Merge pull request #713 from isb-cgc/staging

Staging

docs/source/sections/Hosted-Data.rst

@@ -60,8 +60,8 @@ Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are avail
      - |checkmark|
      - 
    * - `Exceptional Responders <data/EXC_RESPOND_about.html>`_
-     - 
-     - |checkmark| **
+     - |checkmark|
+     - |checkmark|
      - 
    * - `FM <data/FM_about.html>`_
      - |checkmark|
@@ -80,16 +80,16 @@ Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are avail
      - |checkmark|
      - |checkmark|
    * - `MP2PRT <data/MP2PRT_about.html>`_
-     - 
-     - |checkmark| **
+     - |checkmark|
+     - |checkmark| *
      - 
    * - `NCICCR <data/NCICCR_about.html>`_
      - |checkmark|
-     - |checkmark| *
+     - |checkmark| 
      - 
    * - `OHSU <data/OHSU_about.html>`_
      - |checkmark|
-     - |checkmark| *
+     - |checkmark|
      - |checkmark|
    * - `ORGANOID <data/ORGANOID_about.html>`_
      - |checkmark|
@@ -172,6 +172,10 @@ PDC protein expression data are available in ISB-CGC BigQuery tables. The table
      - PDC AWS Cloud Storage
      - ISB-CGC BigQuery Tables
      - ISB-CGC Cohort Builder
+   * - `APOLLO <data/APOLLO1_about.html>`_
+     - 
+     - |checkmark|
+     - 
    * - `CBTN <data/CBTN_about.html>`_  
      - 
      - |checkmark| 
@@ -197,6 +201,7 @@ PDC protein expression data are available in ISB-CGC BigQuery tables. The table
    :maxdepth: 1
    :hidden:
 
+   data/APOLLO1_about
    data/CBTN_about
    data/CPTAC_about
    data/GPRP_about

docs/source/sections/data/APOLLO1_about.rst

@@ -0,0 +1,22 @@
+*****************
+APOLLO Data Set
+*****************
+
+About the Applied Proteogenomics Organizational Learning and Outcomes (APOLLO) Program
+------------------------------------------------------------
+The `Applied Proteogenomics Organizational Learning and Outcomes <https://proteomics.cancer.gov/programs/apollo-network>`_ (APOLLO) network is a collaboration between NCI, the Department of Defense (DoD), and the Department of Veterans Affairs (VA). Its purpose is to incorporate proteogenomics into tumor study to better pinpoint treatment therapies by examing both genetic abnormalities and protein information. It is part of NCI’s Cancer Moonshot Initiative. 
+
+About the Applied Proteogenomics Organizational Learning and Outcomes Data Set
+---------------------------------------------------------------------
+
+The intial studies from project APOLLO1 are available at the `Proteomics Data Commons (PDC) <https://pdc.cancer.gov/pdc/>`_. ISB-CGC has procured this data through the PDC API. This initial data is from lung cancer patients.
+
+Accessing the APOLLO Data in Google BigQuery
+------------------------------------------------
+
+ISB-CGC has APOLLO1 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 APOLLO1 selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
+
+The APOLLO1 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.APOLLO1`` contains the latest tables for each data type.
+- Data set ``isb-cgc-bq.APOLLO1_versioned`` contains previously released tables, as well as the most current table.

docs/source/sections/data/CBTN_about.rst

@@ -14,7 +14,7 @@ CBTN has the Pediatric Brain Cancer Pilot Study available at the `Proteomics Dat
 Accessing the CBTN Data in Google BigQuery
 ------------------------------------------------
 
-ISB-CGC has CBTN data, such as clincial and protein expression, 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 CBTTC selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
+ISB-CGC has CBTN data, such as clinical and protein expression, 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 CBTTC selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
 
 The CBTTC 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>`_.
 

docs/source/sections/data/EXC_RESPOND_about.rst

@@ -16,11 +16,26 @@ For more information on Exceptional Responders data, please refer to the site be
 
 - `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%22EXCEPTIONAL_RESPONDERS%22%5D%7D%7D%5D%7D>`_
 
-
+Accessing the Exceptional Responders 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 Exceptional Responders 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 = 'EXCEPTIONAL_RESPONDERS'
+  AND active.file_gdc_id = GCSurl.file_gdc_id
+
+
 Accessing the Exceptional Responders Data in Google BigQuery
 ------------------------------------------------
 
-ISB-CGC has Exceptional Responders data, such as clinical, 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 EXCEPTIONAL RESPONDERS selected for filter PROGRAM. 
+ISB-CGC has Exceptional Responders data, such as clinical, metadata, RNA-seq and somatic mutation 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 EXCEPTIONAL RESPONDERS selected for filter PROGRAM. 
 To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
 
 The Exceptional Responders 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>`_.

docs/source/sections/data/MP2PRT_about.rst

@@ -16,11 +16,26 @@ For more information on MP2PRT 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%22MP2PRT%22%5D%7D%7D%5D%7D>`_
 
+Accessing the MP2PRT 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 MP2PRT 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 = 'MP2PRT'
+  AND active.file_gdc_id = GCSurl.file_gdc_id
+
 
 Accessing the MP2PRT Data in Google BigQuery
 ------------------------------------------------
 
-ISB-CGC has MP2PRT data, such as clinical, 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 MP2PRT selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
+ISB-CGC has MP2PRT 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 MP2PRT selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
 
 The MP2PRT 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>`_.
 

docs/source/sections/data/NCICCR_about.rst

@@ -35,7 +35,7 @@ Besides accessing the files on the GDC Data Portal, you can also access them fro
 Accessing the NCICCR Data in Google BigQuery
 ------------------------------------------------
 
-ISB-CGC has NCICCR data, such as clinical, 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 NCICCR selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
+ISB-CGC has NCICCR data, such as clinical, metadata and RNA-seq 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 NCICCR selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
 
 The NCICCR 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>`_.
 

docs/source/sections/data/OHSU_about.rst

@@ -35,7 +35,7 @@ Besides accessing the files on the GDC Data Portal, you can also access them fro
 Accessing the OHSU Data in Google BigQuery
 ------------------------------------------------
 
-ISB-CGC has OHSU data, such as clinical, 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 OHSU selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
+ISB-CGC has OHSU data, such as clinical, metadata and RNA-seq 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 OHSU selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
 
 The OHSU 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>`_.