gene-database

Query NCBI Gene via E-utilities and Datasets API for gene metadata.

Updated Mar 30, 2026

Search Tags:#api #ncbi #annotation #datasets #eutilities #gene #batch-lookup

Ready to run

npx skills add https://github.com/ya-way/cytoclaw-skills --skill gene-database-ya-way

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: gene-database
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/labclaw-lit-gene-database
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill gene-database-ya-way

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Retrieves and annotates gene information by symbol, ID, or batch lists from NCBI Gene using E-utilities and the Datasets API, enabling researchers to access authoritative gene metadata quickly.

Core Features & Use Cases

Retrieve gene nomenclature, RefSeqs, chromosomal location, and GO annotations.
Perform batch lookups for large gene lists and cross-database queries to support annotation pipelines.
Export metadata in JSON or XML for integration with downstream analyses and reporting.

Quick Start

Query NCBI Gene data for a given symbol or ID and retrieve comprehensive metadata using E-utilities or the Datasets API.

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 gene annotations from NCBI Gene using E-utilities?▼

Batch lookup of NCBI Gene annotations uses ESearch, ESummary, and EFetch scripts to query large gene lists by symbol or ID, returning structured metadata like RefSeqs and GO annotations in JSON or XML format.

Can I retrieve RefSeqs and GO annotations for a gene symbol across multiple species?▼

Yes, querying NCBI Gene via E-utilities and the Datasets API supports searches by symbol, name, or gene ID across species, retrieving metadata including RefSeqs, GO annotations, and chromosomal locations.

What is the best way to programmatically access NCBI Datasets API for gene metadata?▼

Accessing the NCBI Datasets API programmatically is best done by querying gene symbols or IDs directly, which returns comprehensive gene nomenclature and metadata in structured JSON or XML outputs for downstream analyses.

Does querying NCBI E-utilities handle rate limits and errors for automated gene annotation pipelines?▼

Yes, querying NCBI E-utilities handles rate limits and errors gracefully, ensuring stable automated retrieval of gene metadata for large-scale annotation pipelines without abrupt failures.

How do I export NCBI gene query results in JSON or XML for downstream analysis?▼

Export NCBI gene query results in JSON or XML by using the built-in E-utilities and Datasets API scripts, which output structured metadata directly suitable for integration with downstream analyses and reporting.

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

Using NCBI E-utilities EFetch, you can retrieve gene nomenclature, RefSeqs, chromosomal locations, and GO annotations, providing comprehensive metadata for cross-database queries and annotation pipelines.