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gene-database

Query NCBI Gene data by symbol or ID with batch workflows.

4|1|Updated Jun 18, 2025
Search Tags:#genomics#ncbi#annotation#datasets#gene#e-utils
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill gene-database-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gene-database
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/gene-database
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill gene-database-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

Researchers need programmatic access to accurate gene data from NCBI across symbols, IDs, and batch queries to accelerate annotation and analysis.

Core Features & Use Cases

  • Search genes by symbol or ID using E-utilities (esearch) and retrieve up-to-date identifiers and summaries.
  • Retrieve comprehensive gene information including RefSeqs, GO annotations, chromosomal locations, and phenotypes via esummary, efetch, and Datasets.
  • Batch gene lookups to map symbols to IDs and fetch multi-gene details for annotation pipelines and comparative analyses.
  • Use cases: build gene reference tables for publications, validate gene lists, enrich datasets with gene metadata.

Quick Start

Use batch_gene_lookup.py to fetch IDs and summaries for a list of gene symbols.

Frequently Asked Questions about gene-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I batch query NCBI gene data to map symbols to IDs?▼

NCBI gene data retrieval via E-utilities and Datasets APIs supports batch workflows for mapping symbols to IDs. It fetches comprehensive details including RefSeqs, GO annotations, chromosomal locations, and phenotypes with rate-limited processing and error handling.

Can I retrieve GO annotations and RefSeq data for a list of genes programmatically?▼

Yes, retrieving GO annotations and RefSeq data is supported through esummary, efetch, and Datasets APIs. The Skill performs cross-database enrichment to fetch comprehensive gene information including chromosomal locations and phenotypes, outputting structured JSON or XML formats.

What is the best way to validate gene lists and enrich datasets with NCBI metadata?▼

The best way to validate gene lists and enrich datasets with NCBI metadata is via batch gene lookups using E-utilities. The Skill queries gene data by symbol or ID, retrieving up-to-date identifiers and summaries to build accurate gene reference tables for publications.

Does querying NCBI E-utilities require handling API rate limits for large annotation pipelines?▼

Yes, querying NCBI E-utilities requires handling API rate limits for large annotation pipelines. The Skill implements rate-limited processing and error handling during API interactions to ensure stable batch gene lookups and cross-database enrichment workflows.

How do I fetch chromosomal locations and phenotypes using NCBI gene IDs?▼

Fetching chromosomal locations and phenotypes using NCBI gene IDs is accomplished via esummary, efetch, and Datasets APIs. The Skill retrieves comprehensive gene information and outputs structured JSON or XML data, accelerating annotation and comparative analysis tasks.

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