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.  

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

Contents of this User's Guide