Introduction to the CSSI DCC Portal

Data repositories are important tools in cancer research, providing safe and sustainable locations to store data, providing access to input data for meta-analyses, and allowing researchers to collaborate and share information across a common resource. The Center for Strategic Scientific Initiatives (CSSI) sponsors a diverse array of projects that generate datasets that vary in content and format, yet are related across certain defining characteristics or metadata. Integrated management of the datasets across all sponsored projects  make the data more accessible, easily accessed, and potentially reused by the cancer research community. 

The CSSI Data Coordinating Center (CSSI DCC) stores and manages access to data generated in support of cancer research funded or supported by the CSSI. This data is in the standard Investigation-Study-Assay tab-delimited format (ISA-TAB) format, which describes a scientific investigation, its study or studies, and each study's assay(s). For more information on the ISA-TAB format, refer to the following section, Chapter 1: Getting Started with the CSSI DCC Portal, as well as the ISA-TAB specification .

The CSSI DCC Portal is the repository for CSSI DCC data. It serves the following purposes:

• Provides a common location and web access to data from disparate data types including gene expression results from Next Generation Sequencing, microarray experiments, histopathological images, metabolomics data and proteomics data, allowing for easy access by multiple collaborators and researchers located at different geographic locations. Is flexible enough to handle new and unspecified data types.
• Stores the data in one common location so that you can make biological insights that would otherwise be missed by having data in multiple locations.
• Applies the information gained from one study to multiple studies and projects.
• Allows you to search the metadata from each study to identify datasets of interest.
• Develops data storage and data mining modules that can be applied across studies, avoiding duplication of effort and saving costs.
• Develops and/or adopts common vocabularies, data standards, and ontologies for data representation, storage, and comparison. 

For more information about using the CSSI DCC Portal, see:

• Chapter 2: Browsing, Searching, and Downloading Investigations, and
• Chapter 3: Uploading and Publishing Investigation Data

What is ISA-Tab?

Investigation-Study-Assay tab-delimited format (ISA-Tab) is a format based on the ISA-TAB specification that is used to capture and communicate the complex metadata required to interpret investigations (experiments) employing combinations of technologies. Metadata in ISA-Tab format facilitates standards-compliant collection, curation, management, and reuse of datasets in a wide variety of life science domains. ISA-TAB builds on the existing paradigm that is Microarray Gene Expression - Tabular format (MAGE-TAB)-a tab-delimited format to exchange microarray data.

Investigations, Studies, and Assays are the three entities around which the ISA-Tab framework is built. Investigation is a higher-order object, whose primary role is to group related Studies. Study is the central unit, containing information on the subject under study, its characteristics and any treatments applied. A Study has associated Assays. Assays are measurements performed either on the whole initial subject or on a sample taken from the subject, which produce qualitative or quantitative data. Assays can be characterized as the smallest complete unit of experimentation producing data associated with a subject.

The ISA-Tab specification relies on the ISA data model to order and classify the metadata. The ISA data model uses the following three types of text files to capture the metadata:

• The Investigation file contains all of the information needed to understand the project context, overall goals, and means. An Investigation is a high-level concept that groups related Studies.
• The Study file(s) includes information on the subject under study, its characteristics, and any treatments applied. A Study is the central unit and has associated Assays.
• The Assay file(s) include test steps and analytical measurements. An Assay is a test performed either on material taken from the subject or the whole initial subject, which produces qualitative and quantitative measurements (data).

Each of these files is a tab-delimited text file that researchers can create, view, and edit.

For more information about how the Investigation, Study, and Assay data are linked in the ISA-TAB format, refer to LinkedISA: Semantic Representation of ISA-Tab Experimental Metadata.

The following image shows the structure of the ISA data model.

Source: ISA-Tools.org

Registering to Use the CSSI DCC Portal

Before you can log in for the first time, you must register.

To register on the CSSI DCC Portal

1. Navigate to the CSSI DCC Portal.
   The home page appears.
   
2. Click Login.
   The Please Sign In page appears.
   
3. Click Register.
   The Registration page appears.
   
4. Provide information in all of the following required fields:
   • First name
   • Last name
   • Institution
   • Email address
   • Password
   • Confirm password
5. If you want to upload investigation data to the CSSI DCC portal in the future, select the I would like to upload investigation data box. Doing so ensures that your future submissions are correctly tracked.
6. Select the I'm not a robot box.
7. Click Register.
   A message box appears.
   
8. Check your inbox for an email with the subject line "CSSI DCC Account Activation." Click the link in the email to complete account activation.
9. Get started using the CSSI DCC Portal.

Logging In to the CSSI DCC Portal

Before you can upload investigation data, you must register and then log in.

You do not need to log in to browse, search, and download investigation data.

To log in to the CSSI DCC Portal

1. Navigate to the CSSI DCC Portal.
   The home page appears.
   
2. Click Login.
   The Please Sign In page appears.
   

3. Enter your email address and password you specified when you registered.
   
   

   To reset your password, click Forgot Password? In the window that appears, enter your email address to request a password reset email.

4. Click Sign In.
   The CSSI DCC portal home page appears.

Changing Your Password

1. Log in to the CSSI DCC portal.
   Your email address appears in the upper-right corner of the screen.
2. Click the arrow next to your email address to open the window and then click Change Password.
   The Change Password window appears.
   
3. Your current password is already supplied. Enter your new password twice and click Change Password.
   A message appears confirming that you have changed your password.
4. Click the arrow next to your email address to open the window and then click Change Password.
   The Change Password window appears.
   
5. Your current password is already supplied. Enter your new password twice and click Change Password.
   A message appears confirming that you have changed your password.