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Chepelev LL, Kwan D, Kahn CE, Filice RW, Wang KC. Ontologies in the New Computational Age of Radiology: RadLex for Semantics and Interoperability in Imaging Workflows. Radiographics 2023; 43:e220098. [PMID: 36757882 DOI: 10.1148/rg.220098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
From basic research to the bedside, precise terminology is key to advancing medicine and ensuring optimal and appropriate patient care. However, the wide spectrum of diseases and their manifestations superimposed on medical team-specific and discipline-specific communication patterns often impairs shared understanding and the shared use of common medical terminology. Common terms are currently used in medicine to ensure interoperability and facilitate integration of biomedical information for clinical practice and emerging scientific and educational applications alike, from database integration to supporting basic clinical operations such as billing. Such common terminologies can be provided in ontologies, which are formalized representations of knowledge in a particular domain. Ontologies unambiguously specify common concepts and describe the relationships between those concepts by using a form that is mathematically precise and accessible to humans and machines alike. RadLex® is a key RSNA initiative that provides a shared domain model, or ontology, of radiology to facilitate integration of information in radiology education, clinical care, and research. As the contributions of the computational components of common radiologic workflows continue to increase with the ongoing development of big data, artificial intelligence, and novel image analysis and visualization tools, the use of common terminologies is becoming increasingly important for supporting seamless computational resource integration across medicine. This article introduces ontologies, outlines the fundamental semantic web technologies used to create and apply RadLex, and presents examples of RadLex applications in everyday radiology and research. It concludes with a discussion of emerging applications of RadLex, including artificial intelligence applications. © RSNA, 2023 Quiz questions for this article are available in the supplemental material.
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Affiliation(s)
- Leonid L Chepelev
- From the Joint Department of Medical Imaging, University Health Network, University of Toronto, Toronto General Hospital, 585 University Ave, 1-PMB 286, Toronto, ON, Canada M5G 2N2 (L.L.C.); Insygnia Consulting, Toronto, ON, Canada (D.K.); Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA (C.E.K.); Department of Radiology, MedStar Georgetown University Hospital, Washington, DC (R.W.F.); and Imaging Service, Baltimore VA Medical Center, Baltimore, MD, and Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD (K.C.W.)
| | - David Kwan
- From the Joint Department of Medical Imaging, University Health Network, University of Toronto, Toronto General Hospital, 585 University Ave, 1-PMB 286, Toronto, ON, Canada M5G 2N2 (L.L.C.); Insygnia Consulting, Toronto, ON, Canada (D.K.); Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA (C.E.K.); Department of Radiology, MedStar Georgetown University Hospital, Washington, DC (R.W.F.); and Imaging Service, Baltimore VA Medical Center, Baltimore, MD, and Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD (K.C.W.)
| | - Charles E Kahn
- From the Joint Department of Medical Imaging, University Health Network, University of Toronto, Toronto General Hospital, 585 University Ave, 1-PMB 286, Toronto, ON, Canada M5G 2N2 (L.L.C.); Insygnia Consulting, Toronto, ON, Canada (D.K.); Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA (C.E.K.); Department of Radiology, MedStar Georgetown University Hospital, Washington, DC (R.W.F.); and Imaging Service, Baltimore VA Medical Center, Baltimore, MD, and Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD (K.C.W.)
| | - Ross W Filice
- From the Joint Department of Medical Imaging, University Health Network, University of Toronto, Toronto General Hospital, 585 University Ave, 1-PMB 286, Toronto, ON, Canada M5G 2N2 (L.L.C.); Insygnia Consulting, Toronto, ON, Canada (D.K.); Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA (C.E.K.); Department of Radiology, MedStar Georgetown University Hospital, Washington, DC (R.W.F.); and Imaging Service, Baltimore VA Medical Center, Baltimore, MD, and Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD (K.C.W.)
| | - Kenneth C Wang
- From the Joint Department of Medical Imaging, University Health Network, University of Toronto, Toronto General Hospital, 585 University Ave, 1-PMB 286, Toronto, ON, Canada M5G 2N2 (L.L.C.); Insygnia Consulting, Toronto, ON, Canada (D.K.); Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA (C.E.K.); Department of Radiology, MedStar Georgetown University Hospital, Washington, DC (R.W.F.); and Imaging Service, Baltimore VA Medical Center, Baltimore, MD, and Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD (K.C.W.)
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Gibaud B, Brenet M, Pasquier G, Gil AV, Bardiès M, Stratakis J, Damilakis J, Van Dooren N, Spaltenstein J, Ratib O. A semantic database for integrated management of image and dosimetric data in low radiation dose research in medical imaging. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2021; 2020:492-501. [PMID: 33936422 PMCID: PMC8075532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Medical ionizing radiation procedures and especially medical imaging are a non negligible source of exposure to patients. Whereas the biological effects of high absorbed doses are relatively well known, the effects of low absorbed doses are still debated. This work presents the development of a computer platform called Image and Radiation Dose BioBank (IRDBB) to manage research data produced in the context of the MEDIRAD project, a European project focusing on research on low doses in the context of medical procedures. More precisely, the paper describes a semantic database linking dosimetric data (such as absorbed doses to organs) to the images corresponding to X-rays exposure (such as CT images) or scintigraphic images (such as SPECT or PET images) that allow measuring the distribution of a radiopharmaceutical. The main contributions of this work are: 1) the implementation of the semantic database of the IRDBB system and 2) an ontology called OntoMEDIRAD covering the domain of discourse involved in MEDIRAD research data, especially many concepts from the DICOM standard modelled according to a realist approach.
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Affiliation(s)
| | | | | | - Alex Vergara Gil
- Centre Recherche en Cancérologie de Toulouse, Toulouse, France
- UMR 1037, INSERM, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Manuel Bardiès
- Centre Recherche en Cancérologie de Toulouse, Toulouse, France
- UMR 1037, INSERM, Université Toulouse III Paul Sabatier, Toulouse, France
| | - John Stratakis
- Medical Physics Department, School of Medicine, University of Crete, Heraklion, Greece
| | - John Damilakis
- Medical Physics Department, School of Medicine, University of Crete, Heraklion, Greece
| | | | | | - Osman Ratib
- Institute of Translational Molecular Imaging, Genève
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Rubin DL, Ugur Akdogan M, Altindag C, Alkim E. ePAD: An Image Annotation and Analysis Platform for Quantitative Imaging. ACTA ACUST UNITED AC 2020; 5:170-183. [PMID: 30854455 PMCID: PMC6403025 DOI: 10.18383/j.tom.2018.00055] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Medical imaging is critical for assessing the response of patients to new cancer therapies. Quantitative lesion assessment on images is time-consuming, and adopting new promising quantitative imaging biomarkers of response in clinical trials is challenging. The electronic Physician Annotation Device (ePAD) is a freely available web-based zero-footprint software application for viewing, annotation, and quantitative analysis of radiology images designed to meet the challenges of quantitative evaluation of cancer lesions. For imaging researchers, ePAD calculates a variety of quantitative imaging biomarkers that they can analyze and compare in ePAD to identify potential candidates as surrogate endpoints in clinical trials. For clinicians, ePAD provides clinical decision support tools for evaluating cancer response through reports summarizing changes in tumor burden based on different imaging biomarkers. As a workflow management and study oversight tool, ePAD lets clinical trial project administrators create worklists for users and oversee the progress of annotations created by research groups. To support interoperability of image annotations, ePAD writes all image annotations and results of quantitative imaging analyses in standardized file formats, and it supports migration of annotations from various propriety formats. ePAD also provides a plugin architecture supporting MATLAB server-side modules in addition to client-side plugins, permitting the community to extend the ePAD platform in various ways for new cancer use cases. We present an overview of ePAD as a platform for medical image annotation and quantitative analysis. We also discuss use cases and collaborations with different groups in the Quantitative Imaging Network and future directions.
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Affiliation(s)
- Daniel L Rubin
- Department of Biomedical Data Science, Radiology, and Medicine (Biomedical Informatics Research), Stanford University, Stanford, CA
| | - Mete Ugur Akdogan
- Department of Biomedical Data Science, Radiology, and Medicine (Biomedical Informatics Research), Stanford University, Stanford, CA
| | - Cavit Altindag
- Department of Biomedical Data Science, Radiology, and Medicine (Biomedical Informatics Research), Stanford University, Stanford, CA
| | - Emel Alkim
- Department of Biomedical Data Science, Radiology, and Medicine (Biomedical Informatics Research), Stanford University, Stanford, CA
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Messaoudi R, Mtibaa A, Vacavant A, Gargouri F, Jaziri F. Ontologies for Liver Diseases Representation: A Systematic Literature Review. J Digit Imaging 2019; 33:563-573. [PMID: 31848894 DOI: 10.1007/s10278-019-00303-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ontology, as a useful knowledge engineering technique, has been widely used for reducing ambiguity and helping with information sharing. It is considered originally to be clear, comprehensive, and with well-defined format. It characterizes several domains purposes description through structured and formalized languages. In various areas of research, it has become a significant way to realize successful and powerful accomplishments. Actually, medical ontologies were turned into an efficient application in medical domains. They also become a relevant approach to process large medical data volumes. Consequently, they are behaving as a support decision system in some cases. Also, they ensure diagnosis process acceleration and assistance. Additionally, they have been integrated especially to represent human healthcare concepts. For that reason, plenty of research works applied ontologies to design and treat liver diseases. In this article, we present a general overview of medical ontologies to stand for this type of disease. We expose and discuss these works in details by a complete comparison. Also, we show their performance to arrange clinical data and extract results.
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Affiliation(s)
- Rim Messaoudi
- MIRACL Laboratory, University of Sfax, Sfax, Tunisia.
- Institut Pascal, Université Clermont Auvergne, UMR6602 CNRS/UCA/SIGMA, 63171, Aubière, France.
| | - Achraf Mtibaa
- MIRACL Laboratory, University of Sfax, Sfax, Tunisia
- National School of Electronic and Telecommunications, University of Sfax, Sfax, Tunisia
| | - Antoine Vacavant
- Institut Pascal, Université Clermont Auvergne, UMR6602 CNRS/UCA/SIGMA, 63171, Aubière, France
| | - Faïez Gargouri
- MIRACL Laboratory, University of Sfax, Sfax, Tunisia
- Higher Institute of Computer Science and Multimedia, University of Sfax, Sfax, Tunisia
| | - Faouzi Jaziri
- Institut Pascal, Université Clermont Auvergne, UMR6602 CNRS/UCA/SIGMA, 63171, Aubière, France
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Bibault JE, Zapletal E, Rance B, Giraud P, Burgun A. Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology. PLoS One 2018; 13:e0191263. [PMID: 29351341 PMCID: PMC5774757 DOI: 10.1371/journal.pone.0191263] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 01/01/2018] [Indexed: 12/25/2022] Open
Abstract
Purpose Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources. We present the ontology we developed to address this issue. Methods Radiation Oncology anatomical and target volumes were categorized in anatomical and treatment planning classes. International delineation guidelines specific to radiation oncology were used for lymph nodes areas and target volumes. Hierarchical classes were created to generate The Radiation Oncology Structures (ROS) Ontology. The ROS was then applied to the data from our institution. Results Four hundred and seventeen classes were created with a maximum of 14 children classes (average = 5). The ontology was then converted into a Web Ontology Language (.owl) format and made available online on Bioportal and GitHub under an Apache 2.0 License. We extracted all structures delineated in our department since the opening in 2001. 20,758 structures were exported from our “record-and-verify” system, demonstrating a significant heterogeneity within a single center. All structures were matched to the ROS ontology before integration into our clinical data warehouse (CDW). Conclusion In this study we describe a new ontology, specific to radiation oncology, that reports all anatomical and treatment planning structures that can be delineated. This ontology will be used to integrate dosimetric data in the Assistance Publique—Hôpitaux de Paris CDW that stores data from 6.5 million patients (as of February 2017).
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Affiliation(s)
- Jean-Emmanuel Bibault
- Radiation Oncology Department, Georges Pompidou European Hospital, Assistance Publique – Hôpitaux de Paris (AP-HP), Paris Descartes University, Paris Sorbonne Cité, Paris, France
- INSERM UMR 1138 Team 22: Information Sciences to support Personalized Medicine, Paris Descartes University, Sorbonne Paris Cité, Paris, France
- * E-mail:
| | - Eric Zapletal
- Biomedical Informatics and Public Health Department, Georges Pompidou European Hospital, Assistance Publique – Hôpitaux de Paris (AP-HP), Paris Descartes University, Paris Sorbonne Cité, Paris, France
| | - Bastien Rance
- INSERM UMR 1138 Team 22: Information Sciences to support Personalized Medicine, Paris Descartes University, Sorbonne Paris Cité, Paris, France
- Biomedical Informatics and Public Health Department, Georges Pompidou European Hospital, Assistance Publique – Hôpitaux de Paris (AP-HP), Paris Descartes University, Paris Sorbonne Cité, Paris, France
| | - Philippe Giraud
- Radiation Oncology Department, Georges Pompidou European Hospital, Assistance Publique – Hôpitaux de Paris (AP-HP), Paris Descartes University, Paris Sorbonne Cité, Paris, France
| | - Anita Burgun
- INSERM UMR 1138 Team 22: Information Sciences to support Personalized Medicine, Paris Descartes University, Sorbonne Paris Cité, Paris, France
- Biomedical Informatics and Public Health Department, Georges Pompidou European Hospital, Assistance Publique – Hôpitaux de Paris (AP-HP), Paris Descartes University, Paris Sorbonne Cité, Paris, France
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