cBioPortal as a Hub of Cancer Research
cBioPortal is an open-source web platform used for the interactive exploration of multidimensional cancer genomics data sets. In its WP3, EOSC4Cancer leverages cBioPortal as a platform to make available methods for federated and FAIR analysis of cancer data.
cBioPortal provides an interface for exploring various types of cancer genomics data, such as DNA sequencing data, gene expression data, and clinical data. Users can create custom queries to retrieve and visualise data from multiple studies, perform survival analysis, and generate customised reports. The platform is widely used by cancer researchers and has been adopted by many large-scale cancer genomics projects, including The Cancer Genome Atlas (TCGA), the International Cancer Genome Consortium (ICGC) and the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange (AACR GENIE).
More specifically, EOSC4Cancer deploys a reference installation for the EOSC4Cancer use cases (WP4), provides support for data upload and implementation challenges and distributes a packaged cBioPortal installation.
An initial cBioPortal workshop was already held in March 2023 (view recordings and slides). In March 2024, a functional prototype of an integration between a virtual research environment (e.g. Galaxy) and cBioPortal will be available. In September 2024, integration and visualisation workflows for new data types will be available.