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cosmic-database

Download COSMIC data files via CLI or Python API with authenticated credentials.

4|1|Updated Jun 18, 2025
Search Tags:#authentication#bioinformatics#cosmic#cancer-genomics#data-download#programmatic-access
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill cosmic-database-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: cosmic-database
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/cosmic-database
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill cosmic-database-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

COSMIC data access is essential for researchers who need up-to-date, comprehensive somatic mutation data, Cancer Gene Census annotations, mutational signatures, and structural/genomic context for cancer genomics projects, but obtaining and organizing these data programmatically can be cumbersome and authentication-restricted.

Core Features & Use Cases

  • Programmatic download of core COSMIC data types (mutations, Cancer Gene Census, mutational signatures, structural variants, copy number alterations, gene expression, and resistance mutations) for integration into reproducible pipelines.
  • CLI and Python API access to authenticated COSMIC downloads, enabling seamless incorporation into bioinformatics workflows and analysis scripts.
  • Use cases include retrieving mutation data for cohort analyses, filtering genes via the Cancer Gene Census, performing mutational signature analyses, and integrating COSMIC data into downstream variant interpretation.

Quick Start

Authenticate with your COSMIC account and run the provided script to download the desired data file.

Frequently Asked Questions about cosmic-database

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

FAQPage Schema
How do I download COSMIC data files programmatically for cancer genomics analysis?▼

Yes, the Skill supports programmatic access to download core COSMIC data types including mutations, Cancer Gene Census, mutational signatures, structural variants, copy number alterations, gene expression, and resistance mutations for your bioinformatics workflows.

How do I authenticate to access COSMIC mutation data in a reproducible workflow?▼

Do I need a COSMIC account to download Cancer Gene Census and mutational signature data programmatically?

Do I need a COSMIC account to download Cancer Gene Census and mutational signature data programmatically?▼

Can I integrate COSMIC data download into a Python bioinformatics script?

Can I integrate COSMIC data download into a Python bioinformatics script?▼

What are the limitations of using requests for authenticated COSMIC data access?

What are the limitations of using requests for authenticated COSMIC data access?▼

What is the best way to retrieve structural variants and copy number alterations from COSMIC?

What is the best way to retrieve structural variants and copy number alterations from COSMIC?▼

The best way to retrieve structural variants and copy number alterations is using the provided CLI script or Python API, which authenticates your COSMIC credentials and securely downloads these specific data files to disk for downstream analysis.

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