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gabrielaltay
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tcga-patients-open

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cancer
tcga
clinical
genomics
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gabrielaltay commited on
Commit
b1e6996
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1 Parent(s): 839287e

Add clinical for all 33 TCGA projects (11,428 patients total)

Browse files
Files changed (31) hide show
  1. README.md +123 -3
  2. TCGA-ACC/data.parquet +3 -0
  3. TCGA-BLCA/data.parquet +3 -0
  4. TCGA-BRCA/data.parquet +3 -0
  5. TCGA-CESC/data.parquet +3 -0
  6. TCGA-COAD/data.parquet +3 -0
  7. TCGA-ESCA/data.parquet +3 -0
  8. TCGA-GBM/data.parquet +3 -0
  9. TCGA-HNSC/data.parquet +3 -0
  10. TCGA-KICH/data.parquet +3 -0
  11. TCGA-KIRC/data.parquet +3 -0
  12. TCGA-KIRP/data.parquet +3 -0
  13. TCGA-LAML/data.parquet +3 -0
  14. TCGA-LGG/data.parquet +3 -0
  15. TCGA-LIHC/data.parquet +3 -0
  16. TCGA-LUSC/data.parquet +3 -0
  17. TCGA-MESO/data.parquet +3 -0
  18. TCGA-OV/data.parquet +3 -0
  19. TCGA-PAAD/data.parquet +3 -0
  20. TCGA-PCPG/data.parquet +3 -0
  21. TCGA-PRAD/data.parquet +3 -0
  22. TCGA-READ/data.parquet +3 -0
  23. TCGA-SARC/data.parquet +3 -0
  24. TCGA-SKCM/data.parquet +3 -0
  25. TCGA-STAD/data.parquet +3 -0
  26. TCGA-TGCT/data.parquet +3 -0
  27. TCGA-THCA/data.parquet +3 -0
  28. TCGA-THYM/data.parquet +3 -0
  29. TCGA-UCEC/data.parquet +3 -0
  30. TCGA-UCS/data.parquet +3 -0
  31. TCGA-UVM/data.parquet +3 -0
README.md CHANGED
@@ -9,18 +9,138 @@ tags:
9
  - clinical
10
  - genomics
11
  configs:
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
12
  - config_name: TCGA-CHOL
13
  data_files:
14
  - split: train
15
  path: TCGA-CHOL/data.parquet
 
 
 
 
16
  - config_name: TCGA-DLBC
17
  data_files:
18
  - split: train
19
  path: TCGA-DLBC/data.parquet
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
20
  - config_name: TCGA-LUAD
21
  data_files:
22
  - split: train
23
  path: TCGA-LUAD/data.parquet
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
24
  ---
25
 
26
  # TCGA Patients (Open Access)
@@ -29,8 +149,8 @@ Open-access patient data from The Cancer Genome Atlas (TCGA), pulled from the
29
  National Cancer Institute (NCI) Genomic Data Commons (GDC). One HuggingFace
30
  (HF) subset per TCGA project; one row per patient.
31
 
32
- - **Projects included:** `TCGA-CHOL`, `TCGA-DLBC`, `TCGA-LUAD`
33
- - **Generated:** 2026-05-05 15:19:38 UTC
34
  - **Source:** GDC `/cases` endpoint, open-access tier only.
35
  - **Schema:** derived from the [GDC Data Dictionary][gdc-dict]; the live
36
  dictionary the GDC was serving when the data was fetched is hashed into
@@ -89,7 +209,7 @@ constructed in [`src/tcga2hf/clinical.py`][src-clinical] (the `cases`
89
  table) and [`src/tcga2hf/genomic.py`][src-genomic] (molecular and
90
  provenance tables) of the [`tcga2hf` repo][repo].
91
 
92
- **Projects fetched in this build:** `TCGA-CHOL`, `TCGA-DLBC`, `TCGA-LUAD`.
93
 
94
  ### `POST /cases` → `cases` table
95
 
 
9
  - clinical
10
  - genomics
11
  configs:
12
+ - config_name: TCGA-ACC
13
+ data_files:
14
+ - split: train
15
+ path: TCGA-ACC/data.parquet
16
+ - config_name: TCGA-BLCA
17
+ data_files:
18
+ - split: train
19
+ path: TCGA-BLCA/data.parquet
20
+ - config_name: TCGA-BRCA
21
+ data_files:
22
+ - split: train
23
+ path: TCGA-BRCA/data.parquet
24
+ - config_name: TCGA-CESC
25
+ data_files:
26
+ - split: train
27
+ path: TCGA-CESC/data.parquet
28
  - config_name: TCGA-CHOL
29
  data_files:
30
  - split: train
31
  path: TCGA-CHOL/data.parquet
32
+ - config_name: TCGA-COAD
33
+ data_files:
34
+ - split: train
35
+ path: TCGA-COAD/data.parquet
36
  - config_name: TCGA-DLBC
37
  data_files:
38
  - split: train
39
  path: TCGA-DLBC/data.parquet
40
+ - config_name: TCGA-ESCA
41
+ data_files:
42
+ - split: train
43
+ path: TCGA-ESCA/data.parquet
44
+ - config_name: TCGA-GBM
45
+ data_files:
46
+ - split: train
47
+ path: TCGA-GBM/data.parquet
48
+ - config_name: TCGA-HNSC
49
+ data_files:
50
+ - split: train
51
+ path: TCGA-HNSC/data.parquet
52
+ - config_name: TCGA-KICH
53
+ data_files:
54
+ - split: train
55
+ path: TCGA-KICH/data.parquet
56
+ - config_name: TCGA-KIRC
57
+ data_files:
58
+ - split: train
59
+ path: TCGA-KIRC/data.parquet
60
+ - config_name: TCGA-KIRP
61
+ data_files:
62
+ - split: train
63
+ path: TCGA-KIRP/data.parquet
64
+ - config_name: TCGA-LAML
65
+ data_files:
66
+ - split: train
67
+ path: TCGA-LAML/data.parquet
68
+ - config_name: TCGA-LGG
69
+ data_files:
70
+ - split: train
71
+ path: TCGA-LGG/data.parquet
72
+ - config_name: TCGA-LIHC
73
+ data_files:
74
+ - split: train
75
+ path: TCGA-LIHC/data.parquet
76
  - config_name: TCGA-LUAD
77
  data_files:
78
  - split: train
79
  path: TCGA-LUAD/data.parquet
80
+ - config_name: TCGA-LUSC
81
+ data_files:
82
+ - split: train
83
+ path: TCGA-LUSC/data.parquet
84
+ - config_name: TCGA-MESO
85
+ data_files:
86
+ - split: train
87
+ path: TCGA-MESO/data.parquet
88
+ - config_name: TCGA-OV
89
+ data_files:
90
+ - split: train
91
+ path: TCGA-OV/data.parquet
92
+ - config_name: TCGA-PAAD
93
+ data_files:
94
+ - split: train
95
+ path: TCGA-PAAD/data.parquet
96
+ - config_name: TCGA-PCPG
97
+ data_files:
98
+ - split: train
99
+ path: TCGA-PCPG/data.parquet
100
+ - config_name: TCGA-PRAD
101
+ data_files:
102
+ - split: train
103
+ path: TCGA-PRAD/data.parquet
104
+ - config_name: TCGA-READ
105
+ data_files:
106
+ - split: train
107
+ path: TCGA-READ/data.parquet
108
+ - config_name: TCGA-SARC
109
+ data_files:
110
+ - split: train
111
+ path: TCGA-SARC/data.parquet
112
+ - config_name: TCGA-SKCM
113
+ data_files:
114
+ - split: train
115
+ path: TCGA-SKCM/data.parquet
116
+ - config_name: TCGA-STAD
117
+ data_files:
118
+ - split: train
119
+ path: TCGA-STAD/data.parquet
120
+ - config_name: TCGA-TGCT
121
+ data_files:
122
+ - split: train
123
+ path: TCGA-TGCT/data.parquet
124
+ - config_name: TCGA-THCA
125
+ data_files:
126
+ - split: train
127
+ path: TCGA-THCA/data.parquet
128
+ - config_name: TCGA-THYM
129
+ data_files:
130
+ - split: train
131
+ path: TCGA-THYM/data.parquet
132
+ - config_name: TCGA-UCEC
133
+ data_files:
134
+ - split: train
135
+ path: TCGA-UCEC/data.parquet
136
+ - config_name: TCGA-UCS
137
+ data_files:
138
+ - split: train
139
+ path: TCGA-UCS/data.parquet
140
+ - config_name: TCGA-UVM
141
+ data_files:
142
+ - split: train
143
+ path: TCGA-UVM/data.parquet
144
  ---
145
 
146
  # TCGA Patients (Open Access)
 
149
  National Cancer Institute (NCI) Genomic Data Commons (GDC). One HuggingFace
150
  (HF) subset per TCGA project; one row per patient.
151
 
152
+ - **Projects included:** `TCGA-ACC`, `TCGA-BLCA`, `TCGA-BRCA`, `TCGA-CESC`, `TCGA-CHOL`, `TCGA-COAD`, `TCGA-DLBC`, `TCGA-ESCA`, `TCGA-GBM`, `TCGA-HNSC`, `TCGA-KICH`, `TCGA-KIRC`, `TCGA-KIRP`, `TCGA-LAML`, `TCGA-LGG`, `TCGA-LIHC`, `TCGA-LUAD`, `TCGA-LUSC`, `TCGA-MESO`, `TCGA-OV`, `TCGA-PAAD`, `TCGA-PCPG`, `TCGA-PRAD`, `TCGA-READ`, `TCGA-SARC`, `TCGA-SKCM`, `TCGA-STAD`, `TCGA-TGCT`, `TCGA-THCA`, `TCGA-THYM`, `TCGA-UCEC`, `TCGA-UCS`, `TCGA-UVM`
153
+ - **Generated:** 2026-05-06 00:03:52 UTC
154
  - **Source:** GDC `/cases` endpoint, open-access tier only.
155
  - **Schema:** derived from the [GDC Data Dictionary][gdc-dict]; the live
156
  dictionary the GDC was serving when the data was fetched is hashed into
 
209
  table) and [`src/tcga2hf/genomic.py`][src-genomic] (molecular and
210
  provenance tables) of the [`tcga2hf` repo][repo].
211
 
212
+ **Projects fetched in this build:** `TCGA-ACC`, `TCGA-BLCA`, `TCGA-BRCA`, `TCGA-CESC`, `TCGA-CHOL`, `TCGA-COAD`, `TCGA-DLBC`, `TCGA-ESCA`, `TCGA-GBM`, `TCGA-HNSC`, `TCGA-KICH`, `TCGA-KIRC`, `TCGA-KIRP`, `TCGA-LAML`, `TCGA-LGG`, `TCGA-LIHC`, `TCGA-LUAD`, `TCGA-LUSC`, `TCGA-MESO`, `TCGA-OV`, `TCGA-PAAD`, `TCGA-PCPG`, `TCGA-PRAD`, `TCGA-READ`, `TCGA-SARC`, `TCGA-SKCM`, `TCGA-STAD`, `TCGA-TGCT`, `TCGA-THCA`, `TCGA-THYM`, `TCGA-UCEC`, `TCGA-UCS`, `TCGA-UVM`.
213
 
214
  ### `POST /cases` → `cases` table
215
 
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