On March 29th 2023, EOSC4Cancer held a cBioPortal Workshop as part of their WP4 activities, with two training sessions held for both cBioPortal users and data loaders. Over 50 participants attended the virtual workshop, stemming from various cancer research initiatives, including EOSC4Cancer, CAN.HEAL, UNCAN, and others.
cBioPortal is an open-source web platform used for the interactive exploration of multidimensional cancer genomics data sets. 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).
During the workshop, portal users were given an overview of the functionality of cBioPortal and practised exploring public study material. They also learned how to navigate the portal and use its features to extract valuable insights from the available data. The data-loaders received hands-on experience with the assistance of Health-RI cBioPortal operators, mainly focusing on preparing their environment and loading a study into the Health-RI cBioPortal server. It gives support as well to WP4 members by showing how existing cBioPortal functionality can be applied in cancer research and clinical trial handling (e.g. providing visual support for Molecular Tumour Boards) .
The main takeaway from the Workshop was that EOSC4Cancer will offer a reference installation of cBioPortal for cancer research studies (both in EOSC4Cancer and CAN.HEAL). The project currently investigates how to enhance the capabilities of cBioPortal by enabling it to connect with a wider range of data sources (e.g. linking to biomedical images in an XNAT-OHIF). This will significantly expand the potential applications of cBioPortal in cancer research, and provide researchers with more comprehensive and integrated data resources.
The recording of the webinar is available in three parts. You can access part 1, part 2, and part 3 on YouTube, and read the workshop presentation slides here.