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Hallaj S, Khawaja AP, Rodrigues IAS, Boland MV, Brown EN, Chen A, Stagg BC, Stein JD, Sun CQ, Mahe-Cook AL, Swaminathan SS, Wang SY, Xu BY, Weinreb RN, Baxter SL. Gap Analysis of Glaucoma Examination Concept Representations within Standard SNOMED Clinical Terms. Ophthalmol Glaucoma 2024:S2589-4196(24)00140-6. [PMID: 39147325 DOI: 10.1016/j.ogla.2024.08.001] [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: 03/06/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
PURPOSE Standardization of eye care data is important for clinical interoperability and research . We aimed to address gaps in the representations of glaucoma examination concepts within Systemized Nomenclature of Medicine - Clinical Terms (SNOMED-CT), the preferred terminology of the American Academy of Ophthalmology. DESIGN Study of data elements. METHODS Structured eye exam data fields from two electronic health records (EHR) systems (Epic Systems and Medisoft) were compared against existing SNOMED-CT codes for concepts representing glaucoma examination findings3. Glaucoma specialists from multiple institutions were surveyed to identify high-priority gaps in representation, which were discussed among the SNOMED International Eye Care Clinical Reference Group. Proposals for new codes to address the gaps were formulated and submitted for inclusion in SNOMED-CT. MAIN OUTCOME MEASURES Gaps in SNOMED-CT glaucoma examination concept representations RESULTS: We identified several gaps in SNOMED-CT regarding glaucoma examination concepts. A survey of glaucoma specialists identified high-priority data elements within the categories of tonometry and gonioscopy. For tonometry, there was consensus that we need to define new codes related to maximum intraocular pressure (IOP) and target IOP, and to delineate all methods of measuring IOP. These new codes were proposed and successfully added to SNOMED-CT for future use. Regarding gonioscopy, the current terminology did not include the ability to denote the gonioscopic grading system used (e.g., Shaffer or Spaeth), degree of angle pigmentation, iris configuration (except for plateau iris), and iris approach. There was also no ability to specify eye laterality or angle quadrant for gonioscopic findings. We proposed a framework for representing gonioscopic findings as observable entities in SNOMED-CT. DISCUSSION There are existing gaps in the standardized representation of findings related to tonometry and gonioscopy within SNOMED-CT. These are important areas for evaluating clinical outcomes and enabling secondary use of EHR data for glaucoma research. This international, multi-institutional collaborative process enabled identification of gaps, prioritization, and development of data standards to address these gaps. CONCLUSION Addressing these gaps and augmenting SNOMED-CT coverage of glaucoma examination findings could enhance clinical documentation and future research efforts related to glaucoma.
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Affiliation(s)
- Shahin Hallaj
- Division of Ophthalmology Informatics and Data Science, Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA; Hamilton Glaucoma Center, Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA
| | - Anthony P Khawaja
- National Institute for Health and Care Research Biomedical Research Centre, Moorfields Eye Hospital National Health Service Foundation Trust and University College London Institute of Ophthalmology, London, UK
| | - Ian A S Rodrigues
- Department of Ophthalmology, St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Michael V Boland
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Eric N Brown
- Department of Ophthalmology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Aiyin Chen
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Brian C Stagg
- Department of Ophthalmology and Visual Sciences, John Moran Eye Center, University of Utah, Salt Lake City, Utah; Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | - Joshua D Stein
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan
| | - Catherine Q Sun
- Department of Ophthalmology (C.Q.S.), University of California, San Francisco, California, USA; F.I. Proctor Foundation (C.Q.S.), University of California, San Francisco, California, USA
| | | | - Swarup S Swaminathan
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sophia Y Wang
- Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, California, USA
| | - Benjamin Y Xu
- Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine at the University of Southern California, Los Angeles, California, USA
| | - Robert N Weinreb
- Hamilton Glaucoma Center, Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA
| | - Sally L Baxter
- Division of Ophthalmology Informatics and Data Science, Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA; Hamilton Glaucoma Center, Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA.
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Robertson AJ, Mallett AJ, Stark Z, Sullivan C. It Is in Our DNA: Bringing Electronic Health Records and Genomic Data Together for Precision Medicine. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2024; 5:e55632. [PMID: 38935958 PMCID: PMC11211701 DOI: 10.2196/55632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/08/2024] [Accepted: 04/09/2024] [Indexed: 06/29/2024]
Abstract
Health care is at a turning point. We are shifting from protocolized medicine to precision medicine, and digital health systems are facilitating this shift. By providing clinicians with detailed information for each patient and analytic support for decision-making at the point of care, digital health technologies are enabling a new era of precision medicine. Genomic data also provide clinicians with information that can improve the accuracy and timeliness of diagnosis, optimize prescribing, and target risk reduction strategies, all of which are key elements for precision medicine. However, genomic data are predominantly seen as diagnostic information and are not routinely integrated into the clinical workflows of electronic medical records. The use of genomic data holds significant potential for precision medicine; however, as genomic data are fundamentally different from the information collected during routine practice, special considerations are needed to use this information in a digital health setting. This paper outlines the potential of genomic data integration with electronic records, and how these data can enable precision medicine.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, University of Queensland, Hertson, Australia
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia
- The Genomic Institute, Department of Health, Queensland Government, Brisbane, Australia
| | - Andrew J Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Australian Genomics, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Clair Sullivan
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia
- Centre for Health Services Research, Faculty of Medicine, University of Queensland, Woolloongabba, Australia
- Metro North Hospital and Health Service, Department of Health, Queensland Government, Brisbane, Australia
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3
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Sultan M, Zewdie A, Priyadarshani D, Hassen E, Tilahun M, Geremew T, Beane A, Haniffa R, Berenholtz SM, Checkley W, Hansoti B, Laytin AD. Implementing an ICU registry in Ethiopia-Implications for critical care quality improvement. J Crit Care 2024; 81:154525. [PMID: 38237203 PMCID: PMC10996997 DOI: 10.1016/j.jcrc.2024.154525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 03/14/2024]
Abstract
PURPOSE Intensive care units (ICUs) in low- and middle-income countries have high mortality rates, and clinical data are needed to guide quality improvement (QI) efforts. This study utilizes data from a validated ICU registry specially developed for resource-limited settings to identify evidence-based QI priorities for ICUs in Ethiopia. MATERIALS AND METHODS A retrospective cohort analysis of data from two tertiary referral hospital ICUs in Addis Ababa, Ethiopia from July 2021-June 2022 was conducted to describe casemix, complications and outcomes and identify features associated with ICU mortality. RESULTS Among 496 patients, ICU mortality was 35.3%. The most common reasons for ICU admission were respiratory failure (24.0%), major head injury (17.5%) and sepsis/septic shock (13.3%). Complications occurred in 41.0% of patients. ICU mortality was higher among patients with respiratory failure (46.2%), sepsis (66.7%) and vasopressor requirements (70.5%), those admitted from the hospital ward (64.7%), and those experiencing major complications in the ICU (62.3%). CONCLUSIONS In this study, ICU mortality was high, and complications were common and associated with increased mortality. ICU registries are invaluable tools to understand local casemix and clinical outcomes, especially in resource-limited settings. These findings provide a foundation for QI efforts and a baseline to evaluate their impact.
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Affiliation(s)
- Menbeu Sultan
- St. Paul's Hospital Millennium Medical Center, Addis Ababa, Ethiopia
| | - Ayalew Zewdie
- St. Paul's Hospital Millennium Medical Center, Addis Ababa, Ethiopia; Addis Ababa Burn, Emergency and Trauma Hospital, Addis Ababa, Ethiopia
| | | | - Ephrem Hassen
- St. Paul's Hospital Millennium Medical Center, Addis Ababa, Ethiopia
| | - Melkamu Tilahun
- St. Paul's Hospital Millennium Medical Center, Addis Ababa, Ethiopia
| | - Tigist Geremew
- Addis Ababa Burn, Emergency and Trauma Hospital, Addis Ababa, Ethiopia
| | - Abi Beane
- Centre for Inflammation Research, University of Edinburgh, Scotland, UK.
| | - Rashan Haniffa
- Centre for Inflammation Research, University of Edinburgh, Scotland, UK.
| | - Sean M Berenholtz
- Johns Hopkins University School of Medicine, Department of Anesthesia and Critical Care Medicine, Baltimore, MD, USA.
| | - William Checkley
- Johns Hopkins University School of Medicine, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Baltimore, MD, USA.
| | - Bhakti Hansoti
- Johns Hopkins University School of Medicine, Department of Emergency Medicine, Baltimore, MD, USA.
| | - Adam D Laytin
- Johns Hopkins University School of Medicine, Department of Anesthesia and Critical Care Medicine, Baltimore, MD, USA; Johns Hopkins University School of Medicine, Department of Emergency Medicine, Baltimore, MD, USA.
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Hu R, Shi J, Cui L, Abeysinghe R. An Automated Approach for Identifying Erroneous IS-A Relations in SNOMED CT. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2024; 2024:545-554. [PMID: 38827070 PMCID: PMC11141797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
SNOMED CT is the most comprehensive clinical terminology employed worldwide and enhancing its accuracy is of utmost importance. In this work, we introduce an automated approach to identifying erroneous IS-A relations in SNOMED CT. We first extract linked concept-pairs from which we generate Term Difference Pairs (TDPs) that contain differences between the concepts. Given a TDP, if the reversed TDP also exists and the number of linked-pairs generating this TDP is less than those generating the reversed TDP, then we suggest the former linked-pairs as potentially erroneous IS-A relations. We applied this approach to the Clinical finding and Procedure subhierarchies of the 2022 March US Edition of SNOMED CT, and obtained 52 potentially erroneous IS-A relations and a candidate list of 48 linked-pairs. A domain expert confirmed 41 out of 52 (78.8%) are valid and identified 26 erroneous IS-A relations out of 48 linked-pairs demonstrating the effectiveness of the approach.
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Affiliation(s)
- Ran Hu
- McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX
| | - Jay Shi
- Intermountain Healthcare, Denver, CO
| | - Licong Cui
- McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX
| | - Rashmie Abeysinghe
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
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Tabatabaei Hosseini SA, Kazemzadeh R, Foster BJ, Arpali E, Süsal C. New Tools for Data Harmonization and Their Potential Applications in Organ Transplantation. Transplantation 2024:00007890-990000000-00749. [PMID: 38755748 DOI: 10.1097/tp.0000000000005048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
In organ transplantation, accurate analysis of clinical outcomes requires large, high-quality data sets. Not only are outcomes influenced by a multitude of factors such as donor, recipient, and transplant characteristics and posttransplant events but they may also change over time. Although large data sets already exist and are continually expanding in transplant registries and health institutions, these data are rarely combined for analysis because of a lack of harmonization. Promoted by the digitalization of the healthcare sector, effective data harmonization tools became available, with potential applications also for organ transplantation. We discuss herein the present problems in the harmonization of organ transplant data and offer solutions to enhance its accuracy through the use of emerging new tools. To overcome the problem of inadequate representation of transplantation-specific terms, ontologies and common data models particular to this field could be created and supported by a consortium of related stakeholders to ensure their broad acceptance. Adopting clear data-sharing policies can diminish administrative barriers that impede collaboration between organizations. Secure multiparty computation frameworks and the artificial intelligence (AI) approach federated learning can facilitate decentralized and harmonized analysis of data sets, without sharing sensitive data and compromising patient privacy. A common image data model built upon a standardized format would be beneficial to AI-based analysis of pathology images. Implementation of these promising new tools and measures, ideally with the involvement and support of transplant societies, is expected to produce improved integration and harmonization of transplant data and greater accuracy in clinical decision-making, enabling improved patient outcomes.
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Affiliation(s)
| | - Reza Kazemzadeh
- Transplant Immunology Research Center of Excellence, Koç University Hospital, Istanbul, Turkey
| | - Bethany Joy Foster
- Department of Pediatrics, McGill University, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Emre Arpali
- Transplant Immunology Research Center of Excellence, Koç University Hospital, Istanbul, Turkey
| | - Caner Süsal
- Transplant Immunology Research Center of Excellence, Koç University Hospital, Istanbul, Turkey
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Lee HJ, Schwamm LH, Sansing LH, Kamel H, de Havenon A, Turner AC, Sheth KN, Krishnaswamy S, Brandt C, Zhao H, Krumholz H, Sharma R. StrokeClassifier: ischemic stroke etiology classification by ensemble consensus modeling using electronic health records. NPJ Digit Med 2024; 7:130. [PMID: 38760474 PMCID: PMC11101464 DOI: 10.1038/s41746-024-01120-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/23/2024] [Indexed: 05/19/2024] Open
Abstract
Determining acute ischemic stroke (AIS) etiology is fundamental to secondary stroke prevention efforts but can be diagnostically challenging. We trained and validated an automated classification tool, StrokeClassifier, using electronic health record (EHR) text from 2039 non-cryptogenic AIS patients at 2 academic hospitals to predict the 4-level outcome of stroke etiology adjudicated by agreement of at least 2 board-certified vascular neurologists' review of the EHR. StrokeClassifier is an ensemble consensus meta-model of 9 machine learning classifiers applied to features extracted from discharge summary texts by natural language processing. StrokeClassifier was externally validated in 406 discharge summaries from the MIMIC-III dataset reviewed by a vascular neurologist to ascertain stroke etiology. Compared with vascular neurologists' diagnoses, StrokeClassifier achieved the mean cross-validated accuracy of 0.74 and weighted F1 of 0.74 for multi-class classification. In MIMIC-III, its accuracy and weighted F1 were 0.70 and 0.71, respectively. In binary classification, the two metrics ranged from 0.77 to 0.96. The top 5 features contributing to stroke etiology prediction were atrial fibrillation, age, middle cerebral artery occlusion, internal carotid artery occlusion, and frontal stroke location. We designed a certainty heuristic to grade the confidence of StrokeClassifier's diagnosis as non-cryptogenic by the degree of consensus among the 9 classifiers and applied it to 788 cryptogenic patients, reducing cryptogenic diagnoses from 25.2% to 7.2%. StrokeClassifier is a validated artificial intelligence tool that rivals the performance of vascular neurologists in classifying ischemic stroke etiology. With further training, StrokeClassifier may have downstream applications including its use as a clinical decision support system.
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Affiliation(s)
- Ho-Joon Lee
- Department of Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA.
| | - Lee H Schwamm
- Department of Neurology and Comprehensive Stroke Center, Massachusetts General Hospital and Harvard Medical School Boston, Boston, MA, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Lauren H Sansing
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Hooman Kamel
- Department of Neurology, Weill Cornell Medicine, New York City, NY, USA
| | - Adam de Havenon
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Ashby C Turner
- Department of Neurology and Comprehensive Stroke Center, Massachusetts General Hospital and Harvard Medical School Boston, Boston, MA, USA
| | - Kevin N Sheth
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Smita Krishnaswamy
- Departments of Genetics and Computer Science, Yale School of Medicine, New Haven, CT, USA
| | - Cynthia Brandt
- Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, USA
| | - Hongyu Zhao
- Departments of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Harlan Krumholz
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Richa Sharma
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
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Sheng N, Xie X, Wang Y, Huang L, Zhang S, Gao L, Wang H. A Survey of Deep Learning for Detecting miRNA- Disease Associations: Databases, Computational Methods, Challenges, and Future Directions. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:328-347. [PMID: 38194377 DOI: 10.1109/tcbb.2024.3351752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
MicroRNAs (miRNAs) are an important class of non-coding RNAs that play an essential role in the occurrence and development of various diseases. Identifying the potential miRNA-disease associations (MDAs) can be beneficial in understanding disease pathogenesis. Traditional laboratory experiments are expensive and time-consuming. Computational models have enabled systematic large-scale prediction of potential MDAs, greatly improving the research efficiency. With recent advances in deep learning, it has become an attractive and powerful technique for uncovering novel MDAs. Consequently, numerous MDA prediction methods based on deep learning have emerged. In this review, we first summarize publicly available databases related to miRNAs and diseases for MDA prediction. Next, we outline commonly used miRNA and disease similarity calculation and integration methods. Then, we comprehensively review the 48 existing deep learning-based MDA computation methods, categorizing them into classical deep learning and graph neural network-based techniques. Subsequently, we investigate the evaluation methods and metrics that are frequently used to assess MDA prediction performance. Finally, we discuss the performance trends of different computational methods, point out some problems in current research, and propose 9 potential future research directions. Data resources and recent advances in MDA prediction methods are summarized in the GitHub repository https://github.com/sheng-n/DL-miRNA-disease-association-methods.
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Avery J, Leak-Johnson T, Francis SC. Association between MCU Gene Polymorphisms with Obesity: Findings from the All of Us Research Program. Genes (Basel) 2024; 15:512. [PMID: 38674446 PMCID: PMC11050077 DOI: 10.3390/genes15040512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/09/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Obesity is a public health crisis, and its prevalence disproportionately affects African Americans in the United States. Dysregulation of organelle calcium homeostasis is associated with obesity. The mitochondrial calcium uniporter (MCU) complex is primarily responsible for mitochondrial calcium homeostasis. Obesity is a multifactorial disease in which genetic underpinnings such as single-nucleotide polymorphisms (SNPs) may contribute to disease progression. The objective of this study was to identify genetic variations of MCU with anthropometric measurements and obesity in the All of Us Research Program. METHODS We used an additive genetic model to assess the association between obesity traits (body mass index (BMI), waist and hip circumference) and selected MCU SNPs in 19,325 participants (3221 normal weight and 16,104 obese). Eleven common MCU SNPs with a minor allele frequency ≥ 5% were used for analysis. RESULTS We observed three MCU SNPs in self-reported Black/African American (B/AA) men, and six MCU SNPs in B/AA women associated with increased risk of obesity, whereas six MCU SNPs in White men, and nine MCU SNPs in White women were protective against obesity development. CONCLUSIONS This study found associations of MCU SNPs with obesity, providing evidence of a potential predictor of obesity susceptibility in B/AA adults.
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Affiliation(s)
- Jade Avery
- Department of Physiology, Morehouse School of Medicine, Atlanta, GA 30310, USA;
| | - Tennille Leak-Johnson
- Department of Physiology, Morehouse School of Medicine, Atlanta, GA 30310, USA;
- Institute of Translational Genomic Medicine, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Sharon C. Francis
- Department of Physiology, Morehouse School of Medicine, Atlanta, GA 30310, USA;
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
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Cubas MR, da Silva RS, Primo CC, Brandão MAG, Félix NDDC, Jensen R. Contributions of representing the elements of nursing practice in the ISO 18.104:2023 standard: a theoretical study. Rev Esc Enferm USP 2024; 58:e20230358. [PMID: 38587403 PMCID: PMC11000576 DOI: 10.1590/1980-220x-reeusp-2023-0358en] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 04/09/2024] Open
Abstract
OBJECTIVE To reflect on the contributions of representing nursing practice elements in the ISO 18.104:2023 standard. METHOD This is a theoretical study with standard analysis. Categorical structures were described to represent nursing practice in terminological systems and contributions identified in the parts of the version were analyzed. RESULTS There is innovation in the inclusion of nurse sensitive outcomes, nursing action, nursing diagnosis explanation as an indicator of nursing service demand and complexity of care, representation of concepts through mental maps and suggestion of use of restriction models for nursing actions. It describes that the Nursing Process is constituted by nursing diagnosis, nursing action and nurse sensitive outcomes. FINAL CONSIDERATIONS Indicating a nursing diagnosis as an indicator will bring benefits for knowledge production and decision-making. Although care outcomes are not exclusive responses to nursing action, the modifiable attributes of a nursing diagnosis generate knowledge about clinical practice, nursing action effectiveness and subjects of care' health state. There is coherence in understanding the Nursing Process concept evolution.
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Affiliation(s)
- Marcia Regina Cubas
- Pontifícia Universidade Católica do Paraná, Escola Politécnica, Programa de Pós-Graduação em Tecnologia em Saúde, Curitiba, PR , Brazil
| | | | - Cândida Caniçali Primo
- Universidade Federal do Espírito Santo, Programa de Pós-Graduação em Enfermagem, Vitória, ES, Brazil
| | | | | | - Rodrigo Jensen
- Universidade de São Paulo, Escola de Enfermagem, São Paulo, SP, Brazil
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Gu X, Watson C, Agrawal U, Whitaker H, Elson WH, Anand S, Borrow R, Buckingham A, Button E, Curtis L, Dunn D, Elliot AJ, Ferreira F, Goudie R, Hoang U, Hoschler K, Jamie G, Kar D, Kele B, Leston M, Linley E, Macartney J, Marsden GL, Okusi C, Parvizi O, Quinot C, Sebastianpillai P, Sexton V, Smith G, Suli T, Thomas NPB, Thompson C, Todkill D, Wimalaratna R, Inada-Kim M, Andrews N, Tzortziou-Brown V, Byford R, Zambon M, Lopez-Bernal J, de Lusignan S. Postpandemic Sentinel Surveillance of Respiratory Diseases in the Context of the World Health Organization Mosaic Framework: Protocol for a Development and Evaluation Study Involving the English Primary Care Network 2023-2024. JMIR Public Health Surveill 2024; 10:e52047. [PMID: 38569175 PMCID: PMC11024753 DOI: 10.2196/52047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/02/2024] [Accepted: 01/17/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Prepandemic sentinel surveillance focused on improved management of winter pressures, with influenza-like illness (ILI) being the key clinical indicator. The World Health Organization (WHO) global standards for influenza surveillance include monitoring acute respiratory infection (ARI) and ILI. The WHO's mosaic framework recommends that the surveillance strategies of countries include the virological monitoring of respiratory viruses with pandemic potential such as influenza. The Oxford-Royal College of General Practitioner Research and Surveillance Centre (RSC) in collaboration with the UK Health Security Agency (UKHSA) has provided sentinel surveillance since 1967, including virology since 1993. OBJECTIVE We aim to describe the RSC's plans for sentinel surveillance in the 2023-2024 season and evaluate these plans against the WHO mosaic framework. METHODS Our approach, which includes patient and public involvement, contributes to surveillance objectives across all 3 domains of the mosaic framework. We will generate an ARI phenotype to enable reporting of this indicator in addition to ILI. These data will support UKHSA's sentinel surveillance, including vaccine effectiveness and burden of disease studies. The panel of virology tests analyzed in UKHSA's reference laboratory will remain unchanged, with additional plans for point-of-care testing, pneumococcus testing, and asymptomatic screening. Our sampling framework for serological surveillance will provide greater representativeness and more samples from younger people. We will create a biomedical resource that enables linkage between clinical data held in the RSC and virology data, including sequencing data, held by the UKHSA. We describe the governance framework for the RSC. RESULTS We are co-designing our communication about data sharing and sampling, contextualized by the mosaic framework, with national and general practice patient and public involvement groups. We present our ARI digital phenotype and the key data RSC network members are requested to include in computerized medical records. We will share data with the UKHSA to report vaccine effectiveness for COVID-19 and influenza, assess the disease burden of respiratory syncytial virus, and perform syndromic surveillance. Virological surveillance will include COVID-19, influenza, respiratory syncytial virus, and other common respiratory viruses. We plan to pilot point-of-care testing for group A streptococcus, urine tests for pneumococcus, and asymptomatic testing. We will integrate test requests and results with the laboratory-computerized medical record system. A biomedical resource will enable research linking clinical data to virology data. The legal basis for the RSC's pseudonymized data extract is The Health Service (Control of Patient Information) Regulations 2002, and all nonsurveillance uses require research ethics approval. CONCLUSIONS The RSC extended its surveillance activities to meet more but not all of the mosaic framework's objectives. We have introduced an ARI indicator. We seek to expand our surveillance scope and could do more around transmissibility and the benefits and risks of nonvaccine therapies.
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Affiliation(s)
- Xinchun Gu
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Conall Watson
- Immunisation and Vaccine-Preventable Diseases Division, UK Health Security Agency, London, United Kingdom
| | - Utkarsh Agrawal
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Heather Whitaker
- Statistics, Modelling and Economics Department, UK Health Security Agency, London, United Kingdom
| | - William H Elson
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Sneha Anand
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Ray Borrow
- Vaccine Evaluation Unit, UK Health Security Agency, Manchester, United Kingdom
| | | | - Elizabeth Button
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Lottie Curtis
- Royal College of General Practitioners, London, United Kingdom
| | - Dominic Dunn
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Alex J Elliot
- Real-time Syndromic Surveillance Team, UK Health Security Agency, Birmingham, United Kingdom
| | - Filipa Ferreira
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Rosalind Goudie
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Uy Hoang
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Katja Hoschler
- Respiratory Virus Unit, UK Health Security Agency, London, United Kingdom
| | - Gavin Jamie
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Debasish Kar
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Beatrix Kele
- Respiratory Virus Unit, UK Health Security Agency, London, United Kingdom
| | - Meredith Leston
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Ezra Linley
- Vaccine Evaluation Unit, UK Health Security Agency, Manchester, United Kingdom
| | - Jack Macartney
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Gemma L Marsden
- Royal College of General Practitioners, London, United Kingdom
| | - Cecilia Okusi
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Omid Parvizi
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
- Respiratory Virus Unit, UK Health Security Agency, London, United Kingdom
| | - Catherine Quinot
- Immunisation and Vaccine-Preventable Diseases Division, UK Health Security Agency, London, United Kingdom
| | | | - Vanashree Sexton
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Gillian Smith
- Real-time Syndromic Surveillance Team, UK Health Security Agency, Birmingham, United Kingdom
| | - Timea Suli
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | | | - Catherine Thompson
- Respiratory Virus Unit, UK Health Security Agency, London, United Kingdom
| | - Daniel Todkill
- Real-time Syndromic Surveillance Team, UK Health Security Agency, Birmingham, United Kingdom
| | - Rashmi Wimalaratna
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | | | - Nick Andrews
- Immunisation and Vaccine-Preventable Diseases Division, UK Health Security Agency, London, United Kingdom
| | | | - Rachel Byford
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Maria Zambon
- Virus Reference Department, UK Health Security Agency, London, United Kingdom
| | - Jamie Lopez-Bernal
- Immunisation and Vaccine-Preventable Diseases Division, UK Health Security Agency, London, United Kingdom
| | - Simon de Lusignan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
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11
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Pineda-Moncusí M, Allery F, Delmestri A, Bolton T, Nolan J, Thygesen JH, Handy A, Banerjee A, Denaxas S, Tomlinson C, Denniston AK, Sudlow C, Akbari A, Wood A, Collins GS, Petersen I, Coates LC, Khunti K, Prieto-sAlhambra D, Khalid S. Ethnicity data resource in population-wide health records: completeness, coverage and granularity of diversity. Sci Data 2024; 11:221. [PMID: 38388690 PMCID: PMC10883937 DOI: 10.1038/s41597-024-02958-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/12/2024] [Indexed: 02/24/2024] Open
Abstract
Intersectional social determinants including ethnicity are vital in health research. We curated a population-wide data resource of self-identified ethnicity data from over 60 million individuals in England primary care, linking it to hospital records. We assessed ethnicity data in terms of completeness, consistency, and granularity and found one in ten individuals do not have ethnicity information recorded in primary care. By linking to hospital records, ethnicity data were completed for 94% of individuals. By reconciling SNOMED-CT concepts and census-level categories into a consistent hierarchy, we organised more than 250 ethnicity sub-groups including and beyond "White", "Black", "Asian", "Mixed" and "Other, and found them to be distributed in proportions similar to the general population. This large observational dataset presents an algorithmic hierarchy to represent self-identified ethnicity data collected across heterogeneous healthcare settings. Accurate and easily accessible ethnicity data can lead to a better understanding of population diversity, which is important to address disparities and influence policy recommendations that can translate into better, fairer health for all.
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Affiliation(s)
- Marta Pineda-Moncusí
- Centre for Statistics in Medicine, Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK
| | - Freya Allery
- Institute of Health Informatics, 222 Euston Road, London, NW1 2DA, University College London, London, UK
| | - Antonella Delmestri
- Centre for Statistics in Medicine, Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK
| | - Thomas Bolton
- British Heart Foundation Data Science Centre, Health Data Research UK, London, UK
| | - John Nolan
- British Heart Foundation Data Science Centre, Health Data Research UK, London, UK
| | - Johan H Thygesen
- Institute of Health Informatics, 222 Euston Road, London, NW1 2DA, University College London, London, UK
| | - Alex Handy
- Institute of Health Informatics, 222 Euston Road, London, NW1 2DA, University College London, London, UK
| | - Amitava Banerjee
- Institute of Health Informatics, 222 Euston Road, London, NW1 2DA, University College London, London, UK
| | - Spiros Denaxas
- Institute of Health Informatics, 222 Euston Road, London, NW1 2DA, University College London, London, UK
- British Heart Foundation Data Science Centre, Health Data Research UK, London, UK
- University College London Hospitals Biomedical Research Centre, University College London, London, UK
| | - Christopher Tomlinson
- Institute of Health Informatics, 222 Euston Road, London, NW1 2DA, University College London, London, UK
- University College London Hospitals Biomedical Research Centre, University College London, London, UK
- UK Research and Innovation Centre for Doctoral Training in AI-enabled Healthcare Systems, University College London, London, UK
| | | | - Cathie Sudlow
- British Heart Foundation Data Science Centre, Health Data Research UK, London, UK
| | - Ashley Akbari
- Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales, UK
| | - Angela Wood
- British Heart Foundation Data Science Centre, Health Data Research UK, London, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Gary S Collins
- Centre for Statistics in Medicine, Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK
| | - Irene Petersen
- Department of Primary Care and Population Health, UCL, London, NW3 2PF, UK
- Department of Clinical Epidemiology, Aarhus University, Aarhus N, Aarhus, 8200, Denmark
| | - Laura C Coates
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK
| | - Kamlesh Khunti
- Diabetes Research Centre, University of Leicester, Leicester, UK
| | - Daniel Prieto-sAlhambra
- Centre for Statistics in Medicine, Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK
- Department of Medical Informatics, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Sara Khalid
- Centre for Statistics in Medicine, Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK.
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12
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Mullie L, Afilalo J, Archambault P, Bouchakri R, Brown K, Buckeridge DL, Cavayas YA, Turgeon AF, Martineau D, Lamontagne F, Lebrasseur M, Lemieux R, Li J, Sauthier M, St-Onge P, Tang A, Witteman W, Chassé M. CODA: an open-source platform for federated analysis and machine learning on distributed healthcare data. J Am Med Inform Assoc 2024; 31:651-665. [PMID: 38128123 PMCID: PMC10873779 DOI: 10.1093/jamia/ocad235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/28/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023] Open
Abstract
OBJECTIVES Distributed computations facilitate multi-institutional data analysis while avoiding the costs and complexity of data pooling. Existing approaches lack crucial features, such as built-in medical standards and terminologies, no-code data visualizations, explicit disclosure control mechanisms, and support for basic statistical computations, in addition to gradient-based optimization capabilities. MATERIALS AND METHODS We describe the development of the Collaborative Data Analysis (CODA) platform, and the design choices undertaken to address the key needs identified during our survey of stakeholders. We use a public dataset (MIMIC-IV) to demonstrate end-to-end multi-modal FL using CODA. We assessed the technical feasibility of deploying the CODA platform at 9 hospitals in Canada, describe implementation challenges, and evaluate its scalability on large patient populations. RESULTS The CODA platform was designed, developed, and deployed between January 2020 and January 2023. Software code, documentation, and technical documents were released under an open-source license. Multi-modal federated averaging is illustrated using the MIMIC-IV and MIMIC-CXR datasets. To date, 8 out of the 9 participating sites have successfully deployed the platform, with a total enrolment of >1M patients. Mapping data from legacy systems to FHIR was the biggest barrier to implementation. DISCUSSION AND CONCLUSION The CODA platform was developed and successfully deployed in a public healthcare setting in Canada, with heterogeneous information technology systems and capabilities. Ongoing efforts will use the platform to develop and prospectively validate models for risk assessment, proactive monitoring, and resource usage. Further work will also make tools available to facilitate migration from legacy formats to FHIR and DICOM.
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Affiliation(s)
- Louis Mullie
- Department of Medicine, Centre Hospitalier de l'Université de Montréal, Montréal, H2X 3E4, Canada
- Faculty of Medicine, Université de Montréal, Montréal, H3C 3J7, Canada
- Mila Quebec Artificial Intelligence Institute, Montréal, H2S 3H1, Canada
| | - Jonathan Afilalo
- Department of Medicine, Jewish General Hospital, Montréal, H3T 1E4, Canada
| | - Patrick Archambault
- Department of Emergency Medicine and Family Medicine, Université Laval, Québec, G1V 0A6, Canada
- Department of Anesthesiology and Critical Care Medicine, Université Laval, Québec, G1V 0A6, Canada
- Centre de Recherche Intégré pour un Système Apprenant en santé et Services Sociaux, Centre intégré de santé et de Services Sociaux de Chaudière-Appalaches, Lévis, G6V 3Z1, Canada
| | - Rima Bouchakri
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Université de Montréal, Montréal, H2X 0A9, Canada
| | - Kip Brown
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Université de Montréal, Montréal, H2X 0A9, Canada
| | - David L Buckeridge
- Mila Quebec Artificial Intelligence Institute, Montréal, H2S 3H1, Canada
- Department of Epidemiology and Biostatistics, School of Population and Global Health, McGill University Health Centre, Montréal, H3A 1G1, Canada
| | | | - Alexis F Turgeon
- Department of Anesthesiology and Critical Care Medicine, Université Laval, Québec, G1V 0A6, Canada
- Centre de recherche du CHU de Québec-Université Laval, Université Laval, Québec, G1V 4G2, Canada
| | - Denis Martineau
- Centre de recherche du CHU de Québec-Université Laval, Université Laval, Québec, G1V 4G2, Canada
| | - François Lamontagne
- Centre de recherche du CHUS, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, J1G 2E8, Canada
| | - Martine Lebrasseur
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Université de Montréal, Montréal, H2X 0A9, Canada
| | - Renald Lemieux
- Centre de recherche du CHUS, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, J1G 2E8, Canada
| | - Jeffrey Li
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Université de Montréal, Montréal, H2X 0A9, Canada
| | - Michaël Sauthier
- Faculty of Medicine, Université de Montréal, Montréal, H3C 3J7, Canada
- Department of Pediatrics, Université de Montréal and CHU Sainte-Justine Research Centre, Montréal, H3C 3J7, Canada
| | - Pascal St-Onge
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Université de Montréal, Montréal, H2X 0A9, Canada
| | - An Tang
- Faculty of Medicine, Université de Montréal, Montréal, H3C 3J7, Canada
- Department of Radiology, Centre Hospitalier de l’Université de Montréal, Montréal, H2X 3E4, Canada
| | - William Witteman
- Centre de Recherche Intégré pour un Système Apprenant en santé et Services Sociaux, Centre intégré de santé et de Services Sociaux de Chaudière-Appalaches, Lévis, G6V 3Z1, Canada
| | - Michaël Chassé
- Department of Medicine, Centre Hospitalier de l'Université de Montréal, Montréal, H2X 3E4, Canada
- Faculty of Medicine, Université de Montréal, Montréal, H3C 3J7, Canada
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13
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Friligkou E, Løkhammer S, Cabrera-Mendoza B, Shen J, He J, Deiana G, Zanoaga MD, Asgel Z, Pilcher A, Di Lascio L, Makharashvili A, Koller D, Tylee DS, Pathak GA, Polimanti R. Gene Discovery and Biological Insights into Anxiety Disorders from a Multi-Ancestry Genome-wide Association Study of >1.2 Million Participants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.14.24302836. [PMID: 38405718 PMCID: PMC10889004 DOI: 10.1101/2024.02.14.24302836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
We leveraged information from more than 1.2 million participants to investigate the genetics of anxiety disorders across five continental ancestral groups. Ancestry-specific and cross-ancestry genome-wide association studies identified 51 anxiety-associated loci, 39 of which are novel. Additionally, polygenic risk scores derived from individuals of European descent were associated with anxiety in African, Admixed-American, and East Asian groups. The heritability of anxiety was enriched for genes expressed in the limbic system, the cerebral cortex, the cerebellum, the metencephalon, the entorhinal cortex, and the brain stem. Transcriptome- and proteome-wide analyses highlighted 115 genes associated with anxiety through brain-specific and cross-tissue regulation. We also observed global and local genetic correlations with depression, schizophrenia, and bipolar disorder and putative causal relationships with several physical health conditions. Overall, this study expands the knowledge regarding the genetic risk and pathogenesis of anxiety disorders, highlighting the importance of investigating diverse populations and integrating multi-omics information.
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14
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Newbury A, Liu H, Idnay B, Weng C. The suitability of UMLS and SNOMED-CT for encoding outcome concepts. J Am Med Inform Assoc 2023; 30:1895-1903. [PMID: 37615994 PMCID: PMC10654851 DOI: 10.1093/jamia/ocad161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/14/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
OBJECTIVE Outcomes are important clinical study information. Despite progress in automated extraction of PICO (Population, Intervention, Comparison, and Outcome) entities from PubMed, rarely are these entities encoded by standard terminology to achieve semantic interoperability. This study aims to evaluate the suitability of the Unified Medical Language System (UMLS) and SNOMED-CT in encoding outcome concepts in randomized controlled trial (RCT) abstracts. MATERIALS AND METHODS We iteratively developed and validated an outcome annotation guideline and manually annotated clinically significant outcome entities in the Results and Conclusions sections of 500 randomly selected RCT abstracts on PubMed. The extracted outcomes were fully, partially, or not mapped to the UMLS via MetaMap based on established heuristics. Manual UMLS browser search was performed for select unmapped outcome entities to further differentiate between UMLS and MetaMap errors. RESULTS Only 44% of 2617 outcome concepts were fully covered in the UMLS, among which 67% were complex concepts that required the combination of 2 or more UMLS concepts to represent them. SNOMED-CT was present as a source in 61% of the fully mapped outcomes. DISCUSSION Domains such as Metabolism and Nutrition, and Infections and Infectious Diseases need expanded outcome concept coverage in the UMLS and MetaMap. Future work is warranted to similarly assess the terminology coverage for P, I, C entities. CONCLUSION Computational representation of clinical outcomes is important for clinical evidence extraction and appraisal and yet faces challenges from the inherent complexity and lack of coverage of these concepts in UMLS and SNOMED-CT, as demonstrated in this study.
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Affiliation(s)
- Abigail Newbury
- Department of Biomedical Informatics, Columbia University, New York City, NY 10032, United States
| | - Hao Liu
- Department of Biomedical Informatics, Columbia University, New York City, NY 10032, United States
| | - Betina Idnay
- Department of Biomedical Informatics, Columbia University, New York City, NY 10032, United States
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York City, NY 10032, United States
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15
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Requena G, Joksaite S, Galwey N, Jakes RW. An algorithm-based approach to ascertain patients with rare diseases in electronic health records using hypereosinophilic syndrome as an example. Pharmacoepidemiol Drug Saf 2023; 32:1261-1270. [PMID: 37309054 DOI: 10.1002/pds.5655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/24/2023] [Accepted: 06/08/2023] [Indexed: 06/14/2023]
Abstract
PURPOSE Improved hypereosinophilic syndrome (HES) ascertainment in electronic health record (EHR) databases may improve disease understanding and management. An algorithm to ascertain and characterize this rare condition was therefore developed and validated. METHODS Using the UK clinical practice research datalink (CPRD)-Aurum database linked to the hospital episode statistics database (Admitted Patient Care data) from Jan 2012 to June 2019, this cross-sectional study ascertained patients with a specific HES code (index). Patients with HES were matched (age, sex and index date) 1:29 with a non-HES cohort. An algorithm was developed by identifying pre-defined variables differing between cohorts; model-fitting using Firth logistic regression and statistical determination of the top-five performing models; and internal validation using Leave-One-Out Cross Validation. Final model sensitivity and specificity were determined at an 80% probability threshold. RESULTS The HES and non-HES cohorts included 88 and 2552 patients, respectively; 270 models with four variables each (treatment used for HES, asthma code, white blood cell condition code, and blood eosinophil count [BEC] code) plus age and sex variables were tested. Of the top five models, the sensitivity model performed best (sensitivity, 69% [95% CI: 59%, 79%]; specificity, >99%). The strongest predictors of HES versus non-HES cases (odds >1000 times greater) were an ICD-10 code for white blood cell disorders and a BEC ≥1500 cells/μL in the 24 months pre-index. CONCLUSIONS Using a combination of medical codes, prescribed treatments data and laboratory results, the algorithm can help ascertain patients with HES from EHR databases; this approach may be useful for other rare diseases.
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Affiliation(s)
- Gema Requena
- Epidemiology, Value Evidence and Outcomes, Global Research & Development, GSK, Brentford, Middlesex, UK
| | - Sandra Joksaite
- Real-World Analytics, Value Evidence and Outcomes, Global Research & Development, GSK, Brentford, Middlesex, UK
| | | | - Rupert W Jakes
- Epidemiology, Value Evidence and Outcomes, Global Research & Development, GSK, Brentford, Middlesex, UK
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16
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Mackenzie A, Lewis E, Loveland J. Successes and challenges in extracting information from DICOM image databases for audit and research. Br J Radiol 2023; 96:20230104. [PMID: 37698251 PMCID: PMC10607388 DOI: 10.1259/bjr.20230104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 09/13/2023] Open
Abstract
In radiography, much valuable associated data (metadata) is generated during image acquisition. The current setup of picture archive and communication systems (PACS) can make extraction of this metadata difficult, especially as it is typically stored with the image. The aim of this work is to examine the current challenges in extracting image metadata and to discuss the potential benefits of using this rich information. This work focuses on breast screening, though the conclusions are applicable to other modalities.The data stored in PACS contain information, currently underutilised, and is of great benefit for auditing and improving imaging and radiographic practice. From the literature, we present examples of the potential clinical benefit such as audits of dose, and radiographic practice, as well as more advanced research highlighting the effects of radiographic practice, e.g. cancer detection rates affected by imaging technology.This review considers the challenges in extracting data, namely,• The search tools for data on most PACS are inadequate being both time-consuming and limited in elements that can be searched.• Security and information governance considerations• Anonymisation of data if required• Data curationThe review describes some solutions that have been successfully implemented.• Retrospective extraction: direct query on PACS• Extracting data prospectively• Use of structured reports• Use of trusted research environmentsUltimately, the data access process will be made easier by inclusion during PACS procurement. Auditing data from PACS can be used to improve quality of imaging and workflow, all of which will be a clinical benefit to patients.
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Affiliation(s)
| | | | - John Loveland
- NCCPM, Royal Surrey NHS Foundation Trust, Guildford, United Kingdom
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17
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Lee HJ, Schwamm LH, Sansing L, Kamel H, de Havenon A, Turner AC, Sheth KN, Krishnaswamy S, Brandt C, Zhao H, Krumholz H, Sharma R. StrokeClassifier: Ischemic Stroke Etiology Classification by Ensemble Consensus Modeling Using Electronic Health Records. RESEARCH SQUARE 2023:rs.3.rs-3367169. [PMID: 37961532 PMCID: PMC10635373 DOI: 10.21203/rs.3.rs-3367169/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Determining the etiology of an acute ischemic stroke (AIS) is fundamental to secondary stroke prevention efforts but can be diagnostically challenging. We trained and validated an automated classification machine intelligence tool, StrokeClassifier, using electronic health record (EHR) text data from 2,039 non-cryptogenic AIS patients at 2 academic hospitals to predict the 4-level outcome of stroke etiology determined by agreement of at least 2 board-certified vascular neurologists' review of the stroke hospitalization EHR. StrokeClassifier is an ensemble consensus meta-model of 9 machine learning classifiers applied to features extracted from discharge summary texts by natural language processing. StrokeClassifier was externally validated in 406 discharge summaries from the MIMIC-III dataset reviewed by a vascular neurologist to ascertain stroke etiology. Compared with stroke etiologies adjudicated by vascular neurologists, StrokeClassifier achieved the mean cross-validated accuracy of 0.74 (±0.01) and weighted F1 of 0.74 (±0.01). In the MIMIC-III cohort, the accuracy and weighted F1 of StrokeClassifier were 0.70 and 0.71, respectively. SHapley Additive exPlanation analysis elucidated that the top 5 features contributing to stroke etiology prediction were atrial fibrillation, age, middle cerebral artery occlusion, internal carotid artery occlusion, and frontal stroke location. We then designed a certainty heuristic to deem a StrokeClassifier diagnosis as confidently non-cryptogenic by the degree of consensus among the 9 classifiers, and applied it to 788 cryptogenic patients. This reduced the percentage of the cryptogenic strokes from 25.2% to 7.2% of all ischemic strokes. StrokeClassifier is a validated artificial intelligence tool that rivals the performance of vascular neurologists in classifying ischemic stroke etiology for individual patients. With further training, StrokeClassifier may have downstream applications including its use as a clinical decision support system.
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Affiliation(s)
- Ho-Joon Lee
- Department of Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT
| | - Lee H. Schwamm
- Department of Neurology and Comprehensive Stroke Center, Massachusetts General Hospital and Harvard Medical School Boston, MA
- Department of Neurology, Yale School of Medicine, New Haven, CT
| | - Lauren Sansing
- Department of Neurology, Yale School of Medicine, New Haven, CT
| | - Hooman Kamel
- Department of Neurology, Weill Cornell Medicine, New York City, NY
| | - Adam de Havenon
- Department of Neurology, Yale School of Medicine, New Haven, CT
| | - Ashby C. Turner
- Department of Neurology and Comprehensive Stroke Center, Massachusetts General Hospital and Harvard Medical School Boston, MA
| | - Kevin N. Sheth
- Department of Neurology, Yale School of Medicine, New Haven, CT
| | - Smita Krishnaswamy
- Departments of Genetics and Computer Science, Yale School of Medicine, New Haven, CT
| | - Cynthia Brandt
- Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT
| | - Hongyu Zhao
- Departments of Biostatistics, Yale School of Public Health, New Haven, CT
| | - Harlan Krumholz
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Richa Sharma
- Department of Neurology, Yale School of Medicine, New Haven, CT
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18
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Gholipour M, Khajouei R, Amiri P, Hajesmaeel Gohari S, Ahmadian L. Extracting cancer concepts from clinical notes using natural language processing: a systematic review. BMC Bioinformatics 2023; 24:405. [PMID: 37898795 PMCID: PMC10613366 DOI: 10.1186/s12859-023-05480-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 09/13/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Extracting information from free texts using natural language processing (NLP) can save time and reduce the hassle of manually extracting large quantities of data from incredibly complex clinical notes of cancer patients. This study aimed to systematically review studies that used NLP methods to identify cancer concepts from clinical notes automatically. METHODS PubMed, Scopus, Web of Science, and Embase were searched for English language papers using a combination of the terms concerning "Cancer", "NLP", "Coding", and "Registries" until June 29, 2021. Two reviewers independently assessed the eligibility of papers for inclusion in the review. RESULTS Most of the software programs used for concept extraction reported were developed by the researchers (n = 7). Rule-based algorithms were the most frequently used algorithms for developing these programs. In most articles, the criteria of accuracy (n = 14) and sensitivity (n = 12) were used to evaluate the algorithms. In addition, Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT) and Unified Medical Language System (UMLS) were the most commonly used terminologies to identify concepts. Most studies focused on breast cancer (n = 4, 19%) and lung cancer (n = 4, 19%). CONCLUSION The use of NLP for extracting the concepts and symptoms of cancer has increased in recent years. The rule-based algorithms are well-liked algorithms by developers. Due to these algorithms' high accuracy and sensitivity in identifying and extracting cancer concepts, we suggested that future studies use these algorithms to extract the concepts of other diseases as well.
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Affiliation(s)
- Maryam Gholipour
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Reza Khajouei
- Department of Health Information Sciences, Faculty of Management and Medical Information Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Parastoo Amiri
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Sadrieh Hajesmaeel Gohari
- Medical Informatics Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Leila Ahmadian
- Department of Health Information Sciences, Faculty of Management and Medical Information Sciences, Kerman University of Medical Sciences, Kerman, Iran.
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Menotti L, Silvello G, Atzori M, Boytcheva S, Ciompi F, Di Nunzio GM, Fraggetta F, Giachelle F, Irrera O, Marchesin S, Marini N, Müller H, Primov T. Modelling digital health data: The ExaMode ontology for computational pathology. J Pathol Inform 2023; 14:100332. [PMID: 37705689 PMCID: PMC10495665 DOI: 10.1016/j.jpi.2023.100332] [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: 05/09/2023] [Revised: 07/14/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
Computational pathology can significantly benefit from ontologies to standardize the employed nomenclature and help with knowledge extraction processes for high-quality annotated image datasets. The end goal is to reach a shared model for digital pathology to overcome data variability and integration problems. Indeed, data annotation in such a specific domain is still an unsolved challenge and datasets cannot be steadily reused in diverse contexts due to heterogeneity issues of the adopted labels, multilingualism, and different clinical practices. Material and methods This paper presents the ExaMode ontology, modeling the histopathology process by considering 3 key cancer diseases (colon, cervical, and lung tumors) and celiac disease. The ExaMode ontology has been designed bottom-up in an iterative fashion with continuous feedback and validation from pathologists and clinicians. The ontology is organized into 5 semantic areas that defines an ontological template to model any disease of interest in histopathology. Results The ExaMode ontology is currently being used as a common semantic layer in: (i) an entity linking tool for the automatic annotation of medical records; (ii) a web-based collaborative annotation tool for histopathology text reports; and (iii) a software platform for building holistic solutions integrating multimodal histopathology data. Discussion The ontology ExaMode is a key means to store data in a graph database according to the RDF data model. The creation of an RDF dataset can help develop more accurate algorithms for image analysis, especially in the field of digital pathology. This approach allows for seamless data integration and a unified query access point, from which we can extract relevant clinical insights about the considered diseases using SPARQL queries.
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Affiliation(s)
- Laura Menotti
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Gianmaria Silvello
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Manfredo Atzori
- Information Systems Institute, University of Applied Sciences Western Switzerland, Delémont, Switzerland
- Department of Neuroscience, University of Padua, Padova, Italy
| | | | - Francesco Ciompi
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Fabio Giachelle
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Ornella Irrera
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Stefano Marchesin
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Niccolò Marini
- Information Systems Institute, University of Applied Sciences Western Switzerland, Delémont, Switzerland
| | - Henning Müller
- Information Systems Institute, University of Applied Sciences Western Switzerland, Delémont, Switzerland
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Block LJ, Lozada-Perezmitre E, Cho H, Davies S, Lee J, Lokmic-Tomkins Z, Peltonen LM, Pruinelli L, Reid L, Song J, Topaz M, von Gerich H, Vyas P. Representation of Environmental Concepts Associated with Health Impacts in Computer Standardized Clinical Terminologies. Yearb Med Inform 2023; 32:36-47. [PMID: 38147848 PMCID: PMC10751146 DOI: 10.1055/s-0043-1768746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
OBJECTIVE To evaluate the representation of environmental concepts associated with health impacts in standardized clinical terminologies. METHODS This study used a descriptive approach with methods informed by a procedural framework for standardized clinical terminology mapping. The United Nations Global Indicator Framework for the Sustainable Development Goals and Targets was used as the source document for concept extraction. The target terminologies were the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) and the International Classification for Nursing Practice (ICNP). Manual and automated mapping methods were utilized. The lists of candidate matches were reviewed and iterated until a final mapping match list was achieved. RESULTS A total of 119 concepts with 133 mapping matches were added to the final SNOMED CT list. Fifty-three (39.8%) were direct matches, 37 (27.8%) were narrower than matches, 35 (26.3%) were broader than matches, and 8 (6%) had no matches. A total of 26 concepts with 27 matches were added to the final ICNP list. Eight (29.6%) were direct matches, 4 (14.8%) were narrower than, 7 (25.9%) were broader than, and 8 (29.6%) were no matches. CONCLUSION Following this evaluation, both strengths and gaps were identified. Gaps in terminology representation included concepts related to cost expenditures, affordability, community engagement, water, air and sanitation. The inclusion of these concepts is necessary to advance the clinical reporting of these environmental and sustainability indicators. As environmental concepts encoded in standardized terminologies expand, additional insights into data and health conditions, research, education, and policy-level decision-making will be identified.
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Affiliation(s)
- Lorraine J. Block
- University of British Columbia, School of Nursing, Vancouver, British Columbia, Canada
| | | | - Hwayoung Cho
- University of Florida, Gainesville, Florida, United States
| | | | - Jisan Lee
- Department of Nursing, Gangneung-Wonju National University, Wonju, Republic of Korea
| | - Zerina Lokmic-Tomkins
- School of Nursing and Midwifery, Monash University, 10 Chancellors Walk, Clayton, Melbourne, Victoria 3800, Australia
| | | | | | - Lisa Reid
- Flinders University, Adelaide, South Australia, Australia
| | - Jiyoun Song
- University of Pennsylvania School of Nursing, Philadelphia, PA, USA
| | - Maxim Topaz
- Columbia University & VNS Health, New York, New York, United States
| | - Hanna von Gerich
- University of Turku, Department of Nursing Science, Turku University Hospital, Finland
| | - Pankaj Vyas
- University of Arizona, College of Nursing, Tucson, AZ, United States
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21
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Kempf E, Vaterkowski M, Leprovost D, Griffon N, Ouagne D, Breant S, Serre P, Mouchet A, Rance B, Chatellier G, Bellamine A, Frank M, Guerin J, Tannier X, Livartowski A, Hilka M, Daniel C. How to Improve Cancer Patients ENrollment in Clinical Trials From rEal-Life Databases Using the Observational Medical Outcomes Partnership Oncology Extension: Results of the PENELOPE Initiative in Urologic Cancers. JCO Clin Cancer Inform 2023; 7:e2200179. [PMID: 37167578 DOI: 10.1200/cci.22.00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
PURPOSE To compare the computability of Observational Medical Outcomes Partnership (OMOP)-based queries related to prescreening of patients using two versions of the OMOP common data model (CDM; v5.3 and v5.4) and to assess the performance of the Greater Paris University Hospital (APHP) prescreening tool. MATERIALS AND METHODS We identified the prescreening information items being relevant for prescreening of patients with cancer. We randomly selected 15 academic and industry-sponsored urology phase I-IV clinical trials (CTs) launched at APHP between 2016 and 2021. The computability of the related prescreening criteria (PC) was defined by their translation rate in OMOP-compliant queries and by their execution rate on the APHP clinical data warehouse (CDW) containing data of 205,977 patients with cancer. The overall performance of the prescreening tool was assessed by the rate of true- and false-positive cases of three randomly selected CTs. RESULTS We defined a list of 15 minimal information items being relevant for patients' prescreening. We identified 83 PC of the 534 eligibility criteria from the 15 CTs. We translated 33 and 62 PC in queries on the basis of OMOP CDM v5.3 and v5.4, respectively (translation rates of 40% and 75%, respectively). Of the 33 PC translated in the v5.3 of the OMOP CDM, 19 could be executed on the APHP CDW (execution rate of 58%). Of 83 PC, the computability rate on the APHP CDW reached 23%. On the basis of three CTs, we identified 17, 32, and 63 patients as being potentially eligible for inclusion in those CTs, resulting in positive predictive values of 53%, 41%, and 21%, respectively. CONCLUSION We showed that PC could be formalized according to the OMOP CDM and that the oncology extension increased their translation rate through better representation of cancer natural history.
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Affiliation(s)
- Emmanuelle Kempf
- Sorbonne Université, Inserm, Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances pour la e-Santé, LIMICS, Paris, France
- Department of Medical Oncology, Assistance Publique Hôpitaux de Paris, Henri Mondor Teaching Hospital, Créteil, France
| | - Morgan Vaterkowski
- Innovation and Data, Paris, IT Department, Assistance Publique Hôpitaux de Paris, Paris, France
- EPITA School of Engineering and Computer Science, Paris, France
| | - Damien Leprovost
- Sorbonne Université, Inserm, Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances pour la e-Santé, LIMICS, Paris, France
- Innovation and Data, Paris, IT Department, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Nicolas Griffon
- Sorbonne Université, Inserm, Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances pour la e-Santé, LIMICS, Paris, France
- Innovation and Data, Paris, IT Department, Assistance Publique Hôpitaux de Paris, Paris, France
| | - David Ouagne
- Innovation and Data, Paris, IT Department, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Stéphane Breant
- Innovation and Data, Paris, IT Department, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Patricia Serre
- Innovation and Data, Paris, IT Department, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Alexandre Mouchet
- Innovation and Data, Paris, IT Department, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Bastien Rance
- Department of Medical Informatics, Assistance Publique Hôpitaux de Paris, Centre-Université de Paris (APHP-CUP), Université de Paris, Paris, France
| | - Gilles Chatellier
- Department of Medical Informatics, Assistance Publique Hôpitaux de Paris, Centre-Université de Paris (APHP-CUP), Université de Paris, Paris, France
| | - Ali Bellamine
- Innovation and Data, Paris, IT Department, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Marie Frank
- Department of Medical Information, Paris Saclay Teaching Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | | | - Xavier Tannier
- Sorbonne Université, Inserm, Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances pour la e-Santé, LIMICS, Paris, France
| | | | - Martin Hilka
- Innovation and Data, Paris, IT Department, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Christel Daniel
- Sorbonne Université, Inserm, Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances pour la e-Santé, LIMICS, Paris, France
- Innovation and Data, Paris, IT Department, Assistance Publique Hôpitaux de Paris, Paris, France
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22
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Direito B, Santos A, Mouga S, Lima J, Brás P, Oliveira G, Castelo-Branco M. Design and Implementation of a Collaborative Clinical Practice and Research Documentation System Using SNOMED-CT and HL7-CDA in the Context of a Pediatric Neurodevelopmental Unit. Healthcare (Basel) 2023; 11:healthcare11070973. [PMID: 37046899 PMCID: PMC10094702 DOI: 10.3390/healthcare11070973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
This paper introduces a prototype for clinical research documentation using the structured information model HL7 CDA and clinical terminology (SNOMED CT). The proposed solution was integrated with the current electronic health record system (EHR-S) and aimed to implement interoperability and structure information, and to create a collaborative platform between clinical and research teams. The framework also aims to overcome the limitations imposed by classical documentation strategies in real-time healthcare encounters that may require fast access to complex information. The solution was developed in the pediatric hospital (HP) of the University Hospital Center of Coimbra (CHUC), a national reference for neurodevelopmental disorders, particularly for autism spectrum disorder (ASD), which is very demanding in terms of longitudinal and cross-sectional data throughput. The platform uses a three-layer approach to reduce components’ dependencies and facilitate maintenance, scalability, and security. The system was validated in a real-life context of the neurodevelopmental and autism unit (UNDA) in the HP and assessed based on the functionalities model of EHR-S (EHR-S FM) regarding their successful implementation and comparison with state-of-the-art alternative platforms. A global approach to the clinical history of neurodevelopmental disorders was worked out, providing transparent healthcare data coding and structuring while preserving information quality. Thus, the platform enabled the development of user-defined structured templates and the creation of structured documents with standardized clinical terminology that can be used in many healthcare contexts. Moreover, storing structured data associated with healthcare encounters supports a longitudinal view of the patient’s healthcare data and health status over time, which is critical in routine and pediatric research contexts. Additionally, it enables queries on population statistics that are key to supporting the definition of local and global policies, whose importance was recently emphasized by the COVID pandemic.
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Affiliation(s)
- Bruno Direito
- Coimbra Institute for Biomedical Imaging and Translational Research (CIBIT), Institute of Nuclear Sciences Applied to Health (ICNAS), University of Coimbra, 3000-548 Coimbra, Portugal
- Instituto do Ambiente, Tecnologia e Vida, 3000-214 Coimbra, Portugal
| | - André Santos
- Coimbra Institute for Biomedical Imaging and Translational Research (CIBIT), Institute of Nuclear Sciences Applied to Health (ICNAS), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Susana Mouga
- Coimbra Institute for Biomedical Imaging and Translational Research (CIBIT), Institute of Nuclear Sciences Applied to Health (ICNAS), University of Coimbra, 3000-548 Coimbra, Portugal
| | - João Lima
- Coimbra Institute for Biomedical Imaging and Translational Research (CIBIT), Institute of Nuclear Sciences Applied to Health (ICNAS), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Paulo Brás
- Coimbra Clinical Academic Center, Faculty of Medicine, Coimbra University Hospital, Pediatric Hospital, 3000-602 Coimbra, Portugal
| | - Guiomar Oliveira
- Coimbra Institute for Biomedical Imaging and Translational Research (CIBIT), Institute of Nuclear Sciences Applied to Health (ICNAS), University of Coimbra, 3000-548 Coimbra, Portugal
- Child Developmental Center, Research and Clinical Training Center, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
- University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Miguel Castelo-Branco
- Coimbra Institute for Biomedical Imaging and Translational Research (CIBIT), Institute of Nuclear Sciences Applied to Health (ICNAS), University of Coimbra, 3000-548 Coimbra, Portugal
- Coimbra Clinical Academic Center, Faculty of Medicine, Coimbra University Hospital, Pediatric Hospital, 3000-602 Coimbra, Portugal
- Correspondence:
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23
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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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Lovis C, Vakkuri A, Palojoki S. Systematized Nomenclature of Medicine-Clinical Terminology (SNOMED CT) Clinical Use Cases in the Context of Electronic Health Record Systems: Systematic Literature Review. JMIR Med Inform 2023; 11:e43750. [PMID: 36745498 PMCID: PMC9941898 DOI: 10.2196/43750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The Systematized Medical Nomenclature for Medicine-Clinical Terminology (SNOMED CT) is a clinical terminology system that provides a standardized and scientifically validated way of representing clinical information captured by clinicians. It can be integrated into electronic health records (EHRs) to increase the possibilities for effective data use and ensure a better quality of documentation that supports continuity of care, thus enabling better quality in the care process. Even though SNOMED CT consists of extensively studied clinical terminology, previous research has repeatedly documented a lack of scientific evidence for SNOMED CT in the form of reported clinical use cases in electronic health record systems. OBJECTIVE The aim of this study was to explore evidence in previous literature reviews of clinical use cases of SNOMED CT integrated into EHR systems or other clinical applications during the last 5 years of continued development. The study sought to identify the main clinical use purposes, use phases, and key clinical benefits documented in SNOMED CT use cases. METHODS The Cochrane review protocol was applied for the study design. The application of the protocol was modified step-by-step to fit the research problem by first defining the search strategy, identifying the articles for the review by isolating the exclusion and inclusion criteria for assessing the search results, and lastly, evaluating and summarizing the review results. RESULTS In total, 17 research articles illustrating SNOMED CT clinical use cases were reviewed. The use purpose of SNOMED CT was documented in all the articles, with the terminology as a standard in EHR being the most common (8/17). The clinical use phase was documented in all the articles. The most common category of use phases was SNOMED CT in development (6/17). Core benefits achieved by applying SNOMED CT in a clinical context were identified by the researchers. These were related to terminology use outcomes, that is, to data quality in general or to enabling a consistent way of indexing, storing, retrieving, and aggregating clinical data (8/17). Additional benefits were linked to the productivity of coding or to advances in the quality and continuity of care. CONCLUSIONS While the SNOMED CT use categories were well supported by previous research, this review demonstrates that further systematic research on clinical use cases is needed to promote the scalability of the review results. To achieve the best out-of-use case reports, more emphasis is suggested on describing the contextual factors, such as the electronic health care system and the use of previous frameworks to enable comparability of results. A lesson to be drawn from our study is that SNOMED CT is essential for structuring clinical data; however, research is needed to gather more evidence of how SNOMED CT benefits clinical care and patient safety.
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Affiliation(s)
| | - Anne Vakkuri
- Perioperative, Intensive Care and Pain Medicine, Helsinki University Hospital, Vantaa, Finland
| | - Sari Palojoki
- Unit for Digital Transformation, European Centre for Disease Prevention and Control, Stockholm, Sweden
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CEUSTERS W, PENGPUT A. Axiomatizing SNOMED CT Disorders: Should There Be Room for Interpretation? FORMAL ONTOLOGY IN INFORMATION SYSTEMS : PROCEEDINGS OF THE ... INTERNATIONAL CONFERENCE. FOIS (CONFERENCE) 2023; 377:140-154. [PMID: 38808039 PMCID: PMC11131161 DOI: 10.3233/faia231124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
SNOMED CT is a large concept-based terminology designed according to epistemic, semantic and pragmatic principles relevant to clinicians. Its goal is structured clinical reporting in electronic healthcare records (EHRs). The Basic Formal Ontology (BFO) is an ontology designed on the basis of types claimed to exist in reality based on a domain-independent ontological theory. Its goal is faithful representation of reality within that theory. The Ontology for General Medical Science (OGMS) extends the BFO by providing definitions for types relevant within the clinical domain. Combining SNOMED CT with the ontological rigor of BFO and OGMS might improve clinical reporting by, f.i., preventing data entry mistakes and inconsistencies, and make EHRs more comparable. To that end, we are developing a logical framework capable of exploiting what SNOMED CT offers terminologically and realism-based ontologies such as the BFO and the OGMS ontologically by means of bridging axioms compatible with the BFO, and expressed in the same CLIF-dialect as used in its axiomatization in first order logic. In this paper, we report on our attempts to detect in the combinations of binary relations that are used in the definition of SNOMED CT's definitions of disorder concepts patterns which might at least partially automate the construction of such axioms. Our findings suggest that this partial automation is indeed possible, but to a smaller extent than we had hoped for. We compare our approach with a recent proposal that seeks to bring SNOMED CT and BFO closer together by reinterpreting SNOMED CT disorders as clinical occurrents. The proposal has its merit in providing a realist underpinning for that part of SNOMED CT's concept model in terms of the BFO, but is not discriminatory enough for an automatic translation into OGMS. Key problem is the lack of face validity of SNOMED CT disorder terms as compared to the formal definitions they are given and this in absence of textual definitions.
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Affiliation(s)
- Werner CEUSTERS
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, USA
| | - Anuwat PENGPUT
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, USA
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26
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Leston M, Elson WH, Watson C, Lakhani A, Aspden C, Bankhead CR, Borrow R, Button E, Byford R, Elliot AJ, Fan X, Hoang U, Linley E, Macartney J, Nicholson BD, Okusi C, Ramsay M, Smith G, Smith S, Thomas M, Todkill D, Tsang RS, Victor W, Williams AJ, Williams J, Zambon M, Howsam G, Amirthalingam G, Lopez-Bernal J, Hobbs FDR, de Lusignan S. Representativeness, Vaccination Uptake, and COVID-19 Clinical Outcomes 2020-2021 in the UK Oxford-Royal College of General Practitioners Research and Surveillance Network: Cohort Profile Summary. JMIR Public Health Surveill 2022; 8:e39141. [PMID: 36534462 PMCID: PMC9770023 DOI: 10.2196/39141] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND The Oxford-Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) is one of Europe's oldest sentinel systems, working with the UK Health Security Agency (UKHSA) and its predecessor bodies for 55 years. Its surveillance report now runs twice weekly, supplemented by online observatories. In addition to conducting sentinel surveillance from a nationally representative group of practices, the RSC is now also providing data for syndromic surveillance. OBJECTIVE The aim of this study was to describe the cohort profile at the start of the 2021-2022 surveillance season and recent changes to our surveillance practice. METHODS The RSC's pseudonymized primary care data, linked to hospital and other data, are held in the Oxford-RCGP Clinical Informatics Digital Hub, a Trusted Research Environment. We describe the RSC's cohort profile as of September 2021, divided into a Primary Care Sentinel Cohort (PCSC)-collecting virological and serological specimens-and a larger group of syndromic surveillance general practices (SSGPs). We report changes to our sampling strategy that brings the RSC into alignment with European Centre for Disease Control guidance and then compare our cohort's sociodemographic characteristics with Office for National Statistics data. We further describe influenza and COVID-19 vaccine coverage for the 2020-2021 season (week 40 of 2020 to week 39 of 2021), with the latter differentiated by vaccine brand. Finally, we report COVID-19-related outcomes in terms of hospitalization, intensive care unit (ICU) admission, and death. RESULTS As a response to COVID-19, the RSC grew from just over 500 PCSC practices in 2019 to 1879 practices in 2021 (PCSC, n=938; SSGP, n=1203). This represents 28.6% of English general practices and 30.59% (17,299,780/56,550,136) of the population. In the reporting period, the PCSC collected >8000 virology and >23,000 serology samples. The RSC population was broadly representative of the national population in terms of age, gender, ethnicity, National Health Service Region, socioeconomic status, obesity, and smoking habit. The RSC captured vaccine coverage data for influenza (n=5.4 million) and COVID-19, reporting dose one (n=11.9 million), two (n=11 million), and three (n=0.4 million) for the latter as well as brand-specific uptake data (AstraZeneca vaccine, n=11.6 million; Pfizer, n=10.8 million; and Moderna, n=0.7 million). The median (IQR) number of COVID-19 hospitalizations and ICU admissions was 1181 (559-1559) and 115 (50-174) per week, respectively. CONCLUSIONS The RSC is broadly representative of the national population; its PCSC is geographically representative and its SSGPs are newly supporting UKHSA syndromic surveillance efforts. The network captures vaccine coverage and has expanded from reporting primary care attendances to providing data on onward hospital outcomes and deaths. The challenge remains to increase virological and serological sampling to monitor the effectiveness and waning of all vaccines available in a timely manner.
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Affiliation(s)
- Meredith Leston
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - William H Elson
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Conall Watson
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, Colindale, London, United Kingdom
| | - Anissa Lakhani
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, Colindale, London, United Kingdom
| | - Carole Aspden
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Clare R Bankhead
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Ray Borrow
- Vaccine Evaluation Unit, UK Health Security Agency, Manchester Royal Infirmary, Manchester, United Kingdom
| | - Elizabeth Button
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Rachel Byford
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Alex J Elliot
- Real-time Syndromic Surveillance Team, Field Service, UK Health Security Agency, Birmingham, United Kingdom
| | - Xuejuan Fan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Uy Hoang
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Ezra Linley
- Vaccine Evaluation Unit, UK Health Security Agency, Manchester Royal Infirmary, Manchester, United Kingdom
| | - Jack Macartney
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Brian D Nicholson
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Cecilia Okusi
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Mary Ramsay
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, Colindale, London, United Kingdom
| | - Gillian Smith
- Real-time Syndromic Surveillance Team, Field Service, UK Health Security Agency, Birmingham, United Kingdom
| | - Sue Smith
- Real-time Syndromic Surveillance Team, Field Service, UK Health Security Agency, Birmingham, United Kingdom
| | - Mark Thomas
- Royal College of General Practitioners, London, United Kingdom
| | - Dan Todkill
- Real-time Syndromic Surveillance Team, Field Service, UK Health Security Agency, Birmingham, United Kingdom
| | - Ruby Sm Tsang
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - William Victor
- Royal College of General Practitioners, London, United Kingdom
| | - Alice J Williams
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - John Williams
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Maria Zambon
- Reference Microbiology, UK Health Security Agency, Colindale, London, United Kingdom
| | - Gary Howsam
- Royal College of General Practitioners, London, United Kingdom
| | - Gayatri Amirthalingam
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, Colindale, London, United Kingdom
| | - Jamie Lopez-Bernal
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, Colindale, London, United Kingdom
| | - F D Richard Hobbs
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Simon de Lusignan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
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27
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Chang E. A vector-based semantic relatedness measure using multiple relations within SNOMED CT and UMLS. J Biomed Inform 2022; 131:104118. [PMID: 35690349 DOI: 10.1016/j.jbi.2022.104118] [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: 03/06/2022] [Revised: 05/26/2022] [Accepted: 06/05/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To propose a new vector-based relatedness metric that derives word vectors from the intrinsic structure of biomedical ontologies, without consulting external resources such as large-scale biomedical corpora. MATERIALS AND METHODS SNOMED CT on the mapping layer of UMLS was used as a testbed ontology. Vectors were created for every concept at the end of all semantic relations-attribute-value relations and descendants as well as is_a relation-of the defining concept. The cosine similarity between the averages of those vectors with respect to each defining concept was computed to produce a final semantic relatedness. RESULTS Two benchmark sets that include a total of 62 biomedical term pairs were used for evaluation. Spearman's rank coefficient of the current method was 0.655, 0.744, and 0.742 with the relatedness rated by physicians, coders, and medical experts, respectively. The proposed method was comparable to a word-embedding method and outperformed path-based, information content-based, and another multiple relation-based relatedness metrics. DISCUSSION The current study demonstrated that the addition of attribute relations to the is_a hierarchy of SNOMED CT better conforms to the human sense of relatedness than models based on taxonomic relations. The current approach also showed that it is robust to the design inconsistency of ontologies. CONCLUSION Unlike the previous vector-based approach, the current study exploited the intrinsic semantic structure of an ontology, precluding the need for external textual resources to obtain context information of defining terms. Future research is recommended to prove the validity of the current method with other biomedical ontologies.
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Affiliation(s)
- Eunsuk Chang
- Carolina Health Informatics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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28
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Xiang J, Zhang J, Zhao Y, Wu FX, Li M. Biomedical data, computational methods and tools for evaluating disease-disease associations. Brief Bioinform 2022; 23:6522999. [PMID: 35136949 DOI: 10.1093/bib/bbac006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
In recent decades, exploring potential relationships between diseases has been an active research field. With the rapid accumulation of disease-related biomedical data, a lot of computational methods and tools/platforms have been developed to reveal intrinsic relationship between diseases, which can provide useful insights to the study of complex diseases, e.g. understanding molecular mechanisms of diseases and discovering new treatment of diseases. Human complex diseases involve both external phenotypic abnormalities and complex internal molecular mechanisms in organisms. Computational methods with different types of biomedical data from phenotype to genotype can evaluate disease-disease associations at different levels, providing a comprehensive perspective for understanding diseases. In this review, available biomedical data and databases for evaluating disease-disease associations are first summarized. Then, existing computational methods for disease-disease associations are reviewed and classified into five groups in terms of the usages of biomedical data, including disease semantic-based, phenotype-based, function-based, representation learning-based and text mining-based methods. Further, we summarize software tools/platforms for computation and analysis of disease-disease associations. Finally, we give a discussion and summary on the research of disease-disease associations. This review provides a systematic overview for current disease association research, which could promote the development and applications of computational methods and tools/platforms for disease-disease associations.
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Affiliation(s)
- Ju Xiang
- School of Computer Science and Engineering, Central South University, China
| | - Jiashuai Zhang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Yichao Zhao
- School of Computer Science and Engineering, Central South University, China
| | - Fang-Xiang Wu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Min Li
- Division of Biomedical Engineering and Department of Mechanical Engineering at University of Saskatchewan, Saskatoon, Canada
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