OpenGDC

OpenGDC extracts, integrates, and converts genomic experiments and clinical information from the Genomic Data Commons (GDC) portal to provide harmonized representation and enable analysis of large-scale cancer genomics datasets generated by Next Generation Sequencing.

Key Features:

• Data Harmonization: Implements a Genomic Data Model that represents Genomic Data in Browser Extensible Data (BED) format and stores Metadata in a tab-delimited key-value format.
• Data Integration and Extension: Incorporates annotations and metadata from public databases including GENCODE, HGNC, and miRBase to extend GDC genomic data.
• Automated Metadata Management: Automatically extracts, normalizes, and deduplicates metadata from Clinical/Biospecimen Supplements and the GDC Data Model to ensure consistency across the GDC data portal and API.
• Data Conversion and Export: Converts genomic and clinical data into BED, GTF, CSV, JSON, and XML formats for interoperability with other tools and workflows.
• Repository Creation: Enabled creation of a homogenized and enhanced repository of The Cancer Genome Atlas (TCGA) data totaling approximately 1.3 TB.
• GMQL Compatibility: Ensures compatibility with the GenoMetric Query Language (GMQL) to enable sophisticated queries on transformed TCGA data.
• Implementation: Implemented as a Java-based system.

Scientific Applications:

• Information Retrieval: Facilitates efficient querying and retrieval of complex genomic and clinical data from the GDC and integrated annotation sources.
• Knowledge Discovery Analyses: Supports comprehensive cancer genomics analyses and discovery by providing harmonized, annotated, and queryable TCGA datasets.

Methodology:

The methodology applies the Genomic Data Model to standardize genomic and metadata representation and uses compatibility with the GenoMetric Query Language (GMQL) to support queries on transformed TCGA data from the GDC.