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gene-database

Retrieve NCBI gene metadata by symbol or ID via E-utilities and Datasets API.

1|Updated Jan 26, 2026
Search Tags:#bioinformatics#Datasets API#E-utilities#annotation#NCBI#gene#batch lookup
One-click install
npx skills add https://github.com/Victory-Hugo/S2-Agent-Skill --skill gene-database-victory-hugo
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gene-database
Source: https://github.com/Victory-Hugo/S2-Agent-Skill/tree/main/skills/databases/gene-database
Command: npx skills add https://github.com/Victory-Hugo/S2-Agent-Skill --skill gene-database-victory-hugo

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill enables researchers to quickly retrieve gene metadata from NCBI by gene symbol or gene ID, consolidating key information such as RefSeqs, GO annotations, chromosomal locations, and cross-references for downstream analyses.

Core Features & Use Cases

  • Search by symbol or ID using E-utilities and the NCBI Datasets API.
  • Retrieve comprehensive gene metadata including descriptions, chromosomal coordinates, RefSeqs, transcripts, GO terms, and cross-references.
  • Batch lookups to annotate large gene lists and integrate results into analysis pipelines.
  • Use Case: Given a list of gene symbols, fetch official IDs and annotations to build a gene annotation table for publications or reports.

Quick Start

Example: look up BRCA1 in human using the command below: python scripts/query_gene.py --search "BRCA1[gene] AND human[organism]" --organism human

Frequently Asked Questions about gene-database

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

FAQPage Schema
How do I retrieve NCBI gene annotations using a gene symbol?▼

To retrieve NCBI gene annotations by symbol, use the provided Python script query_gene.py with E-utilities and the Datasets API to fetch metadata like RefSeqs and GO terms.

Can I batch lookup multiple gene IDs for bioinformatics pipelines?▼

Yes, you can batch lookup multiple gene IDs to annotate large gene lists, consolidating official IDs and cross-references for downstream bioinformatics pipeline integration.

What gene metadata is available through the NCBI Datasets API?▼

The NCBI Datasets API provides gene metadata including descriptions, chromosomal coordinates, RefSeqs, transcripts, GO annotations, and cross-references for comprehensive analysis.

How do I query BRCA1 in human using E-utilities?▼

Query BRCA1 in human by executing the Python script with the search string BRCA1[gene] AND human[organism] to retrieve specific gene metadata from the NCBI database.

Does this Skill require external dependencies to fetch GO annotations?▼

No external dependencies are required to fetch GO annotations, as the Skill uses Python scripts under the scripts directory to directly interface with NCBI E-utilities and the Datasets API.

Is this approach better for building gene annotation tables than manual NCBI searches?▼

Using this programmatic approach for building gene annotation tables is faster than manual NCBI searches, enabling automated batch lookups of chromosomal locations and RefSeqs for publications.

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