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kmaneesh

BioPython MCP Server

by kmaneesh

entrez_summary

Retrieve document summaries (DocSums) from NCBI Entrez databases like PubMed, Gene, ClinVar, or Nucleotide. Get key metadata quickly without full records, ideal for lightweight queries and faster results.

Instructions

Get document summaries (DocSums) from NCBI Entrez.

Document summaries are lightweight alternatives to full records, containing key metadata without the full content. Much faster for metadata-only queries.

Args: database: Database name (e.g., 'pubmed', 'gene', 'clinvar', 'nucleotide') ids: Single ID, comma-separated string, or list of IDs use_cache: Whether to use cached results (default: True, TTL: 7 days)

Returns: Dictionary containing: - summaries: List of document summary dictionaries - ids: List of IDs requested - count: Number of summaries returned - database: Database queried - cached: Whether result was from cache (if use_cache=True)

Examples: >>> entrez_summary("pubmed", "12345678") >>> entrez_summary("gene", ["672", "7157"]) # BRCA1, TP53 >>> entrez_summary("clinvar", "12345") >>> entrez_summary("nucleotide", "NM_000207,NM_001127")

Notes: - Much faster than entrez_fetch for metadata-only queries - Fields returned vary by database type - Rate limited to 3 req/sec (or 10 req/sec with API key) - Use this instead of fetch when you don't need full sequence/text - Cached results have 7 day TTL since summary data is relatively static

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
databaseYes
idsYes
use_cacheNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior5/5

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

With no annotations, the description fully discloses behavioral traits: lightweight nature, speed advantage, rate limits (3 req/sec or 10 with API key), 7-day cache TTL, and database-dependent fields. All relevant for safe and effective use.

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?

Well-structured with sections (Args, Returns, Examples, Notes) and front-loaded. Slightly verbose but every sentence adds value; minor room for tightening without losing content.

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?

Covers all aspects: purpose, parameters, usage guidelines, behavioral traits, return format, and examples. With output schema present, the description of return values aligns well. Complete for a query tool.

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?

Schema has 0% parameter descriptions; the description fully compensates by explaining each parameter: database (with examples), ids (single, comma-separated, or list), use_cache (default true, TTL 7 days). Includes multiple usage examples.

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 'Get document summaries (DocSums) from NCBI Entrez', specifying the verb and resource. It distinguishes from siblings by noting it is lighter and faster than entrez_fetch for metadata-only queries, and provides explicit alternatives.

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?

Provides explicit when-to-use (metadata-only, lightweight), when-not-to-use (full content needed), and alternatives (entrez_fetch). Also mentions rate limits and caching behavior, giving clear context for appropriate invocation.

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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