1.7 KiB
1.7 KiB
title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated
| title | task | lineage_type | upstream_source | upstream_sha | imported_at | prompt_class | upstream_changes | author | validated |
|---|---|---|---|---|---|---|---|---|---|
| COSMIC (Catalogue of Somatic Mutations in Cancer) | import | https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/cosmic.md | 9c9bd2e9 | 2026-06-26 | prompt | accepted | upstream | false |
COSMIC (Catalogue of Somatic Mutations in Cancer)
Base URL
https://cancer.sanger.ac.uk/cosmic/api/v1/
Auth
Registration required. Free academic account or paid commercial license.
Login to get JWT token:
POST /auth/login
Content-Type: application/json
{"email": "[email protected]", "password": "yourpassword"}
Pass token as: Authorization: Bearer <token>
Key Endpoints
Search mutations by gene
GET /mutations/search?q={gene_symbol}&page=1&page_size=5
Get gene information
GET /genes/{gene_symbol}
Example: /genes/BRAF
Response includes: gene_symbol, gene_name, chromosome, cancer_census (bool), tier, mutation_count, sample_count
Get specific mutation by COSMIC ID
GET /mutations/{cosmic_mutation_id}
Example: /mutations/COSV56056643
Response includes: gene, cds_mutation, aa_mutation, mutation_type, fathmm_prediction, genomic_coordinates, tissue_distribution
Cancer Gene Census
GET /cancer-gene-census?tier=1&page_size=10
Mutations by tissue/histology
GET /mutations/distribution/{gene_symbol}
Rate Limits
Not officially published. Bulk data requires SFTP download (licensed).
Important
- COSMIC requires authentication for all API calls
- Commercial use requires a paid license
- Bulk data access via SFTP is preferred over API for large queries
- API structure may change across COSMIC versions