GDC Data Portal

The GDC Data Portal is a robust data-driven platform that allows users to search and download cancer data for analysis using modern web technologies.

GDC Data Portal Key Features

Browse Harmonized Data

By browsing through the GDC Data Portal, users can obtain details about specific aspects of the GDC harmonized data, such as the associated project, files, participants and annotations (explanatory comments about the data). Using advanced data modeling, GDC Data Portal users can navigate between pages and results in a seamless and consistent manner. For example, from a project page a user can be redirected to all files or participants within the project. While users are browsing through the portal, they can progressively add more elements to a personalized cart for data download.

Access Legacy Archives

The GDC Data Portal provides access to GDC harmonized data as well as an archive of legacy data from TCGA and other NCI programs. Through the GDC Data Portal, users can launch the Legacy Archive Portal to search and download legacy files.

Visually Identify Data

Due to the large amount of data accessible through the GDC Data Portal, visualization is key in allowing researchers to identify data they are looking for and narrowing their search. The GDC Data Portal uses multiple mechanisms to ease visualization including tables, charts, and plots. Whenever possible, cross-references are enabled so that users can dive into the data directly from a plot.

Search Data with Facets and Smart Search Technology

The GDC Data Portal contains two primary mechanisms for searching data:

1. Using predefined filters (also called facets)
2. Using smart search technology and the smart search advanced query language. When a user clicks on a facet, the GDC smart search is automatically populated to help users get familiar with the advanced query language. At any time, when a need for a more specific query arises, users can switch to smart search and update their query with more specific filters to identify cases or files stored on GDC.

Perform BAM Slicing

The GDC Data Portal allows BAM slicing. Users can submit their slicing request in BED format and download only the requested slice of a BAM file.

Create Personalized Cart

Searching through the GDC Data Portal, allows researchers to add files to their personalized cart. The cart provides detailed statistics about the files it contains in order for the user to have a better understanding of the overall volume of files the user may want to download.

Download Data Quickly and Securely

The GDC Data Portal provides two primary channels to allow users to download data from a cart:

1. Download directly from the browser
2. Download using a dedicated GDC Data Transfer Tool.

When downloading data via the GDC Data Transfer Tool, the GDC Data Portal generates a file manifest that can be easily imported into the GDC Data Transfer Tool to initiate the download. Note that users can only download files they have access to through the NIH database of Genotypes and Phenotypes (dbGaP). Please visit Obtaining Access to GDC Data and Resources for information about how to obtain permission to access controlled data sets through dbGaP.

View Slide Images

The GDC Data Portal provides an image viewing option allowing researchers to view, zoom, and pan slide images associated with a case. Slide images can also be downloaded in the original format (SVS) and are accessible via the GDC API.

Detailed instructions for the above features are available in the GDC Data Portal User's Guide. Information on GDC Data Portal Releases is available in the GDC Data Portal Release Notes.

Accessing the GDC Data Portal

Supported Internet Browsers

The GDC Data Portal is compatible with most modern web browsers, including:

• Most recent supported stable version of Microsoft Edge on Microsoft Windows
• Most recent stable version of Google Chrome
• Most recent stable version of Mozilla Firefox

Release Notes

Release Notes are available on the GDC Data Portal Release Notes page.