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gene-database

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

33.0k|3.2k|Updated Oct 19, 2025
Search Tags:#RefSeq#genomics#functional analysis#gene annotation#Datasets API#NCBI Gene#E-utilities#GO terms
One-click install
npx skills add https://github.com/K-Dense-AI/claude-scientific-skills --skill gene-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gene-database
Source: https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-databases/gene-database
Command: npx skills add https://github.com/K-Dense-AI/claude-scientific-skills --skill gene-database

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Manually searching and retrieving gene information from NCBI Gene, including sequences, annotations, and cross-references, is repetitive and inefficient. This Skill automates access to NCBI's E-utilities and Datasets API, simplifying gene annotation, functional analysis, and batch lookups, saving researchers valuable time.

Core Features & Use Cases

  • Gene Search & Retrieval: Find genes by symbol or ID and fetch detailed information, including RefSeqs for transcripts/proteins, Gene Ontology (GO) annotations, and chromosomal locations.
  • Batch Lookups: Efficiently process lists of genes with built-in rate limiting, ideal for annotating gene panels or large datasets.
  • Functional & Pathway Analysis: Discover genes associated with specific biological contexts, pathways, or phenotypes by leveraging advanced query capabilities.
  • Use Case: Provide a list of 50 gene symbols and automatically retrieve their NCBI Gene IDs, full descriptions, chromosomal locations, and associated RefSeq IDs, compiling a comprehensive annotation table for downstream analysis.

Quick Start

Search for BRCA1 in human using E-utilities

python scripts/query_gene.py --search "BRCA1" --organism "human"

Fetch comprehensive data for a gene ID (e.g., 672 for BRCA1) using Datasets API

python scripts/fetch_gene_data.py --gene-id 672

Perform a batch lookup for multiple genes from a file

(Assuming 'gene_list.txt' contains gene symbols like BRCA1, TP53, EGFR)

python scripts/batch_gene_lookup.py --file gene_list.txt --organism human --output results.json

Frequently Asked Questions about gene-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve gene annotations and RefSeq data from NCBI Gene?▼

Gene annotations and RefSeq data are retrieved by querying NCBI Gene via E-utilities or the Datasets API using gene symbols or IDs. This Skill automates those queries to fetch detailed information including transcripts, proteins, chromosomal locations, and GO annotations for your genes.

Can I batch process multiple gene symbols to get their NCBI IDs and functional information?▼

Yes. Batch lookups process lists of gene symbols with built-in rate limiting, automatically retrieving NCBI Gene IDs, descriptions, chromosomal locations, and RefSeq identifiers. Results compile into structured output formats suitable for downstream annotation pipelines.

What output formats does NCBI gene data retrieval support?▼

Multiple output formats are supported: JSON, XML, GenBank, FASTA, and plain text. Choose the format that best fits your downstream analysis tools or database import requirements.

How do I search for genes across different organisms?▼

Specify the organism parameter when querying NCBI Gene to search across species. The Skill handles organism-specific gene symbol resolution and retrieves organism-appropriate RefSeqs, GO terms, and chromosomal metadata.

Does NCBI gene data retrieval handle API rate limits?▼

Yes. Built-in rate limiting respects NCBI E-utilities quotas and API constraints, ensuring reliable batch processing without hitting request throttles. Single queries and bulk operations both comply with NCBI service policies.

What prerequisites are needed to use NCBI gene lookup and functional analysis?▼

Only the requests library is required. Provide gene symbols or NCBI Gene IDs as input; the Skill handles E-utilities authentication and API communication automatically.

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