Create a local database of TCGA metadata from the GDC API.
Requires uv.
To generate the database:
./run.shUseful links
- TCGA Resources: https://gdc.cancer.gov/about-data/gdc-data-processing/resources-tcga-users
- Code tables: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables
- About barcodes: https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/#reading-barcodes
- Encyclopedia: https://docs.gdc.cancer.gov/Encyclopedia/
Data Model
- https://docs.gdc.cancer.gov/Data/Data_Model/GDC_Data_Model/
- https://docs.gdc.cancer.gov/Data_Dictionary/
- https://docs.gdc.cancer.gov/Data_Dictionary/viewer/
- https://github.com/NCI-GDC/gdcdictionary/tree/develop/src/gdcdictionary/schemas
API
- https://docs.gdc.cancer.gov/Encyclopedia/pages/GDC_API/
- https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/
- https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval
- https://docs.gdc.cancer.gov/API/Users_Guide/Python_Examples/
- https://docs.gdc.cancer.gov/API/Users_Guide/GraphQL_Examples/
- https://docs.gdc.cancer.gov/API/Users_Guide/Additional_Examples/
- https://docs.gdc.cancer.gov/API/Users_Guide/Appendix_A_Available_Fields/
- https://docs.gdc.cancer.gov/API/Users_Guide/Appendix_B_Key_Terms/
- https://docs.gdc.cancer.gov/API/Users_Guide/Appendix_C_Format_of_Submission_Requests_and_Responses/
- https://gdc.cancer.gov/developers/gdc-application-programming-interface-api
- https://github.com/NCI-GDC/gdc-frontend-framework/blob/3aeb60a6/packages/core/src/features/gdcapi/gdcapi.ts#L96
projects: Information about projectscases: Information related to cases, or sample donorsfiles: Information about files stored in the GDChistory: Information related to file version historyannotations: Information about annotations to GDC data
"Search box" endpoint (via query parameter):
https://api.gdc.cancer.gov/v0/all?query=TCGA&size=5
https://api.gdc.cancer.gov/{endpoint}/_mapping
BCR = "Biospecimen Core Resource"