skills.rest
LogauaEngstrom
LogauaEngstromCOMMUNITY
Explore all skills by this author →
GitHub

gene-database

Search NCBI Gene data via E-utilities and Datasets APIs for symbol or ID queries.

18|1|Updated Dec 27, 2025
Search Tags:#ncbi#annotations#datasets#eutilities#gene#batch-lookup
One-click install
npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill gene-database-logauaengstrom
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gene-database
Source: https://github.com/LogauaEngstrom/claude-scientific-skills/tree/main/scientific-skills/gene-database
Command: npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill gene-database-logauaengstrom

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Query and annotate gene information from NCBI across symbols, IDs, and multiple formats, enabling batch lookups and integrated metadata retrieval.

Core Features & Use Cases

  • Symbol and ID searches to retrieve gene names, descriptions, GO annotations, RefSeqs, chromosomal locations, and cross-references.
  • Batch lookups for gene panels or lists, returning structured summaries and detailed records.
  • Integration workflows for data pipelines and publications, with examples for common analyses.

Quick Start

Fetch BRCA1 gene data for Homo sapiens and return a structured JSON with symbol, description, GO terms, and genomic location.

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 using symbols or IDs?▼

You can batch lookup NCBI gene data by passing a list of gene symbols or IDs to the skill, which queries the E-utilities and Datasets APIs and returns structured metadata including RefSeqs, GO annotations, and cross-references.

What gene metadata can I retrieve from NCBI E-utilities and Datasets APIs?▼

NCBI gene metadata retrieval includes gene names, descriptions, GO annotations, RefSeqs, chromosomal locations, and cross-references for downstream analyses, all formatted as structured JSON records.

Can I use NCBI gene queries for data pipelines and publication workflows?▼

Yes, the skill provides integration workflows and Python scripts with error handling and rate-limiting guidance, designed to support reliable gene data retrieval for data pipelines and publication-ready analyses.

How do I get GO annotations and RefSeqs for a specific gene like BRCA1?▼

To get GO annotations and RefSeqs for BRCA1, query the skill with the gene symbol and organism name to receive a structured JSON record containing the symbol, description, GO terms, and genomic location.

What are the limitations of using NCBI E-utilities for batch gene lookups?▼

The main limitation of batch gene lookups with NCBI E-utilities is API rate limiting, which the skill addresses by providing built-in Python scripts with basic error handling and rate-limiting guidance to ensure reliable data retrieval.

Related Skills

Explore More Education & Research Skills→
Hung-3008Hung-3008
1

gene-database

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

Community
Advanced
HolobiomicsLabHolobiomicsLab
4

geo-database

Locate and retrieve GEO datasets and metadata for gene expression studies.

Official
Advanced
K-Dense-AIK-Dense-AI
33.0k

gene-database

Query NCBI Gene data via E-utilities and Datasets API for annotations.

Official
Intermediate
hxk622hxk622
8

gene-database

Query NCBI Gene database for gene annotations and batch lookups.

Community
Intermediate