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gene-database

Retrieve NCBI gene annotations, RefSeqs, mappings, and GO terms by symbol or ID.

1|Updated Mar 11, 2026
Search Tags:#bioinformatics#batch#ncbi#annotation#datasets#eutilities#gene
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill gene-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gene-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/gene-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill gene-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Querying and annotating gene information from NCBI is tedious and error-prone when done manually; this skill consolidates symbol/ID searches, batch lookups, and data retrieval from E-utilities and Datasets API into a repeatable workflow.

Core Features & Use Cases

  • Search genes by symbol or ID using E-utilities.
  • Retrieve detailed metadata including GO annotations, RefSeqs, chromosomal locations, and cross-references.
  • Batch lookups and symbol-to-ID resolution to build annotation tables for panels or studies.
  • Use case: Create a compact gene reference set for a disease panel by fetching metadata for BRCA1, TP53, and EGFR.

Quick Start

Use this skill to fetch BRCA1 gene data from NCBI and display its 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 annotations and RefSeqs using a gene symbol or ID?▼

To retrieve NCBI gene annotations and RefSeqs, query the database by gene symbol or ID to fetch comprehensive metadata, including GO terms and chromosomal locations, directly via E-utilities and Datasets APIs.

Can I perform batch gene lookups and symbol-to-ID resolution for high-throughput studies?▼

Yes, you can perform batch gene lookups and symbol-to-ID resolution to systematically build structured annotation tables for disease panels or high-throughput pipelines.

Does this NCBI gene query tool require an API key for E-utilities?▼

No, an API key is not required, but the tool offers optional API key support for E-utilities to improve query speeds during large batch annotation tasks.

What is the best way to integrate NCBI gene data into a cross-species study pipeline?▼

The best way to integrate NCBI gene data is by exporting structured JSON outputs from your gene queries, which can be directly ingested by downstream high-throughput pipelines for cross-species studies.

How does this approach handle NCBI E-utilities errors during batch annotation?▼

It ensures batch annotation reliability by applying robust error handling to all NCBI E-utilities and Datasets API requests, preventing pipeline failures during data retrieval.

What gene metadata is available when searching NCBI by symbol?▼

Searching NCBI by symbol retrieves comprehensive gene metadata, including GO annotations, RefSeqs, chromosomal locations, and cross-references for cross-species analysis.

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