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kmaneesh

BioPython MCP Server

by kmaneesh

gene_info_fetch

Fetch comprehensive gene information from NCBI Gene by symbol or ID, including summary, chromosome, aliases, and gene type, with organism disambiguation and caching.

Instructions

Fetch comprehensive gene information from NCBI Gene database.

This specialized wrapper provides easy access to gene records with structured output.

Args: gene_symbol: Gene symbol (e.g., "BRCA1", "TP53") gene_id: NCBI Gene ID (e.g., "672" for BRCA1) organism: Organism name (default: "Homo sapiens") use_cache: Whether to use cached results (default: True)

Returns: Dictionary containing: - gene_id: NCBI Gene ID - symbol: Official gene symbol - name: Full gene name - summary: Gene summary/description - organism: Organism name - chromosome: Chromosomal location - aliases: List of gene aliases - type: Gene type (protein-coding, ncRNA, etc.) - cached: Whether result was from cache (if use_cache=True)

Examples: >>> gene_info_fetch(gene_symbol="BRCA1") >>> gene_info_fetch(gene_id="672") >>> gene_info_fetch(gene_symbol="Brca1", organism="Mus musculus")

Notes: - Provide either gene_symbol or gene_id (gene_id takes precedence) - Organism filter helps disambiguate gene symbols - Rate limited (3 req/sec or 10 req/sec with API key) - Cached results inherit TTL from underlying entrez_search and entrez_summary calls

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
gene_symbolNo
gene_idNo
organismNoHomo sapiens
use_cacheNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior5/5

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

Discloses rate limiting, precedence rules (gene_id over gene_symbol), caching behavior, TTL inheritance, and structured output format. No annotations exist, so description carries full burden and does so thoroughly.

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?

Well-organized with clear sections (Args, Returns, Examples, Notes). Every sentence adds value; no redundancy. Front-loaded with purpose.

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: input parameters, output schema, examples, and behavioral notes. No missing information for a tool with this complexity and no annotations.

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 description coverage is 0%, but the description's Args section explains each parameter with defaults, examples, and precedence. Fully compensates for 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?

Clearly states 'Fetch comprehensive gene information from NCBI Gene database' with specific verb and resource. Differentiates from sibling tools like entrez_fetch by being a specialized wrapper for gene records with structured output.

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?

Provides clear context: 'Provide either gene_symbol or gene_id', organism disambiguation, rate limits, and caching. Lacks explicit when-to-use vs alternatives, but examples and purpose imply usage for gene info.

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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