Scientists working to develop better tools in the ongoing fight against COVID-19 have a new resource at their disposal with the launch of the COVIDome Explorer. This new online portal provides access to a multidimensional dataset of COVID-19 patients and negative controls generated through comprehensive analyses conducted at the University of Colorado Anschutz Medical Campus.
The public portal contains information including demographics and clinical data, along with matched analysis of the whole blood transcriptome, plasma analysis, red blood cell metabolome analysis, deep immune phenotyping by mass cytometry and seroconversion assays for each patient. The COVIDome Explorer aims to give researchers from around the world access to a wide dataset for rapid hypotheses testing, hypothesis generation and real-time discoveries, aided through built-in filters and data visualization tools, along with sample level data tables exportable in CSV, Excel and PDF formats.
Each dataset is linked at the sample level with a unique identifier, enabling cross-referencing among platforms. The COVIDome Explorer hosts six dashboards: Cohort, Transcriptome, Proteome, Cytokines, Metabolome and Immune Maps. Each dashboard runs within its own isolated and protected environment.
An open-access paper published in Cell Reports details how the datasets were generated and explains how to use the COVIDome Explorer and dashboards for real-time data analysis, visualization and sharing. The paper further links to data files to guide users, such as catalogs of proteins, metabolites, cytokines and immune cells present in each dataset.
“The global health crisis imposed by the COVID-19 pandemic further emphasizes the need for rapid collaboration, open access to manuscripts under review and data sharing,” said Thomas Flaig, MD, vice chancellor of research at the CU Anschutz Medical Campus. “Now more than ever, with the rise of the COVID-19 Delta variant and breakthrough infection rates rising, it’s critical to have easy and timely access to COVID data to combat the pandemic and advance the best scientific data available.”
The COVIDome explorer was modeled after a similar effort at the Linda Crnic Institute for Down Syndrome, where members of the COVIDome team previously developed the Human Trisome Project and TrisomExplorer data portal. Building on the TrisomExplorer technology allowed the team to create the COVIDome Explorer in a matter of weeks and make it available to the public to help advance COVID-19 research.
“Our mission for the COVIDome Explorer is to enable the development of better prevention, diagnostic and therapeutic tools for the clinical management of COVID-19,” said Joaquin Espinosa, PhD, executive director at the Linda Crnic Institute for Down Syndrome. “Although great progress has been made in all these areas, the speed of research for COVID-19 has been hampered by the lack of widely accessible, public datasets that can be analyzed and reanalyzed in real time by anyone. We expect that this online portal will rapidly accelerate COVID-19 data sharing, hypothesis testing and discoveries worldwide.”