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LeonChaoX
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gene-database

Retrieve NCBI Gene metadata via E-utilities and Datasets API.

783|65|Updated Feb 27, 2026
Search Tags:#bioinformatics#functional analysis#gene annotation#ncbi#batch lookup#datasets api#e-utilities
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill gene-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gene-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/gene-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill gene-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill removes the time-consuming manual lookup process by helping you quickly search NCBI Gene and retrieve structured gene metadata for downstream annotation and functional analysis.

Core Features & Use Cases

  • Gene search by symbol/ID: Find matching Gene IDs using NCBI E-utilities, with optional organism filtering to reduce ambiguity.
  • Rich gene record retrieval: Pull detailed gene information via both E-utilities (ESummary/EFetch) and the NCBI Datasets API (for comprehensive JSON responses).
  • Batch gene lookup: Process many gene symbols or IDs efficiently with rate limiting and chunking, producing analysis-ready summaries.
  • Use Case: Given a gene panel list, fetch each gene’s description, organism, chromosome, map location, and identifiers, then compile the results into a table for a manuscript or functional analysis.

Quick Start

Use the gene-database skill to query BRCA1 in human and return its NCBI Gene metadata.

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 metadata for a list of gene symbols in batch?▼

Batch gene lookup processes multiple gene symbols or IDs using NCBI E-utilities and the Datasets API with rate limiting and chunking, producing analysis-ready structured JSON results containing descriptions, chromosome locations, and identifiers.

What is the best way to search for a gene ID using NCBI E-utilities and filter by organism?▼

Searching NCBI E-utilities with a gene symbol while applying optional organism filtering reduces ambiguity and returns matching Gene IDs, which can then be used to fetch detailed records via ESummary or EFetch.

Can I use the NCBI Datasets API to fetch GO annotations and gene locations?▼

Yes, the NCBI Datasets API pulls comprehensive JSON responses containing rich gene records, including gene locations, GO annotations, and related metadata required for functional and annotation workflows.

Do I need an API key to handle rate limiting when fetching gene records from NCBI?▼

Fetching gene records from NCBI requires deterministic script execution that builds correct Entrez queries and manages API-key headers to handle rate limiting, ensuring reliable retrieval of structured JSON results.

How do I compile gene annotation results into a table for a manuscript?▼

Compiling gene annotation results for a manuscript involves fetching each gene's description, organism, chromosome, map location, and identifiers via batch lookup, then formatting the structured JSON output into a table.

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