, supplying db yields record count, last update, searchable fields, and outbound links. The response_format enum is already fully documented in the schema and is merely restated.

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 first sentence states a specific verb (List / describe) applied to a precise resource (Entrez databases and their searchable fields and links). It cleanly separates the two operating modes (no args = list, db = describe), which lets an agent pick the right call without opening the schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It gives concrete when-to-use examples mapped to inputs ("what fields can I search in PubMed?" -> db="pubmed") and an explicit don't-use case that names the alternative sibling (eutils_egquery) for record counts on a query. The choice between this tool and its closest sibling is fully resolved.

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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