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Scientific Cosmic Database

Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.

5 minutes
By K-Dense AISource
#scientific#claude-code#cosmic-database#bioinformatics#chemistry#database#protein#genomics

You need to know the mutation landscape of your oncology target — which mutations are driver vs. passenger, their frequency across cancer types, and the mutational signatures associated with them. COSMIC is the most comprehensive cancer mutation database, curating somatic mutations, gene fusions, and mutational signatures from published literature and large-scale screens.

Who it's for: cancer researchers studying somatic mutation patterns across tumor types, oncology drug developers validating targets against mutation frequency data, translational scientists identifying patient stratification biomarkers, clinical genomics teams interpreting tumor sequencing results, precision oncology researchers matching patients to targeted therapies

Example

"Query COSMIC for the mutation landscape of EGFR across all cancer types" → Mutation analysis: somatic mutation frequency by cancer type, hotspot mutation identification with functional impact, Cancer Gene Census classification, associated mutational signatures, gene fusion data, and a summary report suitable for target validation documentation

CLAUDE.md Template

New here? 3-minute setup guide → | Already set up? Copy the template below.

# COSMIC Database

## Overview

COSMIC (Catalogue of Somatic Mutations in Cancer) is the world's largest and most comprehensive database for exploring somatic mutations in human cancer. Access COSMIC's extensive collection of cancer genomics data, including millions of mutations across thousands of cancer types, curated gene lists, mutational signatures, and clinical annotations programmatically.

## When to Use This Skill

This skill should be used when:
- Downloading cancer mutation data from COSMIC
- Accessing the Cancer Gene Census for curated cancer gene lists
- Retrieving mutational signature profiles

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README.md

What This Does

COSMIC (Catalogue of Somatic Mutations in Cancer) is the world's largest and most comprehensive database for exploring somatic mutations in human cancer. Access COSMIC's extensive collection of cancer genomics data, including millions of mutations across thousands of cancer types, curated gene lists, mutational signatures, and clinical annotations programmatically.

Quick Start

Step 1: Create a Project Folder

mkdir -p ~/Projects/cosmic-database

Step 2: Download the Template

Click Download above, then:

mv ~/Downloads/CLAUDE.md ~/Projects/cosmic-database/

Step 3: Start Claude Code

cd ~/Projects/cosmic-database
claude

Prerequisites

Account Registration

COSMIC requires authentication for data downloads:

Python Requirements

uv pip install requests pandas

Available Data Types

Core Mutations

Download comprehensive mutation data including point mutations, indels, and genomic annotations.

Common data types:

  • mutations - Complete coding mutations (TSV format)
  • mutations_vcf - Coding mutations in VCF format
  • sample_info - Sample metadata and tumor information
# Download all coding mutations
download_cosmic_file(
    email="user@email.com",
    password="password",
    filepath="GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz"
)

Cancer Gene Census

Access the expert-curated list of ~700+ cancer genes with substantial evidence of cancer involvement.

# Download Cancer Gene Census
download_cosmic_file(
    email="user@email.com",
    password="password",
    filepath="GRCh38/cosmic/latest/cancer_gene_census.csv"
)

Use cases:

  • Identifying known cancer genes
  • Filtering variants by cancer relevance
  • Understanding gene roles (oncogene vs tumor suppressor)
  • Target gene selection for research

Mutational Signatures

Download signature profiles for mutational signature analysis.

# Download signature definitions
download_cosmic_file(
    email="user@email.com",
    password="password",
    filepath="signatures/signatures.tsv"
)

Signature types:

  • Single Base Substitution (SBS) signatures
  • Doublet Base Substitution (DBS) signatures
  • Insertion/Deletion (ID) signatures

Structural Variants and Fusions

Access gene fusion data and structural rearrangements.

Available data types:

  • structural_variants - Structural breakpoints
  • fusion_genes - Gene fusion events
# Download gene fusions
download_cosmic_file(
    email="user@email.com",
    password="password",
    filepath="GRCh38/cosmic/latest/CosmicFusionExport.tsv.gz"
)

Copy Number and Expression

Retrieve copy number alterations and gene expression data.

Available data types:

  • copy_number - Copy number gains/losses
  • gene_expression - Over/under-expression data
# Download copy number data
download_cosmic_file(
    email="user@email.com",
    password="password",
    filepath="GRCh38/cosmic/latest/CosmicCompleteCNA.tsv.gz"
)

Resistance Mutations

Access drug resistance mutation data with clinical annotations.

# Download resistance mutations
download_cosmic_file(
    email="user@email.com",
    password="password",
    filepath="GRCh38/cosmic/latest/CosmicResistanceMutations.tsv.gz"
)

Working with COSMIC Data

Genome Assemblies

COSMIC provides data for two reference genomes:

  • GRCh38 (recommended, current standard)
  • GRCh37 (legacy, for older pipelines)

Specify the assembly in file paths:

# GRCh38 (recommended)
filepath="GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz"

# GRCh37 (legacy)
filepath="GRCh37/cosmic/latest/CosmicMutantExport.tsv.gz"

Versioning

  • Use latest in file paths to always get the most recent release
  • COSMIC is updated quarterly (current version: v102, May 2025)
  • Specific versions can be used for reproducibility: v102, v101, etc.

File Formats

  • TSV/CSV: Tab/comma-separated, gzip compressed, read with pandas
  • VCF: Standard variant format, use with pysam, bcftools, or GATK
  • All files include headers describing column contents

Common Analysis Patterns

Filter mutations by gene:

import pandas as pd

mutations = pd.read_csv('cosmic_mutations.tsv.gz', sep='\t', compression='gzip')
tp53_mutations = mutations[mutations['Gene name'] == 'TP53']

Identify cancer genes by role:

gene_census = pd.read_csv('cancer_gene_census.csv')
oncogenes = gene_census[gene_census['Role in Cancer'].str.contains('oncogene', na=False)]
tumor_suppressors = gene_census[gene_census['Role in Cancer'].str.contains('TSG', na=False)]

Extract mutations by cancer type:

mutations = pd.read_csv('cosmic_mutations.tsv.gz', sep='\t', compression='gzip')
lung_mutations = mutations[mutations['Primary site'] == 'lung']

Work with VCF files:

import pysam

vcf = pysam.VariantFile('CosmicCodingMuts.vcf.gz')
for record in vcf.fetch('17', 7577000, 7579000):  # TP53 region
    print(record.id, record.ref, record.alts, record.info)

Data Reference

For comprehensive information about COSMIC data structure, available files, and field descriptions, see references/cosmic_data_reference.md. This reference includes:

  • Complete list of available data types and files
  • Detailed field descriptions for each file type
  • File format specifications
  • Common file paths and naming conventions
  • Data update schedule and versioning
  • Citation information

Use this reference when:

  • Exploring what data is available in COSMIC
  • Understanding specific field meanings
  • Determining the correct file path for a data type
  • Planning analysis workflows with COSMIC data

Helper Functions

The download script includes helper functions for common operations:

Get Common File Paths

from scripts.download_cosmic import get_common_file_path

# Get path for mutations file
path = get_common_file_path('mutations', genome_assembly='GRCh38')
# Returns: 'GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz'

# Get path for gene census
path = get_common_file_path('gene_census')
# Returns: 'GRCh38/cosmic/latest/cancer_gene_census.csv'

Available shortcuts:

  • mutations - Core coding mutations
  • mutations_vcf - VCF format mutations
  • gene_census - Cancer Gene Census
  • resistance_mutations - Drug resistance data
  • structural_variants - Structural variants
  • gene_expression - Expression data
  • copy_number - Copy number alterations
  • fusion_genes - Gene fusions
  • signatures - Mutational signatures
  • sample_info - Sample metadata

Troubleshooting

Authentication Errors

  • Verify email and password are correct
  • Ensure account is registered at cancer.sanger.ac.uk/cosmic
  • Check if commercial license is required for your use case

File Not Found

  • Verify the filepath is correct
  • Check that the requested version exists
  • Use latest for the most recent version
  • Confirm genome assembly (GRCh37 vs GRCh38) is correct

Large File Downloads

  • COSMIC files can be several GB in size
  • Ensure sufficient disk space
  • Download may take several minutes depending on connection
  • The script shows download progress for large files

Commercial Use

Integration with Other Tools

COSMIC data integrates well with:

  • Variant annotation: VEP, ANNOVAR, SnpEff
  • Signature analysis: SigProfiler, deconstructSigs, MuSiCa
  • Cancer genomics: cBioPortal, OncoKB, CIViC
  • Bioinformatics: Bioconductor, TCGA analysis tools
  • Data science: pandas, scikit-learn, PyTorch

Additional Resources

Citation

When using COSMIC data, cite: Tate JG, Bamford S, Jubb HC, et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Research. 2019;47(D1):D941-D947.

Tips

  • Read the docs: Check the official cosmic-database documentation for latest API changes
  • Start simple: Begin with basic examples before tackling complex workflows
  • Save your work: Keep intermediate results in case of long-running analyses

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