Update PanCancer-Atlas-Mirror.rst

docs/source/sections/PanCancer-Atlas-Mirror.rst

@@ -2,27 +2,25 @@
 PanCancer Atlas BigQuery Data
 *******************************
 
-`The PanCancer BigQuery Mirror <https://console.cloud.google.com/bigquery?project=isb-cgc&page=dataset&d=pancancer_atlas&p=isb-cgc&redirect_from_classic=true>`_ -- produced in
+`The PanCancer BigQuery dataset <https://console.cloud.google.com/bigquery?project=isb-cgc&page=dataset&d=pancancer_atlas&p=isb-cgc&redirect_from_classic=true>`_, produced in
 collaboration with the `TCGA research network <https://cancergenome.nih.gov/>`_,
-the `GDC <https://gdc.cancer.gov/>`_, and the `NCI <https://www.cancer.gov/>`_ -- allows an integrated examination of the full set of tumors characterized in the robust TCGA dataset, thus providing a new way to explore and analyze the processes driving cancer.
+the `GDC <https://gdc.cancer.gov/>`_, and the `NCI <https://www.cancer.gov/>`_ allows an integrated examination of the full set of tumors characterized in the robust TCGA dataset, thus providing a new way to explore and analyze the processes driving cancer.
 
-The availability of PanCancer Atlas data in BigQuery enables easy integration of this
-resource with other public datasets in BigQuery, including other
-open-access datasets made available by the ISB-CGC
+The availability of PanCancer Atlas data in BigQuery enables easy integration of this resource with other public datasets in BigQuery, including other open-access datasets made available by the ISB-CGC
 (see `this <https://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/Hosted-Data.html>`_
 and `that <http://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/data/Reference-Data.html>`_
 for more details on other publicly accessible BigQuery datasets).
 
 About
 #####
 
-The Google BigQuery tables (`here <https://console.cloud.google.com/bigquery?project=isb-cgc&page=dataset&d=pancancer_atlas&p=isb-cgc&redirect_from_classic=true>`_) mirror the files shared by the PanCancer Atlas initiative on the `GDC <https://gdc.cancer.gov/about-data/publications/pancanatlas>`_.
+The PanCancer Atlas BigQuery tables  (`accessed here <https://console.cloud.google.com/bigquery?project=isb-cgc&page=dataset&d=pancancer_atlas&p=isb-cgc&redirect_from_classic=true>`_) mirror the files shared by the PanCancer Atlas initiative on the `GDC <https://gdc.cancer.gov/about-data/publications/pancanatlas>`_.
 
 The tables are generally unmodified uploads of the files in `GDC <https://gdc.cancer.gov/about-data/publications/pancanatlas>`_. The Filtered_* tables were annotated as appropriate with ParticipantBarcode, SampleBarcode, AliquotBarcode, SampleTypeLetterCode, SampleType and TCGA Study, subsequently the tables were filtered using the PanCancer Atlas whitelist. Two exceptions are the (public) *MC3 MAF file* and the *TCGA-CDR resource*, recommended for outcome data. 
 
 Use of the tables starting with Filtered_* is recommended.
 
-For examples of usage, see `Community Notebooks <https://github.com/isb-cgc/Community-Notebooks/tree/master/RegulomeExplorer>`_.
+See examples of statistical Jupyter notebooks using the PanCancer Atlas data `here <https://github.com/isb-cgc/Community-Notebooks/tree/master/RegulomeExplorer>`_.
 
 Getting Started
 ###############
@@ -32,18 +30,15 @@ Getting Started
 Adding the PanCancer Atlas tables to your workspace
 ###################################################
 
-To add public BigQuery datasets and tables to your "view" in the `BigQuery web UI <https://bigquery.cloud.google.com/dataset/isb-cgc:pancancer_atlas>`_ you
+To add public BigQuery datasets and tables to your "view" in the `BigQuery web interface <https://bigquery.cloud.google.com/dataset/isb-cgc:pancancer_atlas>`_ you
 need to know the name of the GCP project that owns the dataset(s). 
-To add the publicly accessible ISB-CGC datasets (project name: ``isb-cgc``) which included the PanCancer Atlas dataset ( dataset name: ``pancancer_atlas``) 
-follow these steps_.
+To add the publicly accessible ISB-CGC datasets (project name: ``isb-cgc``) which includes the PanCancer Atlas dataset ( dataset name: ``pancancer_atlas``) 
+follow these steps_:
 
 .. _steps: http://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/progapi/bigqueryGUI/LinkingBigQueryToIsb-cgcProject.html
 
 You should now be able to see and explore all of the PanCancer Atlas tables and also tables of other ISB-CGC datasets.
-Clicking on the blue triangle next to a dataset name will open it and
-show the list of tables in the dataset. Clicking on a table name will open up
-information about the table in main panel, where you can
-view the Schema, Details, or a Preview of the table.
+Clicking on the blue triangle next to a dataset name will open it and show the list of tables in the dataset. Clicking on a table name will open up information about the table in main panel, where you can view the Schema, Details, or a Preview of the table.
 
 Additional projects with public BigQuery datasets which you may want to explore (repeating
 the same process will add these to your BigQuery side-panel) include genomics-public-data and
@@ -53,7 +48,7 @@ google.com:biggene.
 Interactive Web-based Exploration
 #################################
 
-Ready to query? Great! follow the steps below to run your first BigQuery! More detailas `here <https://cloud.google.com/bigquery/docs/quickstarts/quickstart-web-ui>`_
+Ready to query? Great! Follow the steps below to run your first BigQuery! More details are `here <https://cloud.google.com/bigquery/docs/quickstarts/quickstart-web-ui>`_
 
 * `login <https://accounts.google.com/Login>`_ to your Google account (`Chrome <https://www.google.com/chrome/browser/desktop/index.html>`_ is the preferred browser);
 * go to the `BigQuery web UI <https://console.cloud.google.com/bigquery?project=isb-cgc&page=dataset&d=pancancer_atlas&p=isb-cgc&redirect_from_classic=true>`_  --  if you see a welcome screen inviting you to **Create a Project** then please do so.