1
|
Brady A, Charbonneau A, Grossman RL, Creasy HH, Renner R, Pihl T, Otridge J, Kim E, Barnholtz-Sloan JS, Kerlavage AR. NCI Cancer Research Data Commons: Core Standards and Services. Cancer Res 2024; 84:1384-1387. [PMID: 38488505 PMCID: PMC11067691 DOI: 10.1158/0008-5472.can-23-2655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/05/2024] [Accepted: 02/28/2024] [Indexed: 05/03/2024]
Abstract
The NCI Cancer Research Data Commons (CRDC) is a collection of data commons, analysis platforms, and tools that make existing cancer data more findable and accessible by the cancer research community. In practice, the two biggest hurdles to finding and using data for discovery are the wide variety of models and ontologies used to describe data, and the dispersed storage of that data. Here, we outline core CRDC services to aggregate descriptive information from multiple studies for findability via a single interface and to provide a single access method that spans multiple data commons. See related articles by Wang et al., p. 1388, Pot et al., p. 1396, and Kim et al., p. 1404.
Collapse
Affiliation(s)
- Arthur Brady
- General Dynamics Information Technology, Falls Church, Virginia
| | | | - Robert L. Grossman
- University of Chicago, Center for Translational Data Science, Chicago, Illinois
| | - Heather H. Creasy
- Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland
| | - Robinette Renner
- Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland
| | - Todd Pihl
- Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - John Otridge
- Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Erika Kim
- Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland
| | | | - Jill S. Barnholtz-Sloan
- Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland
- Trans Divisional Research Program, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Anthony R. Kerlavage
- Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland
| |
Collapse
|
2
|
McDonnell KJ. Leveraging the Academic Artificial Intelligence Silecosystem to Advance the Community Oncology Enterprise. J Clin Med 2023; 12:4830. [PMID: 37510945 PMCID: PMC10381436 DOI: 10.3390/jcm12144830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Over the last 75 years, artificial intelligence has evolved from a theoretical concept and novel paradigm describing the role that computers might play in our society to a tool with which we daily engage. In this review, we describe AI in terms of its constituent elements, the synthesis of which we refer to as the AI Silecosystem. Herein, we provide an historical perspective of the evolution of the AI Silecosystem, conceptualized and summarized as a Kuhnian paradigm. This manuscript focuses on the role that the AI Silecosystem plays in oncology and its emerging importance in the care of the community oncology patient. We observe that this important role arises out of a unique alliance between the academic oncology enterprise and community oncology practices. We provide evidence of this alliance by illustrating the practical establishment of the AI Silecosystem at the City of Hope Comprehensive Cancer Center and its team utilization by community oncology providers.
Collapse
Affiliation(s)
- Kevin J McDonnell
- Center for Precision Medicine, Department of Medical Oncology & Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| |
Collapse
|
3
|
Sheffield NC, Bonazzi VR, Bourne PE, Burdett T, Clark T, Grossman RL, Spjuth O, Yates AD. From biomedical cloud platforms to microservices: next steps in FAIR data and analysis. Sci Data 2022; 9:553. [PMID: 36075919 PMCID: PMC9458632 DOI: 10.1038/s41597-022-01619-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Nathan C Sheffield
- Center for Public Health Genomics, School of Medicine, University of Virginia, 22908, Charlottesville, VA, USA.
- School of Data Science, University of Virginia, Charlottesville VA 22904, Charlottesville, VA, USA.
- Department of Biomedical Engineering, School of Medicine, University of Virginia, 22904, Charlottesville, VA, USA.
- Department of Public Health Sciences, School of Medicine, University of Virginia, 22908, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, 22908, Charlottesville, VA, USA.
| | | | - Philip E Bourne
- School of Data Science, University of Virginia, Charlottesville VA 22904, Charlottesville, VA, USA
- Department of Biomedical Engineering, School of Medicine, University of Virginia, 22904, Charlottesville, VA, USA
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Timothy Clark
- School of Data Science, University of Virginia, Charlottesville VA 22904, Charlottesville, VA, USA
- Department of Public Health Sciences, School of Medicine, University of Virginia, 22908, Charlottesville, VA, USA
| | - Robert L Grossman
- Center for Translational Data Science, University of Chicago, Chicago, IL, 60615, USA
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| |
Collapse
|
4
|
Murphy SN, Visweswaran S, Becich MJ, Campion TR, Knosp BM, Melton-Meaux GB, Lenert LA. Research data warehouse best practices: catalyzing national data sharing through informatics innovation. J Am Med Inform Assoc 2022; 29:581-584. [PMID: 35289371 PMCID: PMC8922176 DOI: 10.1093/jamia/ocac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shawn N Murphy
- Research Information Science and Computing, Mass General Brigham, Somerville, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Clinical and Translational Science Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael J Becich
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Clinical and Translational Science Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Thomas R Campion
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York, USA
- Clinical and Translational Science Center, Weill Cornell Medicine, New York, New York, USA
| | - Boyd M Knosp
- Roy J. and Lucille A. Carver College of Medicine and the Institute for Clinical & Translational Science, University of Iowa, Iowa City, Iowa, USA
| | - Genevieve B Melton-Meaux
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Health Informatics (IHI), University of Minnesota, Minneapolis, Minnesota, USA
| | - Leslie A Lenert
- Biomedical Informatics Center (BMIC), Medical University of South Carolina, Charleston, South Carolina, USA
- Health Sciences South Carolina, Columbia, South Carolina, USA
| |
Collapse
|
5
|
O'Hara T, Saldanha A, Trunnell M, Grossman RL, Hota B, Frankenberger C. Economical Utilization of Health Information with Learning Healthcare System Data Commons. PERSPECTIVES IN HEALTH INFORMATION MANAGEMENT 2022; 19:1d. [PMID: 35692848 PMCID: PMC9123530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Finding, accessing, sharing, and analyzing patient data from a clinical setting for collaborative research has continually proven to be a challenge in healthcare organizations. The human and technological architecture required to perform these services exist at the largest academic institutions but are usually under-funded. At smaller, less academically focused healthcare organizations across the United States, where the majority of care is delivered, they are generally absent. Here we propose a solution called the Learning Healthcare System Data Commons where cost is usage-based and the most basic elements are designed to be extensible, allowing it to evolve with the changing landscape of healthcare. Herein we also discuss our reference implementation of this platform tailored specifically for operational sustainability and governance using the data generated in a hospital setting for research, quality, and educational purposes.
Collapse
|