cosmic-database

COSMIC Database - Cancer Somatic Mutation Database Tool

Skill Overview

The COSMIC Database skill allows you to directly access the world’s largest database of cancer somatic mutations via Python scripts and command-line tools, downloading research data such as the Cancer Gene Census, mutation signatures, gene fusions, and more.

Use Cases

1. Cancer Genomics Research

When your research involves cancer mutation analysis, you can use COSMIC to obtain millions of expert-annotated somatic mutation records covering thousands of cancer types, with support for multi-dimensional filtering by gene, cancer type, mutation type, and more.

2. Precision Oncology and Drug Development

Query resistance mutation data, the Cancer Gene Census, and clinical annotation information to help identify oncogenes and tumor suppressor genes, supporting targeted therapy decisions and drug target discovery.

3. Bioinformatics Pipeline Integration

Use COSMIC data as an important reference for variant annotation and mutation signature analysis. It supports standard formats like VCF and TSV and can be seamlessly integrated with commonly used tools such as VEP, ANNOVAR, and SigProfiler.

Core Features

1. Data Download and Query

Provides a Python API and command-line tools to download various data types including mutation data, the Cancer Gene Census, copy number variations, gene fusions, and resistance mutations, with support for GRCh37 and GRCh38 genome builds.

2. Multi-Format Data Support

Downloaded data includes TSV/CSV formats (readable with pandas) and VCF format (processable with pysam, bcftools). All files include complete field descriptions and headers.

3. Flexible Path Management

Built-in quick path mappings for common data types let you obtain the correct file path by simply specifying the data type name, with support for retrieving the latest version or specific historical versions.

Frequently Asked Questions

Is the COSMIC database free?

Academic users can use COSMIC for free—just register an account at cancer.sanger.ac.uk/cosmic. Commercial users need to obtain a commercial license through QIAGEN.

How do I start using the COSMIC Database skill?

First ensure the necessary Python libraries are installed (uv pip install requests pandas), then use the scripts/download_cosmic.py script along with your registered email and password to download data. Supports quick downloads by data type or specifying exact file paths.

What is the difference between COSMIC and TCGA?

COSMIC is an expert-curated cancer mutation database focused on somatic mutations and the Cancer Gene Census; TCGA is the primary cancer genome sequencing project data. COSMIC integrates multiple data sources, including TCGA, and provides unified annotation, making it better suited for querying and variant annotation.