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kmaneesh

BioPython MCP Server

by kmaneesh

entrez_search

Search any NCBI Entrez database (PubMed, Nucleotide, Gene, ClinVar) using query syntax. Returns matching IDs, counts, total found, and query details with optional caching and sorting.

Instructions

Search any NCBI Entrez database using query syntax.

Args: database: Database to search (e.g., 'pubmed', 'nucleotide', 'gene', 'clinvar') query: Search query using Entrez syntax (see module docstring for examples) max_results: Maximum number of results to return (default: 20, max: 10000) sort: Sort order - 'relevance', 'pub_date', 'Author', etc. (default: 'relevance') use_cache: Whether to use cached results (default: True, TTL: 1 hour)

Returns: Dictionary containing: - ids: List of matching record IDs - count: Number of IDs returned - total_found: Total number of matches in database - query: Original query string - database: Database searched - cached: Whether result was from cache (if use_cache=True)

Examples: >>> entrez_search("pubmed", "BRCA1 AND breast cancer", max_results=10) >>> entrez_search("gene", "BRCA1[Gene Name] AND Homo sapiens[Organism]") >>> entrez_search("nucleotide", "Homo sapiens[Organism]", max_results=5) >>> entrez_search("clinvar", "BRCA1[Gene] AND Pathogenic[Clinical Significance]")

Notes: - Uses NCBI Entrez query syntax with field tags and Boolean operators - Rate limited to 3 req/sec (or 10 req/sec with API key) - See module docstring for comprehensive query syntax examples - Cached results have 1 hour TTL to balance freshness and API usage

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
databaseYes
queryYes
max_resultsNo
sortNorelevance
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 provided, the description fully carries the burden of behavioral disclosure. It details rate limits (3 req/sec, 10 with API key), caching behavior (1 hour TTL), and the exact return dictionary structure (ids, count, total_found, query, database, cached). This is comprehensive and transparent.

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-organized with clear sections (intro, Args, Returns, Examples, Notes). It is concise yet comprehensive, with no wasted sentences. The most critical information (purpose, parameters, return format) is front-loaded.

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 tool's complexity (5 parameters, rate limits, caching, output schema), the description is fully complete. It covers purpose, all parameters with defaults, return format, example calls, and behavioral notes. The output schema exists (as per context) and the description aligns with it.

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?

Despite 0% schema description coverage, the description adds rich meaning to each parameter: database is elaborated with examples, query references Entrez syntax with examples, max_results states default and max, sort lists common values, and use_cache explains TTL. This fully compensates for the lack of schema descriptions.

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 'Search any NCBI Entrez database using query syntax', with examples across multiple databases (pubmed, gene, nucleotide, clinvar). This differentiates it from sibling tools like pubmed_search (which is PubMed-specific) and entrez_fetch/entrez_summary (which retrieve details after search).

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 description provides rich usage guidelines including parameters, examples, and notes on rate limiting and caching. It references the module docstring for syntax examples. While it does not explicitly state when not to use this tool (e.g., after search, use entrez_fetch to get full records), the context is clear enough for an AI agent to select it appropriately.

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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