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gene-database

Search NCBI Gene records by symbol or ID and retrieve structured metadata.

21|2|Updated Dec 8, 2025
Search Tags:#bioinformatics#functional analysis#gene lookup#datasets api#e-utilities#ncbi gene#batch annotation
One-click install
npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill gene-database-silverstein
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gene-database
Source: https://github.com/silverstein/claude-scientific-skills-desktop/tree/main/corpus/gene-database
Command: npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill gene-database-silverstein

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires argparse, json, sys, time, urllib.parse, urllib.request, typing, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill removes the friction of manually looking up genes by giving you fast, structured access to NCBI Gene records, including gene metadata and functional annotations.

Core Features & Use Cases

  • Gene search and ID retrieval: Find Gene IDs using NCBI E-utilities (symbol/name plus optional organism filtering).
  • Rich gene annotation lookups: Retrieve gene summaries and detailed records via E-utilities and the NCBI Datasets API.
  • Batch gene annotation workflows: Resolve multiple gene symbols/IDs efficiently with rate limiting and JSON outputs suitable for downstream analysis.

Quick Start

Use the gene-database skill to look up BRCA1 in human by providing the gene’s NCBI Gene ID or by searching by symbol with an organism filter.

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 records and functional annotations in bulk?▼

To fetch NCBI Gene metadata, you search for records by gene symbol or Gene ID using ESearch, then retrieve detailed summaries via ESummary or EFetch. The Datasets API provides additional structured gene metadata, supporting JSON, XML, and text output formats.

Can I search for NCBI Gene IDs by symbol and filter by organism?▼

Yes, you can find NCBI Gene IDs by searching with a gene symbol or name and applying an optional organism filter. This lookup uses NCBI E-utilities to return matched records for targeted annotation and functional analysis.

Does this NCBI gene lookup approach respect API rate limits for batch processing?▼

Yes, batch gene annotation workflows apply rate limiting to respect NCBI E-utilities and Datasets API constraints. This ensures reliable resolution of multiple gene symbols and IDs without exceeding request thresholds.

What is the best way to get GO context and cross-referenced data for gene loci?▼

The best way to get GO context and cross-referenced data for gene loci is using a gene lookup workflow that fetches structured metadata via the NCBI Datasets API and E-utilities. It retrieves aliases, loci, and functional annotations for enrichment.

What output formats are supported when fetching gene metadata from NCBI?▼

Fetching NCBI gene metadata supports JSON, XML, and text output formats. These structured formats allow you to integrate gene summaries, loci, and cross-referenced information directly into downstream bioinformatics pipelines.

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