cosmic-database
Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.
npx skills add BioTender-max/awesome-bio-agent-skills --skill cosmic-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# COSMIC Somatic Cancer Mutations Database ## Overview COSMIC (Catalogue Of Somatic Mutations In Cancer) is the world's largest expert-curated database of somatic mutations in cancer, covering 6.7M+ coding mutations, 40,000+ cancer samples, 19,000+ genes across all cancer types. It includes the Cancer Gene Census (critical cancer genes), mutational signatures (SBS, DBS, ID), drug resistance variants, copy number data, gene expression, and methylation. The REST API v3.1 enables programmatic queries; most features are freely accessible after registration. ## When to Use - Checking whether a specific somatic variant in a cancer gene is annotated in COSMIC (frequency, cancer type distribution) - Retrieving all somatic mutations in a gene of interest across COSMIC cancer samples - Accessing COSMIC Cancer Gene Census classifications (Tier 1/2, role: oncogene/TSG/fusion) - Looking up mutational signature attributions for samples or cancer types - Identifying drug resistance variants (pharmacogenomic data) from COSMIC drug resistance database - Building cancer driver gene lists for bioinformatic pipelines - For germline/inherited variants use `clinvar-database`; for drug-target association
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Query 1: Gene Mutations Search
- Query 2: Cancer Gene Census
- Query 3: Specific Mutation Lookup
- Query 4: Sample-Level Mutation Data
- Query 5: Mutational Signatures
- Query 6: Drug Resistance Variants
- Key Concepts
- Cancer Gene Census Tiers
- Mutation ID Stability
pip install requests pandas Register at https://cancer.sanger.ac.uk/cosmic/register to obtain API credentials
What does the cosmic-database skill do?
Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill cosmic-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.