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gene-database

Search NCBI Gene by symbol or ID and retrieve gene metadata.

75|7|Updated Feb 14, 2026
Search Tags:#ncbi#annotation#datasets#eutilities#gene#batch-lookup
One-click install
npx skills add https://github.com/jiaxiaojunQAQ/SkillJect --skill gene-database-jiaxiaojunqaq
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gene-database
Source: https://github.com/jiaxiaojunQAQ/SkillJect/tree/main/data/skills_sample/gene-database
Command: npx skills add https://github.com/jiaxiaojunQAQ/SkillJect --skill gene-database-jiaxiaojunqaq

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Query NCBI Gene data by symbol or ID and retrieve comprehensive gene data for annotation, analysis, and workflow automation, enabling rapid access to gene metadata across resources.

Core Features & Use Cases

  • Symbol/ID lookups via E-utilities and NCBI Datasets APIs for the Gene database.
  • Retrieve metadata such as RefSeqs, GO annotations, chromosomal locations, phenotypes, and transcripts.
  • Batch lookups to process lists of genes and produce structured outputs for downstream analyses.
  • Use cases include building gene annotation tables, cross-species comparisons, and GO/RefSeq enrichment.

Quick Start

Provide a file named genes.txt containing one gene symbol per line, then run the batch_gene_lookup.py script to generate a JSON annotation file.

Frequently Asked Questions about gene-database

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

FAQPage Schema
How do I batch lookup NCBI Gene data by symbol or ID?▼

Batch lookup NCBI Gene data by providing a text file containing one gene symbol per line, then execute the batch script to generate a structured JSON annotation file via E-utilities and Datasets APIs.

What gene metadata can I retrieve from NCBI using E-utilities?▼

Retrieve comprehensive NCBI Gene metadata including RefSeqs, GO annotations, chromosomal locations, phenotypes, and transcripts via E-utilities and Datasets APIs for downstream analysis.

Can I use an API key for NCBI E-utilities to manage rate limits during batch gene queries?▼

Yes, batch gene lookup supports API-key integration for E-utilities with robust error handling to manage rate limits and failures during large-scale NCBI Gene queries.

Does this NCBI gene retrieval approach work for cross-species comparisons and GO enrichment?▼

Yes, structured outputs from NCBI Gene batch lookups directly support cross-species comparisons, GO enrichment, and building comprehensive gene annotation tables.

What are the limitations of using Datasets API and E-utilities for gene annotation?▼

Limitations include NCBI API rate limits and query failures, mitigated by API-key support and robust error handling to ensure reliable gene annotation retrieval.

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