Public releases¶
Available April 5, 2024¶
CDA is now harmonizing terms as they are incorporated into the CRDC Data Element list. In this release we have included harmonized the values for:
- ethnicity
- file_format
- morphology
- primary_diagnosis
- race
- species
- therapeutic_agent
- source_material_type (cancer/normal)
- treatment_type
- vital_status
In future releases, we expect the harmonization to both broaden and improve. Additionally, in an upcoming release we will provide both the harmonized and original values to make finding the original data easier.
Data extraction and release information¶
- GDC data version 39.0 (extraction date 3/27/2024)
- PDC data version 3.8 (extraction date 3/27/2024)
- IDC data version v17 (extraction date 3/27/2024)
- CDS data version 8.0 (extraction date 3/27/2024)
Known Issues¶
- DICOM was not included in the CRDC Data Element list for file_format, so no IDC files have file_format values
- CDS data includes clashing integer IDs. We included that data with the following changes:
- Ensured that any integer IDs are well-wrapped by project qualifiers to make them unique within CDS
- In instances where the same ID was attached to multiple, conflicting metadata the resulting records will be clobbered copies of one instance. A record of the effected data is available here
beta versions¶
Available September, 12 2023.¶
Data extraction and release information¶
- GDC data version 38.0 (extraction date 9/1/2023)
- PDC data version 3.4 (extraction date 8/24/2023)
- IDC data version 15 (extraction date 7/19/2023)
- CDS data version 3.0 (extraction date 8/31/2023)
Data from Cancer Data Services (CDS) is now available!
Available June 13, 2023.¶
Data extraction and release information¶
- GDC data version 37.0 (extraction date 6/1/2023)
- PDC data version 3.0 (extraction date 6/5/2023)
- IDC data version 14 (extraction date 6/7/2023)
IDC data now contains ethnicity data
Available May 4, 2023.¶
Datasets & Fields¶
Data extraction and release information¶
The current version and release dates for each of the database are:
- GDC data version 37, extraction date - ⅘/2023
- PDC data version 2.16, extraction date - 2/9/2023
- IDC data version 13, extraction date - 4/4/2023
Available November 3, 2022.¶
Datasets & Fields¶
Data extraction and release information¶
The current version and release dates for each of the database are:
- GDC data version - v34.0, GDC extraction date - 09/29/2022
- PDC data version - v2.10, PDC extraction date - 09/29/2022
- IDC data version - v.10.0, IDC extraction date - 09/29/2022
Available September 2022.¶
Datasets & Fields¶
- Versions:
- GDC: v33.1, 06/23/2022
- PDC: v2.7, 06/23/20221
- IDC: v.9.0, 06/24/2022
Early alphas¶
Available as of 7/11/22.¶
The beta 3.0 release of CDA searches across data from the Genomics Data Commons (GDC), the Proteomics Data Commons (PDC), and the Imaging Data Commons (IDC) to aggregate and return data to users via a single application programming interface (API).
Datasets & Fields¶
- All datasets updated as follows
- GDC: v33.1, 06/23/2022
- PDC: v2.7, 06/23/20221
- IDC: v.9.0, 06/24/2022
Metadata Changes¶
- Summary
- Previous table format now called Subjects endpoint
- Replaced all File entities with Files - a list of file ids associated with the entity that the list is located in. e.g
- File -> Files
- ResearchSubject.File -> ResearchSubject.Files
- ResearchSubject.Specimen.File -> ResearchSubject.Specimen.Files
- Replaced all File entities with Files - a list of file ids associated with the entity that the list is located in. e.g
- Files endpoint added:
- Endpoint oriented around File information
- Includes all information regarding the file's associated entities(Subject, ResearchSubject, and Specimen)
- Newly available fields:
- vital_status
- days_to_death
- cause_of_death
- ResearchSubject.Diagnosis.morphology
- ResearchSubject.Diagnosis.method_of_diagnosis
- File.data_modality
- File.dbgap_accession_number
- File.imaging_modality
- File.imaging_series
- ResearchSubject.Diagnosis.Treatment.therapeutic_agent
- ResearchSubject.Diagnosis.Treatment.treatment_anatomic_site
- ResearchSubject.Diagnosis.Treatment.treatment_effect
- ResearchSubject.Diagnosis.Treatment.treatment_end_reason
- ResearchSubject.Diagnosis.Treatment.number_of_cycles
- Renamed fields (old -> new):
- ResearchSubject.associated_project -> ResearchSubject.member_of_research_project
- ResearchSubject.primary_disease_site -> ResearchSubject.primary_diagnosis_site
- ResearchSubject.primary_disease_type -> ResearchSubject.primary_disease_type
- ResearchSubject.Specimen.age_at_collection -> ResearchSubject.Specimen.days_to_collection
- Previous table format now called Subjects endpoint
Known bugs and issues - these will be fixed in an upcoming release¶
- tumor stages are not harmonized, there are redundant terms (complicates query)
- Searches on the subject endpoint incorrectly count files. Please use the file counts for the same query from the files endpoint
- Some PDC files are incorrectly labeled at the specimen level, for e.g. a file may be inappropriately labeled as both cancer and normal.
2.X¶
Version 3.0 is a full rewrite of our code and older versions of cdapython are no longer maintained or supported. If you'd like to see how the project has evolved, you can still access the their documentation here: