72 lines
2.1 KiB
Markdown
72 lines
2.1 KiB
Markdown
---
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title: "TCGA / GDC Data Portal API"
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task: ""
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lineage_type: import
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upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/tcga-gdc.md
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upstream_sha: 9c9bd2e9
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imported_at: 2026-06-26
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prompt_class: prompt
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upstream_changes: accepted
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author: upstream
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validated: false
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---
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# TCGA / GDC Data Portal API
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## Base URL
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```
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https://api.gdc.cancer.gov
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```
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## Auth
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No auth for public data. Token needed only for controlled-access downloads.
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## Key Endpoints
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All search endpoints accept GET or POST (POST preferred for complex filters).
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| Endpoint | Description |
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|----------|-------------|
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| `/projects` | List/filter cancer projects (e.g. TCGA-BRCA) |
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| `/cases` | Search cases (patients/samples) |
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| `/files` | Search/filter files (BAM, VCF, expression) |
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| `/genes` | Search gene-level data |
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| `/ssms` | Search simple somatic mutations |
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| `/ssm_occurrences` | Mutation occurrences across cases |
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| `/files/{uuid}` | File metadata by UUID |
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| `/data/{uuid}` | Download file by UUID |
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## Filter Syntax (POST body)
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```json
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{
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"filters": {
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"op": "in",
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"content": {"field": "cases.project.project_id", "value": ["TCGA-BRCA"]}
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},
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"fields": "file_id,file_name,data_type",
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"format": "JSON",
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"size": 10
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}
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```
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Operators: `in`, `=`, `!=`, `>`, `<`, `>=`, `<=`, `is`, `not`, `and`, `or`
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## Example Calls
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```
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# List projects
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https://api.gdc.cancer.gov/projects?size=5&fields=project_id,name,primary_site
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# BRCA1 mutations (POST)
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curl -X POST https://api.gdc.cancer.gov/ssms \
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-H "Content-Type: application/json" \
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-d '{"filters":{"op":"in","content":{"field":"consequence.transcript.gene.symbol","value":["BRCA1"]}},"fields":"ssm_id,genomic_dna_change","size":5}'
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# Cases in TCGA-LUAD
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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
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```
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## Pagination
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`from` (offset) and `size` (limit, max 10000). Default size is 10.
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## Rate Limits
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No strict limit for metadata queries. Use GDC Transfer Tool for bulk file downloads.
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