73 lines
1.7 KiB
Markdown
73 lines
1.7 KiB
Markdown
---
|
|
title: "COSMIC (Catalogue of Somatic Mutations in Cancer)"
|
|
task: ""
|
|
lineage_type: import
|
|
upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/cosmic.md
|
|
upstream_sha: 9c9bd2e9
|
|
imported_at: 2026-06-26
|
|
prompt_class: prompt
|
|
upstream_changes: accepted
|
|
author: upstream
|
|
validated: 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
|