drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/tcga-gdc.md

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
TCGA / GDC Data Portal API		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/tcga-gdc.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

TCGA / GDC Data Portal API

Base URL

https://api.gdc.cancer.gov

Auth

No auth for public data. Token needed only for controlled-access downloads.

Key Endpoints

All search endpoints accept GET or POST (POST preferred for complex filters).

Endpoint	Description
/projects	List/filter cancer projects (e.g. TCGA-BRCA)
/cases	Search cases (patients/samples)
/files	Search/filter files (BAM, VCF, expression)
/genes	Search gene-level data
/ssms	Search simple somatic mutations
/ssm_occurrences	Mutation occurrences across cases
/files/{uuid}	File metadata by UUID
/data/{uuid}	Download file by UUID

Filter Syntax (POST body)

{
  "filters": {
    "op": "in",
    "content": {"field": "cases.project.project_id", "value": ["TCGA-BRCA"]}
  },
  "fields": "file_id,file_name,data_type",
  "format": "JSON",
  "size": 10
}

Operators: in, =, !=, >, <, >=, <=, is, not, and, or

Example Calls

# List projects
https://api.gdc.cancer.gov/projects?size=5&fields=project_id,name,primary_site

# BRCA1 mutations (POST)
curl -X POST https://api.gdc.cancer.gov/ssms \
  -H "Content-Type: application/json" \
  -d '{"filters":{"op":"in","content":{"field":"consequence.transcript.gene.symbol","value":["BRCA1"]}},"fields":"ssm_id,genomic_dna_change","size":5}'

# Cases in TCGA-LUAD
https://api.gdc.cancer.gov/cases?filters=%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22project.project_id%22%2C%22value%22%3A%5B%22TCGA-LUAD%22%5D%7D%7D&size=3&fields=submitter_id,disease_type

Pagination

from (offset) and size (limit, max 10000). Default size is 10.

Rate Limits

No strict limit for metadata queries. Use GDC Transfer Tool for bulk file downloads.