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Bilaver LA, Wang H, Naidech AM, Luo Y, Das R, Sehgal S, Gupta R. Natural language processing of pediatric progress notes for the identification of food allergy. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:2242-2244.e2. [PMID: 37094730 DOI: 10.1016/j.jaip.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023]
Affiliation(s)
- Lucy A Bilaver
- Center for Food Allergy & Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill.
| | - Hanyin Wang
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Andrew M Naidech
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Yuan Luo
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill; Northwestern University Clinical and Translational Sciences Institute, Northwestern University Feinberg School of Medicine, Chicago, Ill; Institute for Augmented Intelligence in Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Rajeshree Das
- Center for Food Allergy & Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Shruti Sehgal
- Center for Food Allergy & Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Ruchi Gupta
- Center for Food Allergy & Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill; Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
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Gupta RS, Sehgal S, Wlodarski M, Bilaver LA, Wehbe FH, Spergel JM, Wang J, Ciaccio CE, Nimmagadda SR, Assa'ad A, Mahdavinia M, Wasserman RL, Brown E, Sicherer SH, Bird JA, Roberts B, Sharma HP, Mendez K, Holding EG, Mitchell L, Corbett M, Makhija M, Starren JB. Accelerating Food Allergy Research: Need for a Data Commons. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:1063-1067. [PMID: 36796512 DOI: 10.1016/j.jaip.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023]
Abstract
Food allergy is a significant health problem affecting approximately 8% of children and 11% of adults in the United States. It exhibits all the characteristics of a "complex" genetic trait; therefore, it is necessary to look at very large numbers of patients, far more than exist at any single organization, to eliminate gaps in the current understanding of this complex chronic disorder. Advances may be achieved by bringing together food allergy data from large numbers of patients into a Data Commons, a secure and efficient platform for researchers, comprising standardized data, available in a common interface for download and/or analysis, in accordance with the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. Prior data commons initiatives indicate that research community consensus and support, formal food allergy ontology, data standards, an accepted platform and data management tools, an agreed upon infrastructure, and trusted governance are the foundation of any successful data commons. In this article, we will present the justification for the creation of a food allergy data commons and describe the core principles that can make it successful and sustainable.
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Affiliation(s)
- Ruchi S Gupta
- Center for Food Allergy and Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Ill; The Mary Ann & J. Milburn Smith Child Health Outcomes, Research and Evaluation Center, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill.
| | - Shruti Sehgal
- Center for Food Allergy and Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Mark Wlodarski
- Center for Food Allergy and Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Lucy A Bilaver
- Center for Food Allergy and Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Firas H Wehbe
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Jonathan M Spergel
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at University of Pennsylvania, Philadelphia, Pa
| | - Julie Wang
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Christina E Ciaccio
- Departments of Pediatrics and Medicine, the University of Chicago, Chicago, Ill
| | - Sai R Nimmagadda
- Center for Food Allergy and Asthma Research, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Ill; Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Amal Assa'ad
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Mahboobeh Mahdavinia
- Allergy and Immunology Division, Department of Internal Medicine, and Department of Pediatrics, Rush University Medical Center, Chicago, Ill
| | | | | | - Scott H Sicherer
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - J Andrew Bird
- Department of Pediatrics, Division of Allergy and Immunology, University of Texas Southwestern Medical Center, Dallas, Texas
| | | | - Hemant P Sharma
- Division of Allergy and Immunology, Children's National Hospital, Washington, DC
| | | | | | | | - Mark Corbett
- Department of Pediatrics, University of Louisville School of Medicine, Louisville, Ky
| | - Melanie Makhija
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Ill; Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Justin B Starren
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill
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