cBioPortal

What is the EGA cBioPortal?

EGA hosts a dedicated cBioPortal instance that allows authorized researchers to explore and visualize some cancer datasets archived at EGA.

The platform provides interactive tools to analyse genomic and clinical data once access has been granted by the relevant Data Access Committee (DAC).

EGA cBioPortal instance

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How to find and access an EGA cBioPortal Dataset

1. Register as an EGA user
2. Go to the dataset page of interest

If the Dataset is available on the EGA cBioPortal Instance, the cBioPortal icon will be displayed on the Dataset page, as shown below:

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On the dataset page, you will find information about access requirements and whether the dataset is available for visualization in cBioPortal. For more details, please visit Request Access page.

WEBIN actions:

Register metadata for a sequence submission
- Register study, samples, experiments, runs, DAC, policy and dataset/s after file upload.
Register components for your array-based metadata submission
- Register study, samples, DAC or policy before uploading files.
Edit existing submission metadata
- Change or update previously submitted metadata.

Register metadata for a sequence submission

Ensure that all sequence files have been encrypted before uploading them to your submission account using the EgaCryptor.

Go to the EGA Webin and log in using your submission account name (ega-box-XXX) and password.

Register components of your metadata submission

Study
Samples
Data Access Committee (DAC)
Data access policy
Dataset

For array-base submissions: Study, Samples, Data Access Committee (DAC) and Data access policy may all be registered BEFORE file upload and dataset registration through the array-base template.

Register your Study

Go to the “Studies (Projects)” box
Click on “Register Study” and fill in the information related to your study.
Click on “Submit”, this will save the information and generate an EGA study ID.

Field Name	Description
sex	sex of the organism from which the sample was obtained
disease_site	Affected organ
sample type	Affected organ
donor_id **	Identifier of the donor where the sample has been derived from

*Gender should be described as 'male', 'female' or 'unknown'. If 'unknown' due to a known sex chromosome aneuploidy, please create a user defined attribute called 'Sex chromosome karyotype' and add the appropriate value, for example, 'XXY'.

After you have customised the fields for the sample submission, download the template and fill in the information.

Webin_sample

Go to the “Data Access” box
Click on “Register Dacs”
Input the information about the DAC and register at least one main DAC contact.

Register your Data Access Policy

Your Data Access Policy provides the terms and conditions of data use, this is also referred to as the Data Access Agreement (DAA). Completion of a DAA by the applicant/s should form part of the application process to the Data Access Committee (DAC).

Go to the “Data Access” box
Click on “Register Policies”
Select the DAC to which this policy will be linked to and fill in the policy information.

Submitting your Runs and Analyses

Runs Registration

For the templates you have the option to customise the optional fields. To check their description click on “Show Description “

The study and the sequenced samples must be pre-registered before the raw reads are submitted. Please note that each individual study and sample should be registered only once. You will be asked to provide information about the sequencing libraries and instruments.

Submitting your Dataset

The dataset describes the data files, defined by the run (EGARXXXXXXXXXXX) and analysis (EGAZXXXXXXXXXXX) accessions that make up the dataset and links the collection of data files to a specified Data Access Committee and Data Access Policy.

As a result, you must have registered your Reads and experiments, Data Access Committee (DAC) and Data access policy before submitting your Dataset.