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Add treatment timeline to pancan studies #1597

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Apr 17, 2022
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a5426ba
add timeline data
rmadupuri Feb 1, 2022
326c16f
fix header
rmadupuri Feb 1, 2022
a06f7ca
Add timeline data
rmadupuri Feb 2, 2022
3aae89a
Merge branch 'master' into pancan_treatment_data
rmadupuri Feb 2, 2022
35a842c
Add timeline tracks
rmadupuri Feb 10, 2022
fc75553
Merge branch 'master' into pancan_treatment_data
rmadupuri Feb 10, 2022
f57848a
fix validation error
rmadupuri Feb 10, 2022
b1e510b
Merge branch 'pancan_treatment_data' of https://github.com/cBioPortal…
rmadupuri Feb 10, 2022
d32489c
Add initial diagnosis, sample acquisition, new tumor events
rmadupuri Feb 16, 2022
dc9e4ad
Merge branch 'master' into pancan_treatment_data
rmadupuri Feb 22, 2022
f5277d5
remove date, year, month of form completion columns
rmadupuri Feb 22, 2022
429fde1
update sample acquisition data
rmadupuri Feb 23, 2022
4d5c9fd
Merge branch 'master' into pancan_treatment_data
rmadupuri Feb 23, 2022
6818fec
update
rmadupuri Mar 1, 2022
4f6116e
Merge branch 'master' into pancan_treatment_data
rmadupuri Mar 1, 2022
d51a938
remove followup file, add last followup to status track
rmadupuri Mar 1, 2022
fa2215d
add readme
rmadupuri Mar 1, 2022
3fdab21
Merge branch 'master' into pancan_treatment_data
rmadupuri Mar 8, 2022
270704c
Merge branch 'pancan_treatment_data' of https://github.com/cBioPortal…
rmadupuri Apr 12, 2022
ddc7c3d
Merge branch 'master' into pancan_treatment_data
yichaoS Apr 13, 2022
aa8d0fb
Merge branch 'master' into pancan_treatment_data
yichaoS Apr 13, 2022
400a43b
Merge branch 'pancan_treatment_data' of https://github.com/cBioPortal…
rmadupuri Apr 13, 2022
c889615
convert value to camel case, move omf
rmadupuri Apr 14, 2022
f5cbe18
Merge branch 'master' into pancan_treatment_data
yichaoS Apr 17, 2022
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10 changes: 10 additions & 0 deletions public/acc_tcga_pan_can_atlas_2018/README.md
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## Improving PanCancer Atlas Data: (transformation steps for the new data types being added)

### The Timeline/Treatment data:

**Data Source**
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.

**Data Transformation**
- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
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3 changes: 3 additions & 0 deletions public/acc_tcga_pan_can_atlas_2018/data_timeline_status.txt
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cancer_study_identifier: acc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_sample_acquisition.txt
4 changes: 4 additions & 0 deletions public/acc_tcga_pan_can_atlas_2018/meta_timeline_status.txt
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cancer_study_identifier: acc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_status.txt
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cancer_study_identifier: acc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_treatment.txt
10 changes: 10 additions & 0 deletions public/blca_tcga_pan_can_atlas_2018/README.md
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@@ -0,0 +1,10 @@
## Improving PanCancer Atlas Data: (transformation steps for the new data types being added)

### The Timeline/Treatment data:

**Data Source**
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.

**Data Transformation**
- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
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3 changes: 3 additions & 0 deletions public/blca_tcga_pan_can_atlas_2018/data_timeline_status.txt
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cancer_study_identifier: blca_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_sample_acquisition.txt
4 changes: 4 additions & 0 deletions public/blca_tcga_pan_can_atlas_2018/meta_timeline_status.txt
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cancer_study_identifier: blca_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_status.txt
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@@ -0,0 +1,4 @@
cancer_study_identifier: blca_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_treatment.txt
10 changes: 10 additions & 0 deletions public/brca_tcga_pan_can_atlas_2018/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
## Improving PanCancer Atlas Data: (transformation steps for the new data types being added)

### The Timeline/Treatment data:

**Data Source**
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.

**Data Transformation**
- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
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3 changes: 3 additions & 0 deletions public/brca_tcga_pan_can_atlas_2018/data_timeline_status.txt
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cancer_study_identifier: brca_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_sample_acquisition.txt
4 changes: 4 additions & 0 deletions public/brca_tcga_pan_can_atlas_2018/meta_timeline_status.txt
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cancer_study_identifier: brca_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_treatment.txt
10 changes: 10 additions & 0 deletions public/cesc_tcga_pan_can_atlas_2018/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
## Improving PanCancer Atlas Data: (transformation steps for the new data types being added)

### The Timeline/Treatment data:

**Data Source**
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.

**Data Transformation**
- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
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3 changes: 3 additions & 0 deletions public/cesc_tcga_pan_can_atlas_2018/data_timeline_status.txt
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cancer_study_identifier: cesc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_sample_acquisition.txt
4 changes: 4 additions & 0 deletions public/cesc_tcga_pan_can_atlas_2018/meta_timeline_status.txt
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cancer_study_identifier: cesc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_status.txt
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@@ -0,0 +1,4 @@
cancer_study_identifier: cesc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_treatment.txt
10 changes: 10 additions & 0 deletions public/chol_tcga_pan_can_atlas_2018/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
## Improving PanCancer Atlas Data: (transformation steps for the new data types being added)

### The Timeline/Treatment data:

**Data Source**
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.

**Data Transformation**
- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
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3 changes: 3 additions & 0 deletions public/chol_tcga_pan_can_atlas_2018/data_timeline_status.txt
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cancer_study_identifier: chol_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_sample_acquisition.txt
4 changes: 4 additions & 0 deletions public/chol_tcga_pan_can_atlas_2018/meta_timeline_status.txt
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cancer_study_identifier: chol_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: chol_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_treatment.txt
10 changes: 10 additions & 0 deletions public/coadread_tcga_pan_can_atlas_2018/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
## Improving PanCancer Atlas Data: (transformation steps for the new data types being added)

### The Timeline/Treatment data:

**Data Source**
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.

**Data Transformation**
- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
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Original file line number Diff line number Diff line change
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cancer_study_identifier: coadread_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_sample_acquisition.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: coadread_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: coadread_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_treatment.txt
10 changes: 10 additions & 0 deletions public/dlbc_tcga_pan_can_atlas_2018/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
## Improving PanCancer Atlas Data: (transformation steps for the new data types being added)

### The Timeline/Treatment data:

**Data Source**
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.

**Data Transformation**
- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
Git LFS file not shown
3 changes: 3 additions & 0 deletions public/dlbc_tcga_pan_can_atlas_2018/data_timeline_status.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: dlbc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_sample_acquisition.txt
4 changes: 4 additions & 0 deletions public/dlbc_tcga_pan_can_atlas_2018/meta_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: dlbc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: dlbc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_treatment.txt
10 changes: 10 additions & 0 deletions public/esca_tcga_pan_can_atlas_2018/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
## Improving PanCancer Atlas Data: (transformation steps for the new data types being added)

### The Timeline/Treatment data:

**Data Source**
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.

**Data Transformation**
- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
Git LFS file not shown
3 changes: 3 additions & 0 deletions public/esca_tcga_pan_can_atlas_2018/data_timeline_status.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: esca_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_sample_acquisition.txt
4 changes: 4 additions & 0 deletions public/esca_tcga_pan_can_atlas_2018/meta_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: esca_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: esca_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_treatment.txt
10 changes: 10 additions & 0 deletions public/gbm_tcga_pan_can_atlas_2018/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
## Improving PanCancer Atlas Data: (transformation steps for the new data types being added)

### The Timeline/Treatment data:

**Data Source**
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.

**Data Transformation**
- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
Git LFS file not shown
3 changes: 3 additions & 0 deletions public/gbm_tcga_pan_can_atlas_2018/data_timeline_status.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: gbm_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_sample_acquisition.txt
4 changes: 4 additions & 0 deletions public/gbm_tcga_pan_can_atlas_2018/meta_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: gbm_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: gbm_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_treatment.txt
10 changes: 10 additions & 0 deletions public/hnsc_tcga_pan_can_atlas_2018/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
## Improving PanCancer Atlas Data: (transformation steps for the new data types being added)

### The Timeline/Treatment data:

**Data Source**
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.

**Data Transformation**
- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
Git LFS file not shown
3 changes: 3 additions & 0 deletions public/hnsc_tcga_pan_can_atlas_2018/data_timeline_status.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_sample_acquisition.txt
4 changes: 4 additions & 0 deletions public/hnsc_tcga_pan_can_atlas_2018/meta_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_status.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018
genetic_alteration_type: CLINICAL
datatype: TIMELINE
data_filename: data_timeline_treatment.txt
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