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gene-database

Retrieve NCBI Gene data via E-utilities and Datasets APIs for annotation.

Updated Aug 23, 2026
Search Tags:#api#python#ncbi#datasets#gene#batch-lookup
One-click install
npx skills add https://github.com/BKZhao/MIMIC-Papers-Repro-Agent --skill gene-database-bkzhao
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gene-database
Source: https://github.com/BKZhao/MIMIC-Papers-Repro-Agent/tree/main/.codex/skills/gene-database
Command: npx skills add https://github.com/BKZhao/MIMIC-Papers-Repro-Agent --skill gene-database-bkzhao

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Retrieving comprehensive gene information from NCBI Gene can be cumbersome and error-prone when done manually. This skill provides programmatic access to gene data via E-utilities and the Datasets API, enabling scalable search, retrieval, and integration of gene metadata, RefSeqs, GO annotations, chromosomal maps, and transcript data.

Core Features & Use Cases

  • Search genes by symbol or ID across organisms
  • Batch lookup and detailed summaries via E-utilities
  • Retrieve enriched data (GO annotations, RefSeqs, chromosomal locations, transcripts) via Datasets API
  • Export results in JSON/XML for downstream analytics

Quick Start

Process a file of gene symbols and run the batch lookup to generate a structured gene 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 for multiple symbols?▼

Retrieve gene data from NCBI Gene by searching with gene symbols or IDs via E-utilities and Datasets APIs. It returns enriched metadata, RefSeqs, GO annotations, chromosomal locations, and transcript data in JSON format suitable for downstream analysis.

Can I retrieve GO annotations and RefSeqs from NCBI Gene via API?▼

Retrieve GO annotations, RefSeqs, chromosomal locations, and transcript data via the Datasets API for enriched gene summaries. Results are returned in JSON or dataset-formatted outputs, providing comprehensive annotation data for multi-gene analysis.

How do I handle NCBI E-utilities API rate limits for gene queries?▼

Handle NCBI E-utilities API rate limits by using an API key-based approach for gene queries. The skill manages rate limiting and error conditions automatically, returning structured JSON results without manual intervention for batch lookups.

What's the best way to search genes across model organisms using NCBI?▼

Search genes across human and model organisms using symbol- or ID-based queries through NCBI E-utilities. The approach supports multi-gene retrieval and returns JSON-formatted results with gene metadata, chromosomal maps, and transcript data.

How do I export NCBI gene data to JSON for analytics pipelines?▼

Export NCBI gene data to JSON by querying E-utilities and Datasets APIs for gene metadata, GO annotations, and RefSeqs. The structured JSON or dataset-formatted results integrate directly into analytics pipelines for annotation and analysis.

Does the gene batch lookup tool work without external Python dependencies?▼

The gene batch lookup tool operates without external Python dependencies, using scripts and references to query NCBI E-utilities and Datasets APIs. It handles error conditions and rate limits internally, returning structured JSON results.

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