Bioinformatics: Biomarkers of early detection

Issue title: Translational Pathology of Early Cancer

Guest editors: Sudhir Srivastavax and William E. Grizzley

Article type: Research Article

Authors: Crichton, Daniel J.^{a; *} | Mattmann, Chris A.^a | Thornquist, Mark^b | Anton, Kristen^c | Hughes, J. Steven^a

Affiliations: [a] NASA Jet Propulsion Laboratory, Pasadena, CA, USA | [b] Fred Hutchinson Cancer Research Center, Seattle, WA, USA | [c] Dartmouth Medical School, Lebanon, NH, USA | [x] Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA | [y] Department of Pathology, Division of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL, USA

Correspondence: [*] Corresponding author: Daniel Crichton, 4800 Oak Grove Drive MS 301–320, Pasadena, CA 91109, USA. Tel.: +1 818 354 9155; E-mail: Dan.Crichton@jpl.nasa.gov.

Abstract: Capturing, sharing, and publishing cancer biomarker research data are all fundamental challenges of enabling new opportunities to research and understand scientific data. Informatics experts from the National Cancer Institute's (NCI) Early Detection Research Network (EDRN) have pioneered a principled informatics infrastructure to capture and disseminate data from biomarker validation studies, in effect, providing a national-scale, real-world successful example of how to address these challenges. EDRN is a distributed, collaborative network and it requires its infrastructure to support research across cancer research institutions and across their individual laboratories. The EDRN informatics infrastructure is also referred to as the EDRN Knowledge Environment, or EKE. EKE connects information about biomarkers, studies, specimens and resulting scientific data, allowing users to search, download and compare each of these disparate sources of cancer research information. EKE's data is enriched by providing annotations that describe the research results (biomarkers, protocols, studies) and that link the research results to the captured information within EDRN (raw instrument datasets, specimens, etc.). In addition EKE provides external links to public resources related to the research results and captured data. EKE has leveraged and reused data management software technologies originally developed for planetary and earth science research results and has infused those capabilities into biomarker research. This paper will describe the EDRN Knowledge Environment, its deployment to the EDRN enterprise, and how a number of these challenges have been addressed through the capture and curation of biomarker data results.

Keywords: EDRN knowledge environment, data intensive systems, biomarker research, informatics infrastructure, e-science, metadata, data curation, data sharing, biomarker database, Data Grid

DOI: 10.3233/CBM-2011-0180

Journal: Cancer Biomarkers, vol. 9, no. 1-6, pp. 511-530, 2011