<commit_before>*****************
REBC Data Set
*****************

About REBC
------------------------------------------------------------------------

The `REBC data <https://www.trioncology.org/>`_ is a study of Radiation-Related Genomic Profile of Papillary Thyroid Cancer after the Chernobyl Accident

About REBC
---------------------------------------------------------------------------------

The REBC data set includes masked annotations, somatic mutations, gene level copy number scores, and transcript fusion analysis. The program analyzed more than 44,000 cases. The Genomic Data Commons (GDC) currently has MAF, TXT, and TSV controlled data available. 

For more information on GENIE data, please refer to the site below:

- `GDC Data Portal <https://portal.gdc.cancer.gov/projects?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22projects.program.name%22%2C%22value%22%3A%5B%22GENIE%22%5D%7D%7D%5D%7D>`_

Accessing the REBC Data on the Cloud
-------------------------------------------------------------------------------------------

Besides accessing the files on the GDC Data Portal, you can also access them from the GDC Google Cloud Storage Bucket, which means that you don’t need to download them to perform analysis. ISB-CGC stores the cloud file locations in tables in the ``isb-cgc-bq.GDC_case_file_metadata`` data set in BigQuery.

- To access these metadata files, go to the Google BigQuery console.
- Perform SQL queries to find the REBC files. Here is an example:

.. code-block:: sql

  SELECT active.*, file_gdc_url
  FROM `isb-cgc-bq.GDC_case_file_metadata.fileData_active_current` as active, `isb-cgc-bq.GDC_case_file_metadata.GDCfileID_to_GCSurl_current` as GCSurl
  WHERE program_name = 'REBC'
  AND active.file_gdc_id = GCSurl.file_gdc_id
  
Accessing the TRIO Data in Google BigQuery
------------------------------------------------

ISB-CGC has REBC data, such as clinical and metadata, stored in Google BigQuery tables. Information about these tables can be found using the `ISB-CGC BigQuery Table Search <https://isb-cgc.appspot.com/bq_meta_search/>`_ with TRIO selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.

The TRIO tables are in project isb-cgc-bq. To learn more about how to view and query tables in the Google BigQuery console, see the `ISB-CGC BigQuery Tables documentation <../BigQuery.html>`_.

- Data set ``isb-cgc-bq.REBC`` contains the latest tables for each data type.
- Data set ``isb-cgc-bq.REBC_versioned`` contains previously released tables, as well as the most current table.
<commit_msg>Update REBC_about.rst<commit_after>*****************
REBC Data Set
*****************

About REBC
------------------------------------------------------------------------

The `REBC data <https://www.trioncology.org/>`_ is a study of Radiation-Related Genomic Profile of Papillary Thyroid Cancer after the Chernobyl Accident

About REBC
---------------------------------------------------------------------------------

The REBC data set includes masked annotations, somatic mutations, gene level copy number scores, and transcript fusion analysis. The program analyzed more than 44,000 cases. The Genomic Data Commons (GDC) currently has MAF, TXT, and TSV controlled data available. 

For more information on GENIE data, please refer to the site below:

- `GDC Data Portal <https://portal.gdc.cancer.gov/projects?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22projects.program.name%22%2C%22value%22%3A%5B%22GENIE%22%5D%7D%7D%5D%7D>`_

Accessing the REBC Data on the Cloud
-------------------------------------------------------------------------------------------

Besides accessing the files on the GDC Data Portal, you can also access them from the GDC Google Cloud Storage Bucket, which means that you don’t need to download them to perform analysis. ISB-CGC stores the cloud file locations in tables in the ``isb-cgc-bq.GDC_case_file_metadata`` data set in BigQuery.

- To access these metadata files, go to the Google BigQuery console.
- Perform SQL queries to find the REBC files. Here is an example:

.. code-block:: sql

  SELECT active.*, file_gdc_url
  FROM `isb-cgc-bq.GDC_case_file_metadata.fileData_active_current` as active, `isb-cgc-bq.GDC_case_file_metadata.GDCfileID_to_GCSurl_current` as GCSurl
  WHERE program_name = 'REBC'
  AND active.file_gdc_id = GCSurl.file_gdc_id
  
Accessing the TRIO Data in Google BigQuery
------------------------------------------------

ISB-CGC has REBC data, such as clinical and metadata, stored in Google BigQuery tables. Information about these tables can be found using the `ISB-CGC BigQuery Table Search <https://isb-cgc.appspot.com/bq_meta_search/>`_ with REBC selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.

The REBC tables are in project isb-cgc-bq. To learn more about how to view and query tables in the Google BigQuery console, see the `ISB-CGC BigQuery Tables documentation <../BigQuery.html>`_.

- Data set ``isb-cgc-bq.REBC`` contains the latest tables for each data type.
- Data set ``isb-cgc-bq.REBC_versioned`` contains previously released tables, as well as the most current table.

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