Merge pull request #718 from isb-cgc/staging

Staging

docs/source/sections/Hosted-Data.rst

@@ -43,6 +43,10 @@ Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are avail
      - |checkmark|
      - |checkmark|
      - |checkmark|
+   * - `CDDP EAGLE <data/CDDP_EAGLE_about.html>`_
+     - |checkmark|
+     - |checkmark| *
+     - 
    * - `CGCI <data/CGCI_about.html>`_
      - |checkmark|
      - |checkmark|
@@ -75,6 +79,10 @@ Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are avail
      - |checkmark|
      - |checkmark| 
      - 
+   * - `MATCH <data/MATCH_about.html>`_
+     - |checkmark|
+     - |checkmark| *
+     - 
    * - `MMRF <data/MMRF_about.html>`_
      - |checkmark|
      - |checkmark|
@@ -136,6 +144,7 @@ Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are avail
 
    data/BEATAML_about
    data/CCLE_top
+   data/CDDP_EAGLE_about
    data/CGCI_about
    data/CMI_about
    data/CPTAC_about
@@ -144,6 +153,7 @@ Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are avail
    data/FM_about
    data/GENIE_about
    data/HCMI_about
+   data/MATCH_about
    data/MMRF_about
    data/MP2PRT_about
    data/NCICCR_about
@@ -176,6 +186,10 @@ PDC protein expression data are available in ISB-CGC BigQuery tables. The table
      - 
      - |checkmark|
      - 
+   * - Broad Institute
+     - 
+     - |checkmark| 
+     - 
    * - `CBTN <data/CBTN_about.html>`_  
      - 
      - |checkmark| 

docs/source/sections/data/CDDP_EAGLE_about.rst

@@ -0,0 +1,37 @@
+*****************
+CDDP EAGLE Data Set
+*****************
+
+About the CDDP Environment And Genetics in Lung cancer Etiology (EAGLE) Program
+------------------------------------------------------------
+The `Environment And Genetics in Lung cancer Etiology <https://dceg.cancer.gov/research/who-we-study/cancer-cases-controls/eagle-study>`_ (EAGLE) program investigated the genetic and environmental determinants of lung cancer and smoking persistence. It integrated analysis of genetic, environmental, clinical, and behavioral data.
+
+About the CDDP EAGLE Data Set
+---------------------------------------------------------------------
+Data from the CDDP EAGLE Program are available at the `Genomics Data Commons (GDC) <https://portal.gdc.cancer.gov/>`_.  It includes data from the Integrative Analysis of Lung Adenocarcinoma project.
+
+Accessing the CDDP EAGLE 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 CDDP EAGLE 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 = 'CDDP_EAGLE'
+  AND active.file_gdc_id = GCSurl.file_gdc_id
+
+
+Accessing the CDDP EAGLE Data in Google BigQuery
+------------------------------------------------
+
+ISB-CGC has CDDP EAGLE 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 CDDP EAGLE selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
+
+The CDDP_EAGLE 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.CDDP_EAGLE`` contains the latest tables for each data type.
+- Data set ``isb-cgc-bq.CDDP_EAGLE_versioned`` contains previously released tables, as well as the most current table.

docs/source/sections/data/MATCH_about.rst

@@ -0,0 +1,37 @@
+*****************
+MATCH Data Set
+*****************
+
+About the Molecular Analysis for Therapy Choice (MATCH) Program
+------------------------------------------------------------
+`Molecular Analysis for Therapy Choice <https://www.cancer.gov/about-cancer/treatment/clinical-trials/nci-supported/nci-match>`_ (MATCH) is a precision medicine cancer treatment clinical trial which investigated the effectiveness of treating cancer based on the specific genetic changes in a person's tumor.
+
+About the Molecular Analysis for Therapy Choice Data Set
+---------------------------------------------------------------------
+Data from the MATCH Program are available at the `Genomics Data Commons (GDC) <https://portal.gdc.cancer.gov/>`_.  It includes data for over 15 primary sites and at least eight disease types.
+
+Accessing the MATCH 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 MATCH 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 = 'MATCH'
+  AND active.file_gdc_id = GCSurl.file_gdc_id
+
+
+Accessing the MATCH Data in Google BigQuery
+------------------------------------------------
+
+ISB-CGC has MATCH 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 MATCH selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
+
+The MATCH 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.MATCH`` contains the latest tables for each data type.
+- Data set ``isb-cgc-bq.MATCH_versioned`` contains previously released tables, as well as the most current table.