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gabrielaltay
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tcga-patients-open

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Tags:
cancer
tcga
clinical
genomics
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gabrielaltay commited on
Commit
bbcc13a
·
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1 Parent(s): 373cfdd

Add clinical_supplement struct column to patient rows (BCR biotab data: patient/follow_ups/ntes/drugs/radiations/ablations/omfs sub-fields, per-project schema). Patients view now surfaces the same BCR data the tabular view exposes.

Browse files
Files changed (34) hide show
  1. README.md +4 -4
  2. TCGA-ACC/data.parquet +2 -2
  3. TCGA-BLCA/data.parquet +2 -2
  4. TCGA-BRCA/data.parquet +2 -2
  5. TCGA-CESC/data.parquet +2 -2
  6. TCGA-CHOL/data.parquet +2 -2
  7. TCGA-COAD/data.parquet +2 -2
  8. TCGA-DLBC/data.parquet +2 -2
  9. TCGA-ESCA/data.parquet +2 -2
  10. TCGA-GBM/data.parquet +2 -2
  11. TCGA-HNSC/data.parquet +2 -2
  12. TCGA-KICH/data.parquet +2 -2
  13. TCGA-KIRC/data.parquet +2 -2
  14. TCGA-KIRP/data.parquet +2 -2
  15. TCGA-LAML/data.parquet +2 -2
  16. TCGA-LGG/data.parquet +2 -2
  17. TCGA-LIHC/data.parquet +2 -2
  18. TCGA-LUAD/data.parquet +2 -2
  19. TCGA-LUSC/data.parquet +2 -2
  20. TCGA-MESO/data.parquet +2 -2
  21. TCGA-OV/data.parquet +2 -2
  22. TCGA-PAAD/data.parquet +2 -2
  23. TCGA-PCPG/data.parquet +2 -2
  24. TCGA-PRAD/data.parquet +2 -2
  25. TCGA-READ/data.parquet +2 -2
  26. TCGA-SARC/data.parquet +2 -2
  27. TCGA-SKCM/data.parquet +2 -2
  28. TCGA-STAD/data.parquet +2 -2
  29. TCGA-TGCT/data.parquet +2 -2
  30. TCGA-THCA/data.parquet +2 -2
  31. TCGA-THYM/data.parquet +2 -2
  32. TCGA-UCEC/data.parquet +2 -2
  33. TCGA-UCS/data.parquet +2 -2
  34. TCGA-UVM/data.parquet +2 -2
README.md CHANGED
@@ -150,7 +150,7 @@ all 33 TCGA projects.
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  **This view presents one HuggingFace subset per TCGA project**, with one row per patient. See the [`tcga-tabular-open`][tabular] companion for a per-table view of the same underlying data.
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- - **Generated:** 2026-05-09 21:21:40 UTC
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  - **Schema:** derived from the [GDC Data Dictionary][gdc-dict].
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  - **GDC data release:** Data Release 45.0 - December 04, 2025
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@@ -186,8 +186,8 @@ Three sources feed each project's data, all open-access:
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  the BCR-original biotabs preserve. The schema varies by cancer type
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  (e.g. BLCA's BCG-response columns don't exist in CHOL's hepatic-marker
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  forms), so each project's biotabs ship only the columns they actually
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- carry. Discovered via `/files` filtered to `data_type="Clinical
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- Supplement"` + `data_format="bcr biotab"`, downloaded via `/data`.
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  ### Source data filters (canonical)
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@@ -207,7 +207,7 @@ for one source:
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  | GDC `/cases` | nested fields on each patient row (`demographic`, `diagnoses`, `follow_ups`, `exposures`, `family_histories`, `samples`); `gdc_portal_url` link added |
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  | Masked Somatic Mutation MAFs | `samples_masked_somatic_mutation` array on each patient row (sample FKs resolved alongside GDC's aliquot UUIDs) |
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  | Gene Expression Quantification | `samples_gene_expression_quantification` array on each patient row (`stranded_first` / `stranded_second` dropped — GDC harmonizes as unstranded) |
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- | BCR Clinical Supplements | consumed in-memory for the `survival_derived` supplement (see below); not surfaced as columns on the row |
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212
 
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  ### Specific to this view
 
150
 
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  **This view presents one HuggingFace subset per TCGA project**, with one row per patient. See the [`tcga-tabular-open`][tabular] companion for a per-table view of the same underlying data.
152
 
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+ - **Generated:** 2026-05-09 22:03:39 UTC
154
  - **Schema:** derived from the [GDC Data Dictionary][gdc-dict].
155
  - **GDC data release:** Data Release 45.0 - December 04, 2025
156
 
 
186
  the BCR-original biotabs preserve. The schema varies by cancer type
187
  (e.g. BLCA's BCG-response columns don't exist in CHOL's hepatic-marker
188
  forms), so each project's biotabs ship only the columns they actually
189
+ carry. Discovered the same way (`/files` then `/data`) — see the
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+ filter table below.
191
 
192
  ### Source data filters (canonical)
193
 
 
207
  | GDC `/cases` | nested fields on each patient row (`demographic`, `diagnoses`, `follow_ups`, `exposures`, `family_histories`, `samples`); `gdc_portal_url` link added |
208
  | Masked Somatic Mutation MAFs | `samples_masked_somatic_mutation` array on each patient row (sample FKs resolved alongside GDC's aliquot UUIDs) |
209
  | Gene Expression Quantification | `samples_gene_expression_quantification` array on each patient row (`stranded_first` / `stranded_second` dropped — GDC harmonizes as unstranded) |
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+ | BCR Clinical Supplements | `clinical_supplement` struct on each patient row, with sub-fields `patient` (1 dict) and `follow_ups` / `ntes` / `drugs` / `radiations` / `ablations` / `omfs` (lists of dicts). Sub-fields with no data for the project are omitted. |
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  ### Specific to this view
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