Cancer Data Science Pulse

The Cancer Data Science Pulse blog provides insights on trends, policies, initiatives, and innovation in the data science and cancer research communities from professionals dedicated to building a national cancer data ecosystem that enables new discoveries and reduces the burden of cancer.

Dr. Tony Kerlavage, director of NCI’s Center for Biomedical Informatics and Information Technology (CBIIT), sat down to discuss one key component of racial inequality, the issue of health disparities, as it relates to Big Data. As noted by Dr. Kerlavage, representing our diverse U.S. population in research and in the workforce are key, but we also need better data.

Naturally occurring cancers in dogs share similarities with cancer that occurs in humans. The Integrated Canine Data Commons (ICDC), a cloud-based repository of canine cancer data, includes a variety of molecular, clinical, pharmacological, and medical imaging information from pet dogs. Such comparative oncology findings offer researchers greater insight into how best to diagnose, treat, and prevent cancer—in both people and pets.

The explosion of genetic information and direct access to large-scale genomic data not only opens up new areas for exploring today's most pressing research questions, it also serves as a reminder of the importance of collaboration at every stage of the study. NCI’s Dr. Daoud Meerzaman describes a new "circular" way of collaborating that keeps everyone in the loop when devising new genomics studies.

This new blog installment shines a spotlight on the staff who are working to turn data and IT resources into solutions for addressing data-driven cancer research. This spotlight features Sherri de Coronado, program manager in the CBIIT Cancer Informatics Branch.

The use of bioinformatics in cancer research helps organize vast amounts of data to allow researchers to identify information, trends, and correlations, ranging from very large populations of people all the way down to a single molecule. NCI's Dr. Daoud Meerzaman describes how data science is helping pinpoint the contributions of a single protein, bromodomain protein 4 (BRD4), and its effects on the development of tumors and progression of cancer.

NCI initiatives are accumulating a wealth of data from the fields of genomics, proteomics, single-cell, radiology, molecular imaging, clinical findings, and more. The newly awarded Cancer Data Aggregator (CDA) is currently being designed and developed to allow scientists to crosstalk among these very diverse data sets, facilitating interoperability not only within the Cancer Research Data Commons but throughout the larger data ecosystem.

The quest to harmonize data has ushered in a new way of thinking about standardization. Now, rather than expecting everyone to adopt a particular model or standard, we’re seeking to leverage technology that can do some of this work for us. The DREAM Challenge was designed to make aggregating and mapping data to the correct lexicon of terms and metadata a nearly seamless step for researchers. Read more about the Challenge that’s currently underway and how we hope to address harmonization in the future.

This new blog installment shines a spotlight on the staff who are working to turn data and IT resources into solutions for addressing data-driven cancer research. Here we feature Mervi Heiskanen, Ph.D., program manager in the Cancer Informatics Branch at CBIIT. Much of her work focuses on data sharing and creating the tools and resources that help to make open data a reality.

Pooling data from numerous sources strengthens the power of the information, but only if it can be meaningfully connected. Dr. Melissa Haendel, Director of the Translational and Integrative Sciences Laboratory, Oregon State University (OSU), and Principal Investigator for the NCI Center for Cancer Data Harmonization, and Julie McMurry, Associate Director of the Translational and Integrative Sciences Laboratory, OSU, describe the basics of harmonization and how it can help in wrangling massive amounts of data to make them more valuable to research.

NCI’s Dr. Erika Kim and Dr. Chris Kinsinger discuss how the Proteomic Data Commons (PDC) aids cancer researchers in accessing and analyzing proteomic data. The PDC is an integral part of NCI’s Cancer Research Data Commons (CRDC) as it gives researchers access to three types of proteomic data: mass spectra, identified peptides, and protein reports, as well as clinical, biospecimen, and other metadata. The PDC is available for queries and analysis of publicly accessible datasets.