Cancer Data Aggregator (CDA) with CGC: Usage Guide

Overview

This project contains two Data Studio analyses for querying and processing data from the CDA database and importing them to your CGC project(s).

• CDA Release 3 - Import Data to CGC analysis demonstrates usage of cda-python release 3 library, SBG python API and pandas in order to process, manipulate data available in the CDA and import it to the CGC platform.
• CDA Community Notebooks and Tutorials analysis contains notebooks available on the CDA Community Notebook Library.

Using the Cancer Data Aggregator (CDA) and a harmonized data model developed by the NCI Cancer Research Data Commons (CRDC) Data Harmonization teams, users can discover, query, retrieve, and aggregate data according to a variety of search parameters, such as participant, sample, tissue, disease, or study.

More information about the CDA can be found in the official documentation, while the lates cda-python package can be found on the github page.

Use the public project

All Seven Bridges Platform users automatically have copy permissions for this project. This means you can copy the available data to your own projects on the Platform to execute analyses.

You have the options to:

• Copy the entire project - start from the copied project and use available apps to filter a VCF file.
• Copy available Data Studio analyses - alternatively, you can copy the two available Data Studio analyses to any of your projects.

Access the public project

To access the Cancer Data Aggregator (CDA) with CGC: Usage Guide:

1. Click on Public projects from the top navigation bar.
2. Click the title of the project, as shown below.

You'll be taken to the main dashboard of the "Cancer Data Aggregator (CDA) with CGC: Usage Guide" public project. Alternatively, you can choose to copy the project, by clicking Copy project. See below for more information.

Copy the entire project

1. Click Public projects in the top navigation bar.
2. Locate the "Cancer Data Aggregator (CDA) with CGC: Usage Guide" public project and click Copy project in the lower right corner.

4. In the pop-up window, you can name your copy of the project, select the billing group and specify whether this project will contain controlled data.
5. Once you have customized the details, click Copy to copy the entire project.

You will be redirected to the dashboard of your cloned project when it is ready, as shown below.

Copy the Data Studio analysis to your project

The Cancer Data Aggregator (CDA) with CGC public project allows you to copy the accompanying Data Studio analyses to any of your projects. Follow these steps:

1. Click Data Studio in the main navigation of your project.
2. Click the ellipsis menu next to the analysis you want to copy.
   
3. Click Copy.
4. Choose the target project and click Copy.

For the analysis to work properly it will install required dependencies so please make sure network access is turned on for your project. This is needed in order to install necessary requirements within the analysis as well as to be able to communicate with CDA API.

Allowing network access for the project

To allow network access for the project:

1. Click Settings in the upper right corner.
2. Click Allow network access.