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Grosjean J, Dufour F, Benis A, Januel JM, Staccini P, Darmoni SJ. Digital Health Education for the Future: The SaNuRN (Santé Numérique Rouen-Nice) Consortium's Journey. JMIR Med Educ 2024; 10:e53997. [PMID: 38693686 DOI: 10.2196/53997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 05/03/2024]
Abstract
SaNuRN is a five-year project by the University of Rouen Normandy (URN) and the Côte d’Azur University (CAU) consortium to optimize digital health education for medical and paramedical students, professionals, and administrators. The project includes a skills framework, training modules, and teaching resources. In 2027, SaNuRN is expected to train a significant portion of the 400,000 health and paramedical professions students at the French national level. Our purpose is to give a synopsis of the SaNuRN initiative, emphasizing its novel educational methods and how they will enhance the delivery of digital health education. Our goals include showcasing SaNuRN as a comprehensive program consisting of a proficiency framework, instructional modules, and educational materials and explaining how SaNuRN is implemented in the participating academic institutions. SaNuRN is a project aimed at educating and training health-related and paramedics students in digital health. The project results from a cooperative effort between URN and CAU, covering four French departments. The project is based on the French National Referential on Digital Health (FNRDH), which defines the skills and competencies to be acquired and validated by every student in the health, paramedical, and social professions curricula. The SaNuRN team is currently adapting the existing URN and CAU syllabi to FNRDH and developing short-duration video capsules of 20 to 30 minutes to teach all the relevant material. The project aims to ensure that the largest student population earns the necessary skills, and it has developed a two-tier system involving facilitators who will enable the efficient expansion of the project’s educational outreach and support the students in learning the needed material efficiently. With a focus on real-world scenarios and innovative teaching activities integrating telemedicine devices and virtual professionals, SaNuRN is committed to enabling continuous learning for healthcare professionals in clinical practice. The SaNuRN team introduced new ways of evaluating healthcare professionals by shifting from a knowledge-based to a competencies-based evaluation, aligning with the Miller teaching pyramid and using the Objective Structured Clinical Examination and Script Concordance Test in digital health education. Drawing on the expertise of URN, CAU, and their public health and digital research laboratories and partners, the SaNuRN project represents a platform for continuous innovation, including telemedicine training and living labs with virtual and interactive professional activities. The SaNuRN project provides a comprehensive, personalized 30-hour training package for health and paramedical students, addressing all 70 FNRDH competencies. The program is enhanced using AI and NLP to create virtual patients and professionals for digital healthcare simulation. SaNuRN teaching materials are open-access. The project collaborates with academic institutions worldwide to develop educational material in digital health in English and multilingual formats. SaNuRN offers a practical and persuasive training approach to meet the current digital health education requirements.
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Affiliation(s)
- Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratory of Medical Informatics and Knowledge Engineering in e-Health (LIMICS), INSERM U1142, Sorbonne Université, Paris, France
| | - Frank Dufour
- URE Risk Epidemiology Territory INformatics Education and Health (RETINES), Université Côte d'Azur, Nice, France
| | - Arriel Benis
- Department of Digital Medical Technologies, Holon Institute of Technology, Holon, Israel
| | - Jean-Marie Januel
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
| | - Pascal Staccini
- URE Risk Epidemiology Territory INformatics Education and Health (RETINES), Université Côte d'Azur, Nice, France
| | - Stéfan Jacques Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratory of Medical Informatics and Knowledge Engineering in e-Health (LIMICS), INSERM U1142, Sorbonne Université, Paris, France
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Lebel N, Marie I, Grosjean J, Brevet P, Leclercq M, Dumont A, Levesque H, Benhamou Y, Marcelli C, Lequerre T, Vittecoq O. Potential efficacy of T and B lymphocyte-targeted therapies on articular involvement of patients with rheumatoid arthritis and systemic sclerosis overlap syndrome. Results from a 2-centre series of 22 cases. Clin Exp Rheumatol 2024:19981. [PMID: 38489323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/28/2023] [Indexed: 03/17/2024]
Abstract
OBJECTIVES To analyse in routine practice the efficacy of targeted therapies on joint involvement of patients with rheumatoid arthritis/systemic sclerosis (RA/SSc) overlap syndrome. METHODS This was a retrospective analysis of medical records of two academic centres over a 10-year period. Joint response to targeted therapies was measured according to EULAR criteria based on Disease Activity Score (DAS)-28. In addition, changes in CRP level and glucocorticoid consumption were recorded. RESULTS Nineteen patients were included. Methotrexate (n=11) and hydroxychloroquine (n=4) were the most used first-line treatments. Targeted therapies were frequently used (n=14). Tocilizumab was the most selected therapy (n=8), then rituximab (n=5), abatacept and anti-tumour necrosis factor (n=4). Twenty-one treatment sequences were assessed, including 18 with EULAR response criteria. Responses were "good" or "moderate" in 100% (4/4) of patients treated with abatacept, 80% (4/5) with rituximab, 40% (2/5) with tocilizumab, and 25% (1/4) with anti-TNF. T and B lymphocyte-targeted therapies (abatacept, rituximab) resulted more frequently in a "good" or "moderate" response compared to cytokine inhibitors (tocilizumab, etanercept, infliximab) with a significant decrease in DAS-28 at 6 months (-1.75; p=0.016) and a trend to a lower consumption of glucocorticoids. CCONCLUSIONS In patients with RA/SSc overlap syndrome refractory to conventional synthetic-DMARDs, T and B lymphocyte-targeted therapies seem to be a promising therapeutic option to control joint activity.
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Affiliation(s)
- Nans Lebel
- Department of Rheumatology, Rouen University, CHU de Rouen, and CIC-CRB 1404, Inserm 1234, Rouen, France
| | - Isabelle Marie
- Department of Internal Medicine, Rouen University, CHU de Rouen, and Inserm 1234, Rouen, France
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University, CHU de Rouen, and LIMICS U1142, Sorbonne University, Paris, France
| | - Pauline Brevet
- Department of Rheumatology, Rouen University, CHU de Rouen, and CIC-CRB 1404, Inserm 1234, Rouen, France
| | - Mathilde Leclercq
- Department of Internal Medicine, Rouen University, CHU de Rouen, and Inserm 1234, Rouen, France
| | - Anaël Dumont
- Department of Internal Medicine, Normandie Univ, UNICAEN, CHU de Caen, France
| | - Hervé Levesque
- Department of Internal Medicine, Rouen University, CHU de Rouen, and Inserm 1234, Rouen, France
| | - Ygal Benhamou
- Department of Internal Medicine, Rouen University, CHU de Rouen, and Inserm 1234, Rouen, France
| | - Christian Marcelli
- Department of Rheumatology, Normandie Univ, UNICAEN, CHU de Caen, France
| | - Thierry Lequerre
- Department of Rheumatology, Rouen University, CHU de Rouen, and CIC-CRB 1404, Inserm 1234, Rouen, France
| | - Olivier Vittecoq
- Department of Rheumatology, Rouen University, CHU de Rouen, and CIC-CRB 1404, Inserm 1234, Rouen, France.
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Grosjean J, Benis A, Dufour JC, Lejeune É, Disson F, Dahamna B, Cieslik H, Léguillon R, Faure M, Dufour F, Staccini P, Darmoni SJ. Sharing Digital Health Educational Resources in a One-Stop Shop Portal: Tutorial on the Catalog and Index of Digital Health Teaching Resources (CIDHR) Semantic Search Engine. JMIR Med Educ 2024; 10:e48393. [PMID: 38437007 PMCID: PMC10949124 DOI: 10.2196/48393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/13/2023] [Accepted: 12/18/2023] [Indexed: 03/05/2024]
Abstract
BACKGROUND Access to reliable and accurate digital health web-based resources is crucial. However, the lack of dedicated search engines for non-English languages, such as French, is a significant obstacle in this field. Thus, we developed and implemented a multilingual, multiterminology semantic search engine called Catalog and Index of Digital Health Teaching Resources (CIDHR). CIDHR is freely accessible to everyone, with a focus on French-speaking resources. CIDHR has been initiated to provide validated, high-quality content tailored to the specific needs of each user profile, be it students or professionals. OBJECTIVE This study's primary aim in developing and implementing the CIDHR is to improve knowledge sharing and spreading in digital health and health informatics and expand the health-related educational community, primarily French speaking but also in other languages. We intend to support the continuous development of initial (ie, bachelor level), advanced (ie, master and doctoral levels), and continuing training (ie, professionals and postgraduate levels) in digital health for health and social work fields. The main objective is to describe the development and implementation of CIDHR. The hypothesis guiding this research is that controlled vocabularies dedicated to medical informatics and digital health, such as the Medical Informatics Multilingual Ontology (MIMO) and the concepts structuring the French National Referential on Digital Health (FNRDH), to index digital health teaching and learning resources, are effectively increasing the availability and accessibility of these resources to medical students and other health care professionals. METHODS First, resource identification is processed by medical librarians from websites and scientific sources preselected and validated by domain experts and surveyed every week. Then, based on MIMO and FNRDH, the educational resources are indexed for each related knowledge domain. The same resources are also tagged with relevant academic and professional experience levels. Afterward, the indexed resources are shared with the digital health teaching and learning community. The last step consists of assessing CIDHR by obtaining informal feedback from users. RESULTS Resource identification and evaluation processes were executed by a dedicated team of medical librarians, aiming to collect and curate an extensive collection of digital health teaching and learning resources. The resources that successfully passed the evaluation process were promptly included in CIDHR. These resources were diligently indexed (with MIMO and FNRDH) and tagged for the study field and degree level. By October 2023, a total of 371 indexed resources were available on a dedicated portal. CONCLUSIONS CIDHR is a multilingual digital health education semantic search engine and platform that aims to increase the accessibility of educational resources to the broader health care-related community. It focuses on making resources "findable," "accessible," "interoperable," and "reusable" by using a one-stop shop portal approach. CIDHR has and will have an essential role in increasing digital health literacy.
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Affiliation(s)
- Julien Grosjean
- Department of Digital Health, Rouen University Hospital, Rouen, France
- LIMICS, INSERM U1142, Sorbonne Université, Paris, France
| | - Arriel Benis
- Department of Digital Medical Technologies, Holon Institute of Technology, Holon, Israel
- European Federation for Medical Informatics, Le Mont-sur-Lausanne, Switzerland
| | - Jean-Charles Dufour
- SESSTIM, Aix Marseille Univ, APHM, INSERM, IRD, Hop Timone, BioSTIC, Marseille, France
| | - Émeline Lejeune
- Department of Digital Health, Rouen University Hospital, Rouen, France
| | - Flavien Disson
- Department of Digital Health, Rouen University Hospital, Rouen, France
| | - Badisse Dahamna
- Department of Digital Health, Rouen University Hospital, Rouen, France
- LIMICS, INSERM U1142, Sorbonne Université, Paris, France
| | - Hélène Cieslik
- Department of Digital Health, Rouen University Hospital, Rouen, France
| | - Romain Léguillon
- Department of Digital Health, Rouen University Hospital, Rouen, France
- LIMICS, INSERM U1142, Sorbonne Université, Paris, France
- Department of Pharmacy, Rouen University Hospital, Rouen, France
| | | | - Frank Dufour
- RETINES, Université de Nice Côté d'Azur, Nice, France
| | | | - Stéfan Jacques Darmoni
- Department of Digital Health, Rouen University Hospital, Rouen, France
- LIMICS, INSERM U1142, Sorbonne Université, Paris, France
- European Federation for Medical Informatics, Le Mont-sur-Lausanne, Switzerland
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Litovsky J, Hacard F, Tétart F, Boccon-Gibod I, Soria A, Staumont-Sallé D, Doutre MS, Amsler E, Mansard C, Dezoteux F, Darrigade AS, Milpied B, Bernier C, Perrot JL, Raison-Peyron N, Paryl M, Droitcourt C, Demoly P, Grosjean J, Mura T, Du-Thanh A. Omalizumab Drug Survival in Chronic Urticaria: A Retrospective Multicentric French Study. J Allergy Clin Immunol Pract 2023; 11:3752-3762.e2. [PMID: 37652349 DOI: 10.1016/j.jaip.2023.08.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Omalizumab (OMA) dramatically improves disease control and quality of life in patients with chronic urticaria (CU). OBJECTIVE We aimed to evaluate the discontinuation patterns of OMA and their determinants in a cohort of French patients with CU. METHODS We conducted a retrospective multicenter study in 9 French tertiary referral hospitals. All patients diagnosed with either spontaneous (CSU) and/or inducible (CIndU) CU who received at least 1 injection of OMA between 2009 and 2021 were included. We analyzed OMA drug survival and investigated possible determinants using Kaplan-Meier curves and log-rank tests. RESULTS A total of 878 patients were included in this study; 48.8% had CSU, 10.1% CIndU, and 41.1% a combination of both. OMA was discontinued in 408 patients, but the drug was later reintroduced in 50% of them. The main reason for discontinuing treatment was the achievement of a well-controlled disease in 50% of patients. Half of the patients were still being treated with OMA 2.4 years after the initiation of treatment. Drug survival was shorter in patients with CIndU and in those with an autoimmune background. In atopic patients, OMA was discontinued earlier in patients achieving a well-controlled disease. A longer OMA drug survival was observed in patients with a longer disease duration at initiation. CONCLUSION In French patients with CU, the drug survival of OMA appears to be longer than that observed in previous studies conducted elsewhere, highlighting discrepancies in prescription and reimbursement possibilities. Further studies are warranted to develop customized OMA treatment schemes based on individual patterns.
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Affiliation(s)
- Julie Litovsky
- Département de Dermatologie, C.H.U de Montpellier, Montpellier, France
| | - Florence Hacard
- Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Service d'Allergologie et Immunologie Clinique, Pierre Bénite, France
| | - Florence Tétart
- Centre Erik Satie-Allergologie, Rouen University Hospital, Rouen, France
| | - Isabelle Boccon-Gibod
- Service de Médecine Interne, Centre National de Référence des Angioedèmes, CHU de Grenoble, Échirolles, France
| | - Angèle Soria
- Service de Dermatologie et Allergologie, Hôpital Tenon AP-HP, Sorbonne Université, Paris, France
| | - Delphine Staumont-Sallé
- CHU Lille, Service de Dermatologie, Université de Lille, INSERM U1286, Lille Inflammation Translational Research Institute (INFINITE) F-59000, Lille, France
| | | | - Emmanuelle Amsler
- Service de Dermatologie et Allergologie, Hôpital Tenon AP-HP, Sorbonne Université, Paris, France
| | - Catherine Mansard
- Service de Médecine Interne, Centre National de Référence des Angioedèmes, CHU de Grenoble, Échirolles, France
| | - Frédéric Dezoteux
- CHU Lille, Service de Dermatologie, Université de Lille, INSERM U1286, Lille Inflammation Translational Research Institute (INFINITE) F-59000, Lille, France
| | | | | | - Claire Bernier
- Plateforme Transversale d'Allergologie, Hôtel-Dieu-CHU de Nantes, Nantes, France
| | - Jean-Luc Perrot
- Service Dermatologie-Allergologie-Oncologie, CHU Nord Saint-Étienne U1059 INSERM, Saint-Priest-en-Jarez, France
| | | | - Marie Paryl
- Laboratoire de Biostatistiques, Épidémiologie, Santé Publique et Innovation Médicale Bespim, CHU De Nîmes, Nîmes, France
| | - Catherine Droitcourt
- Service de Dermatologie, CHU Rennes, Rennes, France; Université Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, Rennes, France
| | - Pascal Demoly
- Department of Allergology, University Hospital of Montpellier, Montpellier, France; IDESP UA11 University Montpellier, Montpellier, France
| | - Julien Grosjean
- Département d'Informatique BioMédicale, CHU de Rouen & LIMICS, U1142, Sorbonne Université, Paris, France
| | - Thibault Mura
- Laboratoire de Biostatistiques, Épidémiologie, Santé Publique et Innovation Médicale Bespim, CHU De Nîmes, Nîmes, France
| | - Aurélie Du-Thanh
- Département de Dermatologie, C.H.U de Montpellier, Montpellier, France.
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Benis A, Haghi M, Tamburis O, Darmoni SJ, Grosjean J, Deserno TM. Digital Emergency Management for a Complex One Health Landscape: the Need for Standardization, Integration, and Interoperability. Yearb Med Inform 2023; 32:27-35. [PMID: 38147847 PMCID: PMC10751113 DOI: 10.1055/s-0043-1768742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
OBJECTIVE Planning reliable long-term planning actions to handle disruptive events requires a timely development of technological infrastructures, as well as the set-up of focused strategies for emergency management. The paper aims to highlight the needs for standardization, integration, and interoperability between Accident & Emergency Informatics (A&EI) and One Digital Health (ODH), as fields capable of dealing with peculiar dynamics for a technology-boosted management of emergencies under an overarching One Health panorama. METHODS An integrative analysis of the literature was conducted to draw attention to specific foci on the correlation between ODH and A&EI, in particular: (i) the management of disruptive events from private smart spaces to diseases spreading, and (ii) the concepts of (health-related) quality of life and well-being. RESULTS A digitally-focused management of emergency events that tackles the inextricable interconnectedness between humans, animals, and surrounding environment, demands standardization, integration, and systems interoperability. A consistent and finalized process of adoption and implementation of methods and tools from the International Standard Accident Number (ISAN), via findability, accessibility, interoperability, and reusability (FAIR) data principles, to Medical Informatics and Digital Health Multilingual Ontology (MIMO) - capable of looking at different approaches to encourage the integration between the ODH framework and the A&EI vision, provides a first answer to these needs. CONCLUSIONS ODH and A&EI look at different scales but with similar goals for converging health and environmental-related data management standards to enable multi-sources, interdisciplinary, and real-time data integration and interoperability. This allows holistic digital health both in routine and emergency events.
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Affiliation(s)
- Arriel Benis
- Department of Digital Medical Technologies, Holon Institute of Technology, Holon, Israel
- IMIA Working Group One Digital Health (WG ODH)
| | - Mostafa Haghi
- Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany
- IMIA Working Group Accident & Emergency Informatics (WG A&EI)
| | - Oscar Tamburis
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
- IMIA Working Group One Digital Health (WG ODH)
| | - Stéfan J. Darmoni
- Department of Digital Health, Rouen University Hospital, France
- LIMICS Laboratory of Medical Informatics and Knowledge Engineering in e-Health, Inserm U1142, Sorbonne Université, France
| | - Julien Grosjean
- Department of Digital Health, Rouen University Hospital, France
- LIMICS Laboratory of Medical Informatics and Knowledge Engineering in e-Health, Inserm U1142, Sorbonne Université, France
| | - Thomas M. Deserno
- Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany
- IMIA Working Group Accident & Emergency Informatics (WG A&EI)
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Gosselin L, Leguillon R, Rollin L, Lejeune E, Darmoni SJ, Grosjean J. Trends in computerized provider order entry: 20-year bibliometric overview. Front Digit Health 2023; 5:1217694. [PMID: 37497185 PMCID: PMC10367087 DOI: 10.3389/fdgth.2023.1217694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/28/2023] [Indexed: 07/28/2023] Open
Abstract
Background Drug-related problems (DRPs) can lead to serious health issues and have significant economic impacts on healthcare systems. One solution to address this issue is the use of computerized physician order entry systems (CPOE), which can help prevent DRPs by reducing the risk of medication errors. Objective The purpose of this study is to provide an analysis on scientific production of the past 20 years in order to describe trends in academic publishing on CPOE and to identify the major topics as well as the predominant actors (journals, countries) involved in this field. Methods A PubMed search was carried out to extract articles related to computerized provider order entry during the period January 1st 2003- December 31st 2022 using a specific query. Data were downloaded from PubMed in Extensible Markup Language (XML) and were processed through a dedicated parser. Results A total of 2,946 articles were retrieved among 623 journals. One third of these articles were published in eight journals. Publications grew strongly from 2002 to 2006, with a dip in 2008 followed by an increase again in 2009. After 2009, there follows a decreasing until 2022.The most producing countries are the USA with 51.39% of the publication over the period by France (3.80%), and Canada (3.77%). About disciplines, the top 3 is: "medical informatics" (21.62% of articles), "pharmacy" (19.04%), and "pediatrics" (6.56%). Discussion This study provides an overview of publication trends related to CPOE, which exhibited a significant increase in the first decade of the 21st century followed by a decline after 2009. Possible reasons for this decline include the emergence of digital health tools beyond CPOE, as well as healthcare professionals experiencing alert fatigue of the current system. Conclusion Future research should focus on analyzing publication trends in the field of medical informatics and decision-making tools to identify other areas of interest that may have surpassed the development of CPOE.
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Affiliation(s)
- Laura Gosselin
- Department of Digital Health, Rouen University Hospital, Rouen, France
- Department of Pharmacy, Rouen University Hospital, Rouen, France
| | - Romain Leguillon
- Department of Digital Health, Rouen University Hospital, Rouen, France
- Department of Pharmacy, Rouen University Hospital, Rouen, France
- Laboratoire D'Informatique Médicale et D'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Laetitia Rollin
- Laboratoire D'Informatique Médicale et D'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
- Institute of Occupational Medicine, Rouen University Hospital, Rouen, France
| | - Emeline Lejeune
- Department of Digital Health, Rouen University Hospital, Rouen, France
| | - Stéfan J. Darmoni
- Department of Digital Health, Rouen University Hospital, Rouen, France
- Laboratoire D'Informatique Médicale et D'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Julien Grosjean
- Department of Digital Health, Rouen University Hospital, Rouen, France
- Laboratoire D'Informatique Médicale et D'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
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Léguillon R, Gosselin L, Carnoy C, Pressat-Laffouilhere T, Letord C, Dahamna B, Darmoni SJ, Grosjean J. Integrating a new knowledge organisation system for monoclonal antibodies for therapeutic use authorised in Europe into HeTOP terminology-ontology server. J Biomed Inform 2023; 140:104325. [PMID: 36870586 DOI: 10.1016/j.jbi.2023.104325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 02/06/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023]
Abstract
Monoclonal antibodies (MAs) are increasingly used in the therapeutic arsenal. Clinical Data Warehouses (CDWs) offer unprecedented opportunities for research on real-word data. The objective of this work is to develop a knowledge organization system on MAs for therapeutic use (MATUs) applicable in Europe to query CDWs from a multi-terminology server (HeTOP). After expert consensus, three main health thesauri were selected: the MeSH thesaurus, the National Cancer Institute thesaurus (NCIt) and the SNOMED CT. These thesauri contain 1,723 MAs concepts, but only 99 (5.7 %) are identified as MATUs. The knowledge organisation system proposed in this article is a six-level hierarchical system according to their main therapeutic target. It includes 193 different concepts organised in a cross lingual terminology server, which will allow the inclusion of semantic extensions. Ninety nine (51.3 %) MATUs concepts and 94 (48.7 %) hierarchical concepts composed the knowledge organisation system. Two separates groups (an expert group and a validation group) carried out the selection, creation and validation processes. Queries identify, for unstructured data, 83 out of 99 (83.8 %) MATUs corresponding to 45,262 patients, 347,035 hospital stays and 427,544 health documents, and for structured data, 61 out of 99 (61.6 %) MATUs corresponding to 9,218 patients, 59,643 hospital stays and 104,737 hospital prescriptions. The volume of data in the CDW demonstrated the potential for using these data in clinical research, although not all MATUs are present in the CDW (16 missing for unstructured data and 38 for structured data). The knowledge organisation system proposed here improves the understanding of MATUs, the quality of queries and helps clinical researchers retrieve relevant medical information. The use of this model in CDW allows for the rapid identification of a large number of patients and health documents, either directly by a MATU of interest (e.g. Rituximab) but also by searching for parent concepts (e.g. Anti-CD20 Monoclonal Antibody).
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Affiliation(s)
- Romain Léguillon
- Department of Digital Health, Rouen University Hospital, Rouen, France; Department of Pharmacy, Rouen University Hospital, Rouen, France; Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France.
| | - Laura Gosselin
- Department of Digital Health, Rouen University Hospital, Rouen, France; Department of Pharmacy, Rouen University Hospital, Rouen, France
| | - Christophe Carnoy
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France; GIVRE, Univ-Lille, France
| | - Thibaut Pressat-Laffouilhere
- Clinique Ambroise Paré, groupe ELSAN Department of medical information, 387 Rte de Saint-Simon, F-31100 Toulouse, France
| | - Catherine Letord
- Department of Digital Health, Rouen University Hospital, Rouen, France; Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Badisse Dahamna
- Department of Digital Health, Rouen University Hospital, Rouen, France; Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Stéfan J Darmoni
- Department of Digital Health, Rouen University Hospital, Rouen, France; Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Julien Grosjean
- Department of Digital Health, Rouen University Hospital, Rouen, France; Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
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8
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Lagassy M, Laffouilhere TP, Grosjean J, Leblond L, Dordain S, Mahay G, Couderc L, Dumant-Forest C, Sabourin JC, Martinet J, Thiebaut PA, Coëffier M. Résultats préliminaires de l’étude Immune-Eo : différents profils d’œsophagite à éosinophiles (allergique et non allergique) selon de multiples immunomarquages tissulaires. Revue Française d'Allergologie 2023. [DOI: 10.1016/j.reval.2022.103271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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9
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Gosselin L, Letord C, Leguillon R, Soualmia LF, Dahamna B, Mouazer A, Disson F, Darmoni SJ, Grosjean J. Modeling and integrating interactions involving the CYP450 enzyme system in a multi-terminology server: Contribution to information extraction from a clinical data warehouse. Int J Med Inform 2023; 170:104976. [PMID: 36599261 DOI: 10.1016/j.ijmedinf.2022.104976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022]
Abstract
INTRODUCTION The cytochrome P450 (CYP450) enzyme system is involved in the metabolism of certain drugs and is responsible for most drug interactions. These interactions result in either an enzymatic inhibition or an enzymatic induction mechanism that has an impact on the therapeutic management of patients. Detecting these drug interactions will allow for better predictability in therapeutic response. Therefore, computerized solutions can represent a valuable help for clinicians in their tasks of detection. OBJECTIVE The objective of this study is to provide a structured data-source of interactions involving the CYP450 enzyme system. These interactions are aimed to be integrated in the cross-lingual multi-terminology server HeTOP (Health Terminologies and Ontologies Portal), to support the query processing of the clinical data warehouse (CDW) EDSaN (Entrepôt de Données de Santé Normand). MATERIAL AND METHODS A selection and curation of drug components (DCs) that share a relationship with the CYP450 system was performed from several international data sources. The DCs were linked according to the type of relationship which can be substrate, inhibitor, or inducer. These relationships were then integrated into the HeTOP server. To validate the CYP450 relationships, a semantic query was performed on the CDW, whose search engine is founded on HeTOP data (concepts, terms, and relations). RESULTS A total of 776 DCs are associated by a new interaction relationship, integrated in HeTOP, by 14 enzymes. These are CYP450 1A2, 2A6, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 3A4, 3A7, 11B1,11B2 mitochondrial and P-glycoprotein, constituting a total of 2,088 relationships. A general modelling of cytochromic interactions was performed. From this model, 233,006 queries were processed in less than two hours, demonstrating the usefulness and performance of our CDW implementation. Moreover, they showed that in our university hospital, the concurrent prescription that could cause a cytochromic interaction is Bisoprolol with Amiodarone by enzymatic inhibition for 2,493 patients. DISCUSSION The queries submitted to the CDW EDSaN allowed to highlight the most prescribed molecules simultaneously and potentially responsible for cytochromic interactions. In a second step, it would be interesting to evaluate the real clinical impact by looking for possible adverse effects of these interactions in the patients' files. Other computational solutions for cytochromic interactions exist. The impact of CYP450 is particularly important for drugs with narrow therapeutic window (NTW) as they can lead to increased toxicity or therapeutic failure. It is also important to define which drug component is a pro-drug and to considerate the many genetic polymorphisms of patients. CONCLUSION The HeTOP server contains a non-negligible number of relationships between drug components and CYP450 from multiple reference sources. These data allow us to query our Clinical Data Warehouse to highlight these cytochromic interactions. It would be interesting in the future to assess the actual clinical impact in hospital reports.
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Affiliation(s)
- Laura Gosselin
- Department of Digital Health, Rouen University Hospital, Rouen, France; Department of Pharmacy, Rouen University Hospital, Rouen, France.
| | - Catherine Letord
- Department of Digital Health, Rouen University Hospital, Rouen, France; Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Romain Leguillon
- Department of Digital Health, Rouen University Hospital, Rouen, France; Department of Pharmacy, Rouen University Hospital, Rouen, France; Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Lina F Soualmia
- Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France; Normandy University, UNIROUEN, LITIS-TIBS, UR 4108 Rouen, France
| | - Badisse Dahamna
- Department of Digital Health, Rouen University Hospital, Rouen, France; Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Abdelmalek Mouazer
- Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Flavien Disson
- Department of Digital Health, Rouen University Hospital, Rouen, France
| | - Stéfan J Darmoni
- Department of Digital Health, Rouen University Hospital, Rouen, France; Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Julien Grosjean
- Department of Digital Health, Rouen University Hospital, Rouen, France; Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
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Melot B, Amsilli M, Drouet F, Rodriguez L, Salomon J, Grosjean J, Duclos C. Appropriateness of Antibiotic Prescription During Teleconsultation. Stud Health Technol Inform 2022; 298:142-146. [PMID: 36073473 DOI: 10.3233/shti220924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Teleconsultation has become a new means of using care which has taken off significantly since the COVID crisis, The pooling of the technological environment within the TC makes it possible to set up practice reviews by reusing the data collected. Our aim was to evaluate the relevance of antibiotic therapy during teleconsultations carried out on the national teleconsultation platform "Qare" in 4 common infections. 143,428 TCs with structured prescriptions were analyzed, with an appropriate prescription in more than 82% of cases, higher than in the literature. The use of data makes it possible to quickly assess practices and inform doctors to improve their practices.
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Affiliation(s)
- B Melot
- Qare, Paris, France
- Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, Sorbonne Université, INSERM, F-93000, Bobigny, France
| | | | | | | | | | - J Grosjean
- Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, Sorbonne Université, INSERM, F-93000, Bobigny, France
- Department of Digital Health, Rouen University Hospital, Rouen France
| | - C Duclos
- Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, Sorbonne Université, INSERM, F-93000, Bobigny, France
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Dahlweid M, Rausch D, Hinske C, Darmoni S, Grosjean J, Santi J, Marin L, Yasini M. Clinical Knowledge Platform (CKP): A Collaborative Ecosystem to Share Interoperable Clinical Forms, Viewers, and Order Sets with Various EMRs. Stud Health Technol Inform 2022; 298:117-121. [PMID: 36073468 DOI: 10.3233/shti220919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A large number of Electronic Medical Records (EMR) are currently available with a variety of features and architectures. Existing studies and frameworks presented some solutions to overcome the problem of specification and application of clinical guidelines toward the automation of their use at the point of care. However, they could not yet support thoroughly the dynamic use of medical knowledge in EMRs according to the clinical contexts and provide local application of international recommendations. This study presents the development of the Clinical Knowledge Platform (CKP): a collaborative interoperable environment to create, use, and share sets of information elements that we entitled Clinical Use Contexts (CUCs). A CUC could include medical forms, patient dashboards, and order sets that are usable in various EMRs. For this purpose, we have identified and developed three basic requirements: an interoperable, inter-mapped dictionary of concepts leaning on standard terminologies, the possibility to define relevant clinical contexts, and an interface for collaborative content production via communities of professionals. Community members work together to create and/or modify, CUCs based on different clinical contexts. These CUCs will then be uploaded to be used in clinical applications in various EMRs. With this method, each CUC is, on the one hand, specific to a clinical context and on the other hand, could be adapted to the local practice conditions and constraints. Once a CUC has been developed, it could be shared with other potential users that can consume it directly or modify it according to their needs.
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Affiliation(s)
| | | | - Christian Hinske
- Department of Data Management and Clinical Decision Support, University of Augsburg, Germany
| | - Stefan Darmoni
- Department of Digital Health, Rouen University Hospital & LIMICS INSERM, Sorbonne Université, France
| | - Julien Grosjean
- Department of Digital Health, Rouen University Hospital & LIMICS INSERM, Sorbonne Université, France
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Darmoni S, Benis A, Lejeune E, Disson F, Dahamna B, Weber P, Staccini P, Grosjean J. Digital Health Multilingual Ontology to Index Teaching Resources. Stud Health Technol Inform 2022; 298:19-23. [PMID: 36073449 DOI: 10.3233/shti220900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The aim of this paper is to present the use of Medical Informatics Multilingual Ontology (MIMO) to index digital health resources that are (and will be) included in SaNuRN (project to teach digital health). MIMO currently contains 1,379 concepts and is integrated into HeTOP, which is a cross-lingual multiterminogy server. Existing teaching resources have been reindexed with MIMO concepts and integrated into a dedicated website. A total of 345 resources have been indexed with MIMO concepts and are freely available at https://doccismef.chu-rouen.fr/dc/#env=sanurn. The development of a multilingual MIMO for enhancing the quality and the efficiency of international projects is challenging. A specific semantic search engine has been deployed to give access to digital health teaching resources.
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Affiliation(s)
- Stéfan Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, France
- LIMICS Laboratory of Medical Informatics and Knowledge Engineering in e-Health, INSERM U1142, Sorbonne Université, France
| | - Arriel Benis
- Faculty of Industrial Engineering and Technology Management, Holon Institute of Technology, Israel
- Faculty of Digital Technologies in Medicine, Holon Institute of Technology, Israel
| | - Emeline Lejeune
- Department of Biomedical Informatics, Rouen University Hospital, France
- LIMICS Laboratory of Medical Informatics and Knowledge Engineering in e-Health, INSERM U1142, Sorbonne Université, France
| | - Flavien Disson
- Department of Biomedical Informatics, Rouen University Hospital, France
- LIMICS Laboratory of Medical Informatics and Knowledge Engineering in e-Health, INSERM U1142, Sorbonne Université, France
| | - Badisse Dahamna
- Department of Biomedical Informatics, Rouen University Hospital, France
- LIMICS Laboratory of Medical Informatics and Knowledge Engineering in e-Health, INSERM U1142, Sorbonne Université, France
| | | | | | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, France
- LIMICS Laboratory of Medical Informatics and Knowledge Engineering in e-Health, INSERM U1142, Sorbonne Université, France
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13
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Gehanno JF, Grosjean J, Darmoni SJ, Rollin L. Reliability of citations of medRxiv preprints in articles published on COVID-19 in the world leading medical journals. PLoS One 2022; 17:e0264661. [PMID: 35947594 PMCID: PMC9365132 DOI: 10.1371/journal.pone.0264661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction Preprints have been widely cited during the COVID-19 pandemics, even in the major medical journals. However, since subsequent publication of preprint is not always mentioned in preprint repositories, some may be inappropriately cited or quoted. Our objectives were to assess the reliability of preprint citations in articles on COVID-19, to the rate of publication of preprints cited in these articles and to compare, if relevant, the content of the preprints to their published version. Methods Articles published on COVID in 2020 in the BMJ, The Lancet, the JAMA and the NEJM were manually screened to identify all articles citing at least one preprint from medRxiv. We searched PubMed, Google and Google Scholar to assess if the preprint had been published in a peer-reviewed journal, and when. Published articles were screened to assess if the title, data or conclusions were identical to the preprint version. Results Among the 205 research articles on COVID published by the four major medical journals in 2020, 60 (29.3%) cited at least one medRxiv preprint. Among the 182 preprints cited, 124 were published in a peer-reviewed journal, with 51 (41.1%) before the citing article was published online and 73 (58.9%) later. There were differences in the title, the data or the conclusion between the preprint cited and the published version for nearly half of them. MedRxiv did not mentioned the publication for 53 (42.7%) of preprints. Conclusions More than a quarter of preprints citations were inappropriate since preprints were in fact already published at the time of publication of the citing article, often with a different content. Authors and editors should check the accuracy of the citations and of the quotations of preprints before publishing manuscripts that cite them.
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Affiliation(s)
- Jean-Francois Gehanno
- Department of Occupational Medicine, Rouen University Hospital, Rouen, France
- Inserm, Rouen University, Sorbonne University, University of Paris 13, Laboratory of Medical Informatics and Knowledge Engineering in e-Health, LIMICS, Paris, France
- * E-mail:
| | - Julien Grosjean
- Inserm, Rouen University, Sorbonne University, University of Paris 13, Laboratory of Medical Informatics and Knowledge Engineering in e-Health, LIMICS, Paris, France
- Department of Biomedical Informatics, Rouen University Hospital, Rouen France
| | - Stefan J. Darmoni
- Inserm, Rouen University, Sorbonne University, University of Paris 13, Laboratory of Medical Informatics and Knowledge Engineering in e-Health, LIMICS, Paris, France
- Department of Biomedical Informatics, Rouen University Hospital, Rouen France
| | - Laetitia Rollin
- Department of Occupational Medicine, Rouen University Hospital, Rouen, France
- Inserm, Rouen University, Sorbonne University, University of Paris 13, Laboratory of Medical Informatics and Knowledge Engineering in e-Health, LIMICS, Paris, France
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Benis A, Grosjean J, Billey K, Gustavo Montanha Meireles Martins J, Dornauer V, Crisan-Vida M, Hackl WO, Stoicu-Tivadar L, Darmoni S. Medical Informatics and Digital Health Multilingual Ontology (MIMO): a tool to improve international collaborations. Int J Med Inform 2022; 167:104860. [PMID: 36084537 PMCID: PMC9582075 DOI: 10.1016/j.ijmedinf.2022.104860] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/10/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022]
Abstract
Background Even if English is the leading language for international communication, it is essential to keep in mind that research runs at the local level by local teams generally communicating in their local/national language, especially in Europe among European projects. Objective Therefore, the European Federation for Medical Informatics - Working Group on Health Informatics for Inter-regional Cooperation” has one objective: To develop a multilingual ontology focusing on Health Informatics and Digital Health as a collaboration tool that improves international and, in particular, European collaborations. Results We have developed the Medical Informatics and Digital Health Multilingual Ontology (MIMO). Hosted on the Health Terminology/Ontology Portal (HeTOP), MIMO contains around 1,000 concepts, 460 MeSH Descriptors, 220 MeSH Concepts, and more than 300 newly created concepts. MIMO is continuously updated to comprise as recent as possible concepts and their translations in more than 30 languages. Moreover, the MIMO’s development team constantly improves MIMO content and supporting information. Thus, during workshop discussions and one-on-one exchanges, the MIMO team has collected domain experts’ opinions about the community’s interests and suggestions for future enhancements. Moreover, MIMO will be integrated to support the annotation and categorization of research products into the HosmartAI European project involving more than 20 countries around Europe and worldwide. Conclusion MIMO is hosted by HeTOP (Health Terminology/Ontology Portal), which integrates 100 terminologies and ontologies in 55 languages. MIMO is freely available online. MIMO is portable to other knowledge platforms as part of MIMO’s main aims to facilitate communication between medical librarians, translators, and researchers as well as to support students’ self-learning.
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Zana I, Grosjean J, Letord C, Charlet J, Rio J, Darmoni ETN, Duclos C, Darmoni SJ. Qualitative Evaluation of a Drug Terminology Server. Stud Health Technol Inform 2022; 290:1002-1003. [PMID: 35673176 DOI: 10.3233/shti220238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Although the drug is finished, identifiable, there is no universally accepted standard for naming them. The objective of this work is to evaluate qualitatively the HeTOP drug terminology server by two categories of students: (a) pharmacy students and (b) a control group. METHODS A formal evaluation was built to measure the perception of users about the HeTOP drug server, using the three mains questions about "teaching interest", "skill interest" (or competence) and "ergonomics". RESULTS The three pharmacy student subgroups gave the best and the worst score to the same categories. CONCLUSION All three criteria are rated above 6.5 out of 10. The HeTOP drug terminology server is freely available to "non drug" specialists (URL: www.hetop.eu/hetop/drugs/).
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Affiliation(s)
- Ilan Zana
- Faculty of pharmacy, Université de Paris, Paris
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, 76031 Rouen Cedex, France
- Sorbonne Université, INSERM, Université Paris 13, LIMICS, Paris, France
| | - Catherine Letord
- Department of Biomedical Informatics, Rouen University Hospital, 76031 Rouen Cedex, France
- Sorbonne Université, INSERM, Université Paris 13, LIMICS, Paris, France
| | - Jean Charlet
- Sorbonne Université, INSERM, Université Paris 13, LIMICS, Paris, France
- Assistance Publique-Hôpitaux de Paris, DRCI, Paris, France
| | - Julien Rio
- Department of Biomedical Informatics, Rouen University Hospital, 76031 Rouen Cedex, France
| | | | - Catherine Duclos
- Sorbonne Université, INSERM, Université Paris 13, LIMICS, Paris, France
- Assistance Publique-Hôpitaux de Paris, DRCI, Paris, France
| | - Stéfan J Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, 76031 Rouen Cedex, France
- Sorbonne Université, INSERM, Université Paris 13, LIMICS, Paris, France
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Grosjean J, Pressat-Laffouilhère T, Ndangang M, Leroy JP, Darmoni SJ. Using Clinical Data Warehouse to Optimize the Vaccination Strategy Against COVID-19: A Use Case in France. Stud Health Technol Inform 2022; 290:150-153. [PMID: 35672989 DOI: 10.3233/shti220050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Clinical Data Warehouses (CDW) are gold mines and may be useful to manage the COVID-19 outbreak. This article details the use of CDW in order to retrieve patients for vaccination purposes. A list of 34 diseases (or conditions) was published by French Health Authorities to target individuals at a high risk of developing a severe form of COVID. Using a multilevel search engine, 23 queries were built based on structured or unstructured data using natural language processing features. The Diagnosis Related Group coding system was used alone in three queries (13.0%), coupled with unstructured data in four queries (17.4%), and unstructured data were used alone in 16 queries (69.6%). Eleven diseases (conditions) were too broad to be translated into queries. Finally, 6,006 unique re-identified patients were retrieved. This use case demonstrates the usefulness of the Rouen University Hospital CDW in retrieving patients for other purposes than translational research.
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Affiliation(s)
- Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, U1142, INSERM, Sorbonne Université & Sorbonne Paris Nord, Paris, France
| | - Thibaut Pressat-Laffouilhère
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratoire LITIS EA4108, Rouen Normandie University, France
| | - Marie Ndangang
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
| | - Jean-Philippe Leroy
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
| | - Stéfan J Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, U1142, INSERM, Sorbonne Université & Sorbonne Paris Nord, Paris, France
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Pressat Laffouilhère T, Grosjean J, Bénichou J, Darmoni SJ, Soualmia LF. OntoBioStat: Supporting Causal Diagram Design and Analysis. Stud Health Technol Inform 2022; 294:302-306. [PMID: 35612081 DOI: 10.3233/shti220463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Suitable causal inference in biostatistics can be best achieved by knowledge representation thanks to causal diagrams or directed acyclic graphs. However, necessary and sufficient causes are not easily represented. Since existing ontologies do not fill this gap, we designed OntoBioStat in order to enable covariate selection support based on causal relation representations. OntoBioStat automatic ontological causal diagram construction and inferences are detailed in this study. OntoBioStat inferences are allowed by Semantic Web Rule Language rules and axioms. First, statements made by the users include outcome, exposure, covariate, and causal relation specification. Then, reasoning enable automatic construction using generic instances of Meta_Variable and Necessary_Variable classes. Finally, inferred classes highlighted potential bias such as confounder-like. Ontological causal diagram built with OntoBioStat was compared to a standard causal diagram (without OntoBioStat) in a theoretical study. It was found that confounding and bias were not completely identified by the standard causal diagram, and erroneous covariate sets were provided. Further research is needed in order to make OntoBioStat more usable.
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Affiliation(s)
- Thibaut Pressat Laffouilhère
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- CHU Rouen, Department of Biostatistics, F-76000 Rouen, France
- Normandie Univ, UNIROUEN, LITIS-TIBS EA 4108, F-76000 Rouen, France
| | - Julien Grosjean
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
| | - Jacques Bénichou
- CHU Rouen, Department of Biostatistics, F-76000 Rouen, France
- INSERM U1018, CESP, Université Paris-Saclay, Paris, France
| | - Stefan J Darmoni
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
| | - Lina F Soualmia
- Normandie Univ, UNIROUEN, LITIS-TIBS EA 4108, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
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Duclos C, Griffon N, Daniel C, Bouzillé G, Delamarre D, Darmoni S, Toubiana L, Grosjean J. Reliability of Drug-Drug Interaction Measurement on Real-Word Data: The ReMIAMes Project. Stud Health Technol Inform 2022; 294:151-152. [PMID: 35612045 DOI: 10.3233/shti220425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The ReMIAMes project proposes a methodological framework to provide a reliable and reproducible measurement of the frequency of drug-drug interactions (DDI) when performed on real-world data. This framework relies on (i) a fine-grained and contextualized definition of DDIs, (ii) a shared minimum information model to select the appropriate data for the correct interpretation of potential DDIs, (iii) an ontology-based inference module able to handle missing data to classify prescription lines with potential DDIs, (iv) a report generator giving the value of the measurement and explanations when potential false positive are detected due to a lack of available data. All the tools developed are intended to be publicly shared under open license.
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Affiliation(s)
- Catherine Duclos
- Sorbonne Université, Université Sorbonne Paris Nord, INSERM, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, F-75006 Paris, France
| | - Nicolas Griffon
- Sorbonne Université, Université Sorbonne Paris Nord, INSERM, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, F-75006 Paris, France
- Innovation and Data, IT Department, AP-HP, Paris, France
| | - Christel Daniel
- Sorbonne Université, Université Sorbonne Paris Nord, INSERM, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, F-75006 Paris, France
- Innovation and Data, IT Department, AP-HP, Paris, France
| | - Guillaume Bouzillé
- Inserm, Laboratoire Traitement du Signal et de l'Image - UMR 1099, Centre Hospitalier Universitaire de Rennes, Université de Rennes 1, Rennes, France
| | - Denis Delamarre
- Inserm, Laboratoire Traitement du Signal et de l'Image - UMR 1099, Centre Hospitalier Universitaire de Rennes, Université de Rennes 1, Rennes, France
| | - Stefan Darmoni
- Sorbonne Université, Université Sorbonne Paris Nord, INSERM, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, F-75006 Paris, France
- Department of Digital Health, Rouen University Hospital, France
| | - Laurent Toubiana
- Sorbonne Université, Université Sorbonne Paris Nord, INSERM, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, F-75006 Paris, France
| | - Julien Grosjean
- Sorbonne Université, Université Sorbonne Paris Nord, INSERM, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, F-75006 Paris, France
- Department of Digital Health, Rouen University Hospital, France
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19
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Lelong R, Dahamna B, Berthelot H, Duville W, Letord C, Grosjean J, Duclos C. When Context Matters for Credible Measurement of Drug-Drug Interactions Based on Real-World Data. Stud Health Technol Inform 2022; 294:38-42. [PMID: 35612012 DOI: 10.3233/shti220392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The frequency of potential drug-drug interactions (DDI) in published studies on real world data considerably varies due to the methodological framework. Contextualization of DDI has a proven effect in limiting false positives. In this paper, we experimented with the application of various DDIs contexts elements to see their impact on the frequency of potential DDIs measured on the same set of prescription data collected in EDSaN, the clinical data warehouse of Rouen University Hospital. Depending on the context applied, the frequency of daily prescriptions with potential DDI ranged from 0.89% to 3.90%. Substance-level analysis accounted for 48% of false positives because it did not account for some drug-related attributes. Consideration of the patient's context could eliminate up to an additional 29% of false positives.
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Affiliation(s)
- Romain Lelong
- Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, SorbonneUniversité, INSERM, F-93000, Bobigny, France.,Department of Digital Health, Rouen University Hospital, Rouen, France
| | - Badisse Dahamna
- Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, SorbonneUniversité, INSERM, F-93000, Bobigny, France.,Department of Digital Health, Rouen University Hospital, Rouen, France
| | - Hélène Berthelot
- Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, SorbonneUniversité, INSERM, F-93000, Bobigny, France
| | - Willy Duville
- Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, SorbonneUniversité, INSERM, F-93000, Bobigny, France
| | - Catherine Letord
- Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, SorbonneUniversité, INSERM, F-93000, Bobigny, France.,Department of Digital Health, Rouen University Hospital, Rouen, France
| | - Julien Grosjean
- Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, SorbonneUniversité, INSERM, F-93000, Bobigny, France.,Department of Digital Health, Rouen University Hospital, Rouen, France
| | - Catherine Duclos
- Université Sorbonne Paris Nord, Laboratoire d'Informatique Médicale et d'Ingénierie des connaissances en e-Santé, LIMICS, SorbonneUniversité, INSERM, F-93000, Bobigny, France
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20
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Dusenne M, Billey K, Desgrippes F, Benis A, Darmoni SJ, Grosjean J. WikiMeSH: Multi Lingual MeSH Translations via Wikipedia. Stud Health Technol Inform 2022; 294:403-404. [PMID: 35612105 DOI: 10.3233/shti220483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVE The aim of this paper is to propose an extended translation of the MeSH thesaurus based on Wikipedia pages. METHODS A mapping was realized between each MeSH descriptor (preferred terms and synonyms) and corresponding Wikipedia pages. RESULTS A tool called "WikiMeSH" has been developed. Among the top 20 languages of this study, seven have currently no MeSH translations: Arabic, Catalan, Farsi (Iran), Mandarin Chinese, Korean, Serbian, and Ukrainian. For these seven languages, WikiMeSH is proposing a translation for 47% for Arabic to 34% for Serbian. CONCLUSION WikiMeSH is an interesting tool to translate the MeSH thesaurus and other health terminologies and ontologies based on a mapping to Wikipedia pages.
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Affiliation(s)
- Mikaël Dusenne
- Department of Digital Health, Rouen University Hospital, France
| | - Kévin Billey
- Department of Digital Health, Rouen University Hospital, France
| | | | - Arriel Benis
- Faculty of Industrial Engineering and Technology Management, Holon Institute of Technology, Holon, Israel
| | - Stéfan Jacques Darmoni
- Department of Digital Health, Rouen University Hospital, France.,Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
| | - Julien Grosjean
- Department of Digital Health, Rouen University Hospital, France.,Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé (LIMICS), U1142, INSERM, Sorbonne Université, Paris, France
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21
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Bouteiller F, Pulido M, Brain E, Paillaud E, Grosjean J, Mina W, Caillet P, Tassy L, Soubeyran P, Rifi N, Falandry C, Carola E. Feasibility of palbociclib in women aged 70 and older with resistant and/or pretreated advanced breast cancer in the PALOMAGE study. Rev Epidemiol Sante Publique 2022. [DOI: 10.1016/j.respe.2022.03.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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22
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Pressat-Laffouilhère T, Balayé P, Dahamna B, Lelong R, Billey K, Darmoni SJ, Grosjean J. Correction to: Evaluation of Doc'EDS: a French semantic search tool to query health documents from a clinical data warehouse. BMC Med Inform Decis Mak 2022; 22:107. [PMID: 35459201 PMCID: PMC9027664 DOI: 10.1186/s12911-022-01839-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Thibaut Pressat-Laffouilhère
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France.,LITIS EA4108, Rouen University, Normandy, France
| | - Pierre Balayé
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France
| | - Badisse Dahamna
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France.,LIMICS U1142 INSERM, Sorbonne Université & Sorbonne Paris Nord, Paris, France
| | - Romain Lelong
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France.,LIMICS U1142 INSERM, Sorbonne Université & Sorbonne Paris Nord, Paris, France
| | - Kévin Billey
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France.,LITIS EA4108, Rouen University, Normandy, France
| | - Stéfan J Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France.,LIMICS U1142 INSERM, Sorbonne Université & Sorbonne Paris Nord, Paris, France
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France. .,LIMICS U1142 INSERM, Sorbonne Université & Sorbonne Paris Nord, Paris, France.
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23
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Gourcerol G, Melchior C, Wuestenberghs F, Desprez C, Prevost G, Grosjean J, Leroi AM, Tavolacci MP. Delayed gastric emptying as an independent predictor of mortality in gastroparesis. Aliment Pharmacol Ther 2022; 55:867-875. [PMID: 35187671 DOI: 10.1111/apt.16827] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/01/2021] [Accepted: 02/03/2022] [Indexed: 12/18/2022]
Abstract
BACKGROUND Whether gastroparesis is associated with a shortened life expectancy remains uncertain as no systematic study has evaluated the impact of gastroparesis on mortality, based on gastric emptying (GE) tests. AIM This study aimed to assess whether delayed GE was predictive of mortality. METHODS GE was measured using a 13C-octanoic acid breath test in 1563 consecutive patients. Delayed GE at baseline defined the gastroparesis group. Patients were followed up for a mean of 8.9 years, yielding 13 466 patients per year. Mortality was assessed using the French CepiDc database with data from local civil registries. The cause of death was determined from medical records. Mortality rates were assessed using the Kaplan-Meier method and hazard ratio (HR) was calculated using the Cox regression model. RESULTS Age and symptoms severity were not different among patients with normal GE (n = 1179) and with delayed GE (n = 384) while diabetes mellitus was more frequent in the gastroparesis group. Kaplan-Meier analysis showed increased mortality in the gastroparesis group compared to patients with normal GE. Cox regression model identified delayed GE as independently associated with increased mortality (HR = 1.63[1.09-2.42]; P = 0.02). Other independent factors associated with increased mortality included age, male sex, and diabetes. No difference was observed between groups for the cause of death, with cancer and cardiovascular disease being the leading causes. CONCLUSION This study has shown that gastroparesis, diagnosed on GE tests, was associated with increased mortality, independently of age, sex, BMI or diabetes status (NCT04918329).
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Affiliation(s)
- Guillaume Gourcerol
- Digestive Physiology Department, Rouen University Hospital, Rouen, France
- Clinical Investigation Centre, CIC-CRB 1404, Rouen University Hospital, Rouen, France
- Nutrition, Brain and Gut Laboratory, INSERM Unit 1073, Rouen University Hospital, Rouen, France
| | - Chloé Melchior
- Clinical Investigation Centre, CIC-CRB 1404, Rouen University Hospital, Rouen, France
- Hepato-Gastroenterology Department, Rouen University Hospital, Rouen, France
| | - Fabien Wuestenberghs
- Digestive Physiology Department, Rouen University Hospital, Rouen, France
- Nutrition, Brain and Gut Laboratory, INSERM Unit 1073, Rouen University Hospital, Rouen, France
| | - Charlotte Desprez
- Digestive Physiology Department, Rouen University Hospital, Rouen, France
- Nutrition, Brain and Gut Laboratory, INSERM Unit 1073, Rouen University Hospital, Rouen, France
| | - Gaëtan Prevost
- Clinical Investigation Centre, CIC-CRB 1404, Rouen University Hospital, Rouen, France
- Endocrinology Department, Rouen University Hospital, Rouen, France
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France
| | - Anne Marie Leroi
- Digestive Physiology Department, Rouen University Hospital, Rouen, France
- Clinical Investigation Centre, CIC-CRB 1404, Rouen University Hospital, Rouen, France
- Nutrition, Brain and Gut Laboratory, INSERM Unit 1073, Rouen University Hospital, Rouen, France
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24
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Douze L, Pelayo S, Messaadi N, Grosjean J, Kerdelhué G, Marcilly R. Designing Formulae for Ranking Search Results: Mixed Methods Evaluation Study. JMIR Hum Factors 2022; 9:e30258. [PMID: 35333180 PMCID: PMC8994140 DOI: 10.2196/30258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/07/2021] [Accepted: 01/09/2022] [Indexed: 11/20/2022] Open
Abstract
Background A major factor in the success of any search engine is the relevance of the search results; a tool should sort the search results to present the most relevant documents first. Assessing the performance of the ranking formula is an important part of search engine evaluation. However, the methods currently used to evaluate ranking formulae mainly collect quantitative data and do not gather qualitative data, which help to understand what needs to be improved to tailor the formulae to their end users. Objective This study aims to evaluate 2 different parameter settings of the ranking formula of LiSSa (the French acronym for scientific literature in health care; Department of Medical Informatics and Information), a tool that provides access to health scientific literature in French, to adapt the formula to the needs of the end users. Methods To collect quantitative and qualitative data, user tests were carried out with representative end users of LiSSa: 10 general practitioners and 10 registrars. Participants first assessed the relevance of the search results and then rated the ranking criteria used in the 2 formulae. Verbalizations were analyzed to characterize each criterion. Results A formula that prioritized articles representing a consensus in the field was preferred. When users assess an article’s relevance, they judge its topic, methods, and value in clinical practice. Conclusions Following the evaluation, several improvements were implemented to give more weight to articles that match the search topic and to downgrade articles that have less informative or scientific value for the reader. Applying a qualitative methodology generates valuable user inputs to improve the ranking formula and move toward a highly usable search engine.
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Affiliation(s)
- Laura Douze
- Inserm, Centre d'Investigation Clinique pour les Innovations Technologiques 1403, Institut Coeur-Poumon, Lille, France.,Unité Labellisée de Recherche 2694 - METRICS : Évaluation des technologies de santé et des pratiques médicales, Univ. Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Sylvia Pelayo
- Inserm, Centre d'Investigation Clinique pour les Innovations Technologiques 1403, Institut Coeur-Poumon, Lille, France.,Unité Labellisée de Recherche 2694 - METRICS : Évaluation des technologies de santé et des pratiques médicales, Univ. Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Nassir Messaadi
- Département de médecine générale, Univ. Lille, Lille, France
| | - Julien Grosjean
- Département d'Informatique et d'Information Médicales, Centre hospitalier universitaire de Rouen, Rouen, France.,Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, Inserm 1142, Sorbonne Paris Nord University, Sorbonne Paris Cité, Villetaneuse, France
| | - Gaétan Kerdelhué
- Département d'Informatique et d'Information Médicales, Centre hospitalier universitaire de Rouen, Rouen, France.,Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, Inserm 1142, Sorbonne Paris Nord University, Sorbonne Paris Cité, Villetaneuse, France
| | - Romaric Marcilly
- Inserm, Centre d'Investigation Clinique pour les Innovations Technologiques 1403, Institut Coeur-Poumon, Lille, France.,Unité Labellisée de Recherche 2694 - METRICS : Évaluation des technologies de santé et des pratiques médicales, Univ. Lille, Centre Hospitalier Universitaire de Lille, Lille, France
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25
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Pressat-Laffouilhère T, Balayé P, Dahamna B, Lelong R, Billey K, Darmoni SJ, Grosjean J. Evaluation of Doc'EDS: a French semantic search tool to query health documents from a clinical data warehouse. BMC Med Inform Decis Mak 2022; 22:34. [PMID: 35135538 PMCID: PMC8822768 DOI: 10.1186/s12911-022-01762-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Unstructured data from electronic health records represent a wealth of information. Doc'EDS is a pre-screening tool based on textual and semantic analysis. The Doc'EDS system provides a graphic user interface to search documents in French. The aim of this study was to present the Doc'EDS tool and to provide a formal evaluation of its semantic features. METHODS Doc'EDS is a search tool built on top of the clinical data warehouse developed at Rouen University Hospital. This tool is a multilevel search engine combining structured and unstructured data. It also provides basic analytical features and semantic utilities. A formal evaluation was conducted to measure the impact of Natural Language Processing algorithms. RESULTS Approximately 18.1 million narrative documents are stored in Doc'EDS. The formal evaluation was conducted in 5000 clinical concepts that were manually collected. The F-measures of negative concepts and hypothetical concepts were respectively 0.89 and 0.57. CONCLUSION In this formal evaluation, we have shown that Doc'EDS is able to deal with language subtleties to enhance an advanced full text search in French health documents. The Doc'EDS tool is currently used on a daily basis to help researchers to identify patient cohorts thanks to unstructured data.
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Affiliation(s)
- Thibaut Pressat-Laffouilhère
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France.,LITIS EA4108, Rouen University, Normandy, France
| | - Pierre Balayé
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France
| | - Badisse Dahamna
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France.,LIMICS U1142 INSERM, Sorbonne Université & Sorbonne Paris Nord, Paris, France
| | - Romain Lelong
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France.,LIMICS U1142 INSERM, Sorbonne Université & Sorbonne Paris Nord, Paris, France
| | - Kévin Billey
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France.,LITIS EA4108, Rouen University, Normandy, France
| | - Stéfan J Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France.,LIMICS U1142 INSERM, Sorbonne Université & Sorbonne Paris Nord, Paris, France
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France. .,LIMICS U1142 INSERM, Sorbonne Université & Sorbonne Paris Nord, Paris, France.
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26
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Lelong R, Dahamna B, Leguillon R, Grosjean J, Letord C, Darmoni SJ, Soualmia LF. Assisting Data Retrieval with a Drug Knowledge Graph. Stud Health Technol Inform 2022; 289:260-263. [PMID: 35062142 DOI: 10.3233/shti210909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The Normandy health data warehouse EDSaN integrates the medication orders from the University Hospital of Rouen (France). This study aims at describing the design and the evaluation of an information retrieval system founded on a complex and semantically augmented knowledge graph dedicated to EDSaN drugs' prescriptions. The system is intended to help the selection of drugs in the search process by health professionals. The manual evaluation of the relevance of the returned drugs showed encouraging results as expected. A deeper analysis in order to improve the ranking method is needed and will be performed in a future work.
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Affiliation(s)
- Romain Lelong
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
| | - Badisse Dahamna
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
| | - Romain Leguillon
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
| | - Julien Grosjean
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
| | - Catherine Letord
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
| | - Stéfan J Darmoni
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
| | - Lina F Soualmia
- LIMICS U1142, Sorbonne Université, Paris, France
- Normandie Univ, UNIROUEN, TIBS-LITIS EA 4108, F-76000 Rouen, France
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27
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Morin A, Pressat-Laffouilhere T, Sarazin M, Lagarde J, Roue-Jagot C, Olivieri P, Paquet C, Cognat E, Dumurgier J, Pasquier F, Lebouvier T, Ceccaldi M, Godefroy O, Martinaud O, Grosjean J, Zarea A, Maltête D, Wallon D. Telemedicine in French Memory Clinics During the COVID-19 Pandemic. J Alzheimers Dis 2022; 86:525-530. [PMID: 34974434 DOI: 10.3233/jad-215459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This multicenter study was conducted in French memory clinics during the first COVID-2019 lockdown (March-May 2020). The objective was to evaluate the effect of a telemedicine consultation on treatment modification in dementia care. Among 874 patients who had a telemedicine consultation, 103 (10.7%) had treatment modifications, in particular those living with a relative or diagnosed with Alzheimer's disease. A control group of patients referred March-May 2019 was also included. Treatment modification rate was similar between periods with an adjusted percentage difference of -4% (p = 0.27). Telemedicine consultations allowed treatment modifications with only a minor short-term negative impact on therapeutic strategies.
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Affiliation(s)
- Alexandre Morin
- CHU Rouen, Department of Neurology and CIC-CRB1404, Rouen, France
| | | | - Marie Sarazin
- Department of Neurology of Memory and Language, GHU Paris Psychiatry and Neurosciences, Hôpital Sainte Anne, Paris, France.,Université de Paris, Paris, France.,Université Paris-Saclay, BioMaps, CEA, CNRS, Inserm, Orsay, France
| | - Julien Lagarde
- Department of Neurology of Memory and Language, GHU Paris Psychiatry and Neurosciences, Hôpital Sainte Anne, Paris, France.,Université de Paris, Paris, France.,Université Paris-Saclay, BioMaps, CEA, CNRS, Inserm, Orsay, France
| | - Carole Roue-Jagot
- Department of Neurology of Memory and Language, GHU Paris Psychiatry and Neurosciences, Hôpital Sainte Anne, Paris, France.,Université de Paris, Paris, France.,Université Paris-Saclay, BioMaps, CEA, CNRS, Inserm, Orsay, France
| | - Pauline Olivieri
- Department of Neurology of Memory and Language, GHU Paris Psychiatry and Neurosciences, Hôpital Sainte Anne, Paris, France.,Université de Paris, Paris, France.,Université Paris-Saclay, BioMaps, CEA, CNRS, Inserm, Orsay, France
| | - Claire Paquet
- Université de Paris, Cognitive Neurology Center, Lariboisiere - Fernand Widal Hospital, APHP, Paris, France
| | - Emmanuel Cognat
- Université de Paris, Cognitive Neurology Center, Lariboisiere - Fernand Widal Hospital, APHP, Paris, France
| | - Julien Dumurgier
- Université de Paris, Cognitive Neurology Center, Lariboisiere - Fernand Widal Hospital, APHP, Paris, France
| | | | | | - Matthieu Ceccaldi
- Department of Neurology, Marseille University Hospital, APHM, Marseille, France
| | - Olivier Godefroy
- Department of Neurology, Amiens University Hospital, Amiens, France
| | - Olivier Martinaud
- Department of Neurology, Caen University Hospital, Caen, France.,Normandie UNIV, UNICAEN, PSL Research University, EPHE, INSERM, CHU de Caen, Neuropsychologie et Imagerie de la mémoire humaine, Caen, France
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France.,LIMICS, INSERM U1142, Sorbonne Université, Paris, France
| | - Aline Zarea
- CHU Rouen, Department of Neurology and CIC-CRB1404, Rouen, France.,Normandie Univ, UNIROUEN, Inserm U1245 and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - David Maltête
- CHU Rouen, Department of Neurology and CIC-CRB1404, Rouen, France
| | - David Wallon
- CHU Rouen, Department of Neurology and CIC-CRB1404, Rouen, France.,Normandie Univ, UNIROUEN, Inserm U1245 and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Rouen, France
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28
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Morin A, Pressat‐Laffouilhere T, Sarazin M, Lagarde J, Roue‐Jagot C, Paquet C, Cognat E, Dumurgier J, Pasquier F, Lebouvier T, Ceccaldi M, Godefroy O, Martinaud O, Grosjean J, Zarea A, Maltête D, Wallon D. Telemedicine in French memory clinics during Covid‐19 crisis. Alzheimers Dement 2021. [PMCID: PMC9011636 DOI: 10.1002/alz.052037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background In early 2020, COVID‐19 outbreak struck France leading to a national lockdown between March 17th and May 11th. While standard in‐person medical consultation was complicated, telemedicine dramatically expanded. In order to evaluate the impact of this unpreceded situation on clinical practice and use of psychoactive drug in dementia care, we conducted a nationwide clinical prospective and retrospective study. Method During the lockdown period, telemedicine patients’ demographic and clinical data were retrospectively collected from 7 French memory clinics (telemedicine cohort). Clinical diagnoses, treatment changes, cognitive modifications since last consultations and living conditions during the lockdown were systematically retrieved. In Rouen site, we also included patients only reached by a secretary to propose a postponed visit after lockdown (no‐telemedicine cohort) and patients seen in 2019 during the same period of the year (Rouen‐2019). The primary outcome was any change in psychoactive drug and a specific analysis on sedative treatment increase was the secondary outcome, defined as any increase in the prescriptions of antipsychotics or benzodiazepines. Result The telemedicine cohort included 874 patients (73 from Rouen), while no‐telemedicine control cohort and Rouen‐2019 cohorts included respectively 86 and 234 patients (table 1). In the telemedicine cohort, treatments were modified for 10.7% of the patients with more treatment modification among the patients living with a relative (+5.8% (CI95% [0.2%; 11.4%] p=0.04) and among the patients with Alzheimer’s disease (+12.2% (CI95% [7.1%; 17.3%] p<0.001). When comparing therapeutic strategies in 2020 and 2019 for Rouen site, 24.6% of the patients had their treatment modified in 2020 and 12.4% in 2019. That difference was however not statically significant with an adjusted percentage difference of ‐4% (CI95% [‐10.8%; 3.4%] p=0.27, including the telemedicine and no‐telemedicine cohorts for 2020. Conclusion Telemedicine seems to have had only minor negative impacts on clinical practice in memory clinics.
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Affiliation(s)
- Alexandre Morin
- Department of Neurology, Rouen University Hospital, F‐76000, Rouen, FR Paris France
| | | | - Marie Sarazin
- Neurology of Memory and Language, Université Paris Descartes, Sorbonne Paris Cité, INSERM UMR S894, Centre Hospitalier Sainte Anne Paris France
- Université Paris‐Saclay, CEA, CNRS, Inserm, BioMaps Orsay France
| | - Julien Lagarde
- Université Paris‐Saclay, CEA, CNRS, Inserm, BioMaps Orsay France
- Neurologie de la Mémoire et du Langage, Université Paris Descartes, Sorbonne Paris Cité, INSERM UMR S894, Centre Hospitalier Sainte Anne Paris France
| | | | - Claire Paquet
- Université de Paris APHP GHU Nord Centre de Neurologie Cognitive Lariboisière Hospital INSERMU1144 Paris France
- Université Paris Diderot, INSERM U942, AP‐HP, Cognitive Neurology Center Paris France
- INSERM UMR‐S1144 Paris France
| | - Emmanuel Cognat
- INSERM UMR‐S942 Université Paris Diderot Paris France
- Cognitive Neurology Center, GH Saint‐Louis ‐ Lariboisière ‐ Fernand‐Widal, APHP Paris France
| | - Julien Dumurgier
- Paris Diderot University Paris France
- Cognitive Neurology Center, Hôpital Lariboisière‐Fernand Widal APHP Paris France
| | - Florence Pasquier
- INSERM 1172 Lille France
- Université de Lille Lille France
- CHU, CNR‐MAJ, Labex Distalz, LiCENDLille Lille France
| | - Thibaud Lebouvier
- INSERM U1172 / National Reference Centre for Young Onset Dementia / Neurology Department/DistAlz, University Hospital Lille France
- Univ. Lille, Inserm, CHU‐Lille, Lille Neuroscience & Cognition, F‐59000 Lille France
| | - Mathieu Ceccaldi
- Aix Marseille University Marseille France
- Memory Resource and Research Center of Marseille, CHU de Marseille, Hôpital de La Timone Marseille France
| | - Olivier Godefroy
- Memory Resource and Research Center of Amiens, CHU Amiens Picardie, Hôpital Nord Amiens France
- CHU Amiens Amiens France
| | | | | | - Aline Zarea
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Neurology and CNR‐MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine Rouen France
| | - David Maltête
- Rouen University Hospital, F‐76000, Rouen, FR Rouen France
| | - David Wallon
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Neurology and CNR‐MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine Rouen France
- CNR‐MAJ & Neurology, Rouen University Hospital Rouen France
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29
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Dezoteux F, El Mesbahi S, Tedbirt B, Grosjean J, Gautier S, Lannoy D, Nassar C, Tétart F, Staumont-Sallé D. Immunomodulatory or/and immunosuppressive drugs should not avoid skin test for the assessment of drug allergy. Br J Dermatol 2021; 186:742-744. [PMID: 34811738 DOI: 10.1111/bjd.20901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/25/2021] [Accepted: 11/17/2021] [Indexed: 12/01/2022]
Abstract
The use of immunomodulatory and/or immunosuppressive therapy (IT) is increasingly common in the management of chronic inflammatory disease. Skin reactions to any drug (IT or not) are not rare in these patients, justifying allergological investigations. The influence of IT on allergological tests for drugs is not clearly described. IT cannot be interrupted due to the underlying disease. The data assessing the benefit and the safety of allergological test for drug allergy in patients under IT are missing.
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Affiliation(s)
- F Dezoteux
- CHU Lille, Service de Dermatologie, F-59000, Lille, France.,Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, F-59000, Lille, France
| | - S El Mesbahi
- CHU Lille, Service de Dermatologie, F-59000, Lille, France
| | - B Tedbirt
- Clinique de dermatologie, CHU Rouen, Centre Erik Satie allergologie
| | - J Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France.,Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, U1142, INSERM, Sorbonne Université, Paris, France
| | - S Gautier
- CHU Lille, Centre régional de Pharmacovigilance, F-59000, Lille, France
| | - D Lannoy
- CHU Lille, Institut de Pharmacie, F-59000, Lille, France.,Univ. Lille, ULR7365 GRITA Groupe de Recherche sur les Formes Injectables et les Technologies Associées, F-59000, Lille, France
| | - C Nassar
- CHU Lille, Centre régional de Pharmacovigilance, F-59000, Lille, France
| | - F Tétart
- Clinique de dermatologie, CHU Rouen, Centre Erik Satie allergologie
| | - D Staumont-Sallé
- CHU Lille, Service de Dermatologie, F-59000, Lille, France.,Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, F-59000, Lille, France
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30
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Deroualle T, Dominique S, Monti F, Grosjean J, Darmoni S, Lequerré T, Vittecoq O. Rheumatologic manifestations of sarcoidosis and increased risk of spondyloarthritis occurrence. A retrospective single center case-control study. Joint Bone Spine 2021; 88:105247. [PMID: 34216754 DOI: 10.1016/j.jbspin.2021.105247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/22/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Tiffany Deroualle
- Department of Rheumatology & CIC/CRB 1404, Rouen University Hospital, Normandy, France
| | | | - Francesco Monti
- Department of Biostatistics, Rouen University Hospital, Normandy, France
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France; LIMICS U1142, Sorbonne University, Paris, France
| | - Stéfan Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France; LIMICS U1142, Sorbonne University, Paris, France
| | - Thierry Lequerré
- Department of Rheumatology & CIC/CRB 1404, Rouen University Hospital, Normandy, France
| | - Olivier Vittecoq
- Department of Rheumatology & CIC/CRB 1404, Rouen University Hospital, Normandy, France.
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31
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Karkampouna S, La Manna F, Benjak A, Kiener M, De Menna M, Zoni E, Grosjean J, Klima I, Garofoli A, Bolis M, Vallerga A, Theurillat J, De Filippo M, Genitsch V, Keller D, Booij T, Stirnimann C, Eng K, Sboner A, Ng C, Piscuoglio S, Gray P, Rubin M, Thalmann G, Kruithof-De J. Patient-derived xenografts and organoids model therapy response in prostate cancer. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)00805-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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Pressat Laffouilhère T, Grosjean J, Bénichou J, Darmoni SJ, Soualmia LF. Ontological Models Supporting Covariates Selection in Observational Studies. Stud Health Technol Inform 2021; 281:1095-1096. [PMID: 34042854 DOI: 10.3233/shti210361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In the context of causal inference, biostatisticians use causal diagrams to select covariates in order to build multivariate models. These diagrams represent datasets variables and their relations but have some limitations (representing interactions, bidirectional causal relations). The MetBrAYN project aims at building an ontological-based process to tackle these issues. The knowledge acquired by the biostatistician during a methodological consultation for a research question will be represented in a general ontology. In order to aggregate various forms of knowledge the ontology will act as a wrapper. Ontology-based causal diagrams will be semi-automatically built. Founded on inference rules, the global system will help biostatisticians to curate it and to visualize recommended covariates for their research question.
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Affiliation(s)
- Thibaut Pressat Laffouilhère
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- CHU Rouen, Department of Biostatistics, F-76000 Rouen, France
- Normandie Univ, UNIROUEN, LITIS EA 4108, F-76000 Rouen, France
| | - Julien Grosjean
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
| | | | - Stefan J Darmoni
- CHU Rouen, Department of Biomedical Informatics, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
| | - Lina F Soualmia
- Normandie Univ, UNIROUEN, LITIS EA 4108, F-76000 Rouen, France
- LIMICS U1142, Sorbonne Université, Paris, France
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33
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Tejedor I, Boulard C, Bauvin O, Grosjean J, Joly P, Tetart F. Évaluation de l’impact du bilan allergologique dans l’hypersensibilité aux produits de contraste iodés. Ann Dermatol Venereol 2020. [DOI: 10.1016/j.annder.2020.09.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Brain E, Grosjean J, Pulido M, Paillaud E, Carola E, Jovenin N, Guillem O, Chehimi M, Mina W, Caillet P, Tassy L, Falandry C, Rifi N, Vauthier J. Real-world analysis of patients’ clinical and geriatric characteristics aged ≥70 years with advanced breast cancer receiving palbociclib with endocrine therapy in the French cohort PALOMAGE. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)30568-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
Background: Childhood obesity (CO) has become a true epidemic and a subject of increasing publications. The aim of this study was to assess if the number of publications in that field increases over time in proportion to the epidemic, and also according to socioeconomic factors. Methods: A PubMed search was carried out to extract articles related to CO published between 1945 and 2017. Data were downloaded from PubMed and processed through a dedicated parser. Socioeconomic data were collected from international organizations. Results: Overall, 36,554 articles were retrieved among 3329 journals, one-third of them being concentrated in 44 journals. The annual growth rate of publications on CO was on average 11.6% per year between 1990 and 2016, whereas the growth rate of articles on pediatrics or of the total articles indexed in MEDLINE was 2.6% and 4.4%, respectively. The most productive countries were the United States (37.80%), the United Kingdom (6.24%), and Italy (4.56%). There was a significant relationship between publications on CO in a country and prevalence of CO in that country (p = 0.002) and between evolution of the number of publications and evolution of the Human Development Index (p = 0.01). Following exponential growth, CO publications reached a plateau in 2013, whereas publications targeted on obesity in infants continue to increase. Conclusions: Research on CO has risen markedly in the last two decades, with a higher growth rate than biomedical research overall, as a result of the worldwide obesity epidemic and also due to specific socioeconomic factors.
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Affiliation(s)
- Jean-Francois Gehanno
- 1 Sorbonne Université, Inserm, Université Paris 13, Laboratoire d'informatique Médicale et d'ingénierie des Connaissances en e-santé, LIMICS, Paris, France.,2 Department of Occupational and Environmental Medicine, Rouen University Hospital, Rouen, France
| | - Bogna Gehanno
- 3 Department of Pediatrics, LADAPT, Caudebec-lès-Elbeuf, Rouen, France
| | - Mathieu Schuers
- 1 Sorbonne Université, Inserm, Université Paris 13, Laboratoire d'informatique Médicale et d'ingénierie des Connaissances en e-santé, LIMICS, Paris, France.,4 Department of General Medicine, Rouen University Hospital, Rouen, France
| | - Julien Grosjean
- 1 Sorbonne Université, Inserm, Université Paris 13, Laboratoire d'informatique Médicale et d'ingénierie des Connaissances en e-santé, LIMICS, Paris, France.,5 Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
| | - Laetitia Rollin
- 1 Sorbonne Université, Inserm, Université Paris 13, Laboratoire d'informatique Médicale et d'ingénierie des Connaissances en e-santé, LIMICS, Paris, France.,2 Department of Occupational and Environmental Medicine, Rouen University Hospital, Rouen, France
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Kerdelhué G, Grosjean J, Lejeune E, Letord C, Darmoni S, Oviève JM, Martin L, Gedda M. Kinedoc, CISMeF et COVID-19 : la nécessité de référencer les brochures pédagogiques pour le patient. Kinésithérapie, la Revue 2020. [PMCID: PMC7218388 DOI: 10.1016/j.kine.2020.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gaétan Kerdelhué
- LIMICS INSERM U1142, Département de l’informatique et de l’information médicales (D2IM), Université de Rouen, Sorbonne Université, CHU de Rouen, Rouen, France
- Auteur correspondant : LIMICS INSERM U1142, Département de l’informatique et de l’information médicales (D2IM), Université de Rouen, Sorbonne Université, CHU de Rouen, Rouen, France.
| | - Julien Grosjean
- LIMICS INSERM U1142, Département de l’informatique et de l’information médicales (D2IM), Université de Rouen, Sorbonne Université, CHU de Rouen, Rouen, France
| | - Emeline Lejeune
- LIMICS INSERM U1142, Département de l’informatique et de l’information médicales (D2IM), Université de Rouen, Sorbonne Université, CHU de Rouen, Rouen, France
| | - Catherine Letord
- LIMICS INSERM U1142, Département de l’informatique et de l’information médicales (D2IM), Université de Rouen, Sorbonne Université, CHU de Rouen, Rouen, France
| | - Stéfan Darmoni
- LIMICS INSERM U1142, Département de l’informatique et de l’information médicales (D2IM), Université de Rouen, Sorbonne Université, CHU de Rouen, Rouen, France
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Karkampouna S, La Manna F, De Filippo M, De Menna M, Zoni E, Grosjean J, Klima I, Garofoli A, Genitsch V, Keller D, Booij T, Stirnimann C, Sboner A, Ng C, Piscuoglio S, Spahn M, Mark A, Thalmann G, Kruithof-De Julio M. Personalised organoid drug treatment and therapy resistance characterization based on novel BRCA2 prostate cancer xenograft of SPOP-like phenotype and microsatellite instability. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)33823-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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38
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Grosjean J, Billey K, Charlet J, Darmoni SJ. Manual Evaluation of the Automatic Mapping of International Classification of Diseases (ICD)-11 (in French). Stud Health Technol Inform 2020; 270:1335-1336. [PMID: 32570646 DOI: 10.3233/shti200429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A lexical method was used to map ICD-11 to the terminologies included in the HeTOP server. About half of ICD-11 codes (47.76%) were mapped to at least one concept. The developed tool reached a global precision of 0.98 and a recall of 0.66. Lexical methods are powerful methods to map health terminologies. Supervised and manual mapping is still necessary to complete the mapping.
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Affiliation(s)
- Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France
- LIMICS U1142 INSERM, Sorbonne Université, Paris & Rouen University, France
| | - Kévin Billey
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France
- LITIS EA4108, Rouen University, France
| | - Jean Charlet
- LIMICS U1142 INSERM, Sorbonne Université, Paris & Rouen University, France
- Assistance Publique-Hôpitaux de Paris, DRCI, Paris, France
| | - Stefan J Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, Normandy, France
- LIMICS U1142 INSERM, Sorbonne Université, Paris & Rouen University, France
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39
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Massonnaud CR, Kerdelhué G, Grosjean J, Lelong R, Griffon N, Darmoni SJ. Identification of the Best Semantic Expansion to Query PubMed Through Automatic Performance Assessment of Four Search Strategies on All Medical Subject Heading Descriptors: Comparative Study. JMIR Med Inform 2020; 8:e12799. [PMID: 32496201 PMCID: PMC7303830 DOI: 10.2196/12799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/20/2020] [Accepted: 03/23/2020] [Indexed: 12/04/2022] Open
Abstract
Background With the continuous expansion of available biomedical data, efficient and effective information retrieval has become of utmost importance. Semantic expansion of queries using synonyms may improve information retrieval. Objective The aim of this study was to automatically construct and evaluate expanded PubMed queries of the form “preferred term”[MH] OR “preferred term”[TIAB] OR “synonym 1”[TIAB] OR “synonym 2”[TIAB] OR …, for each of the 28,313 Medical Subject Heading (MeSH) descriptors, by using different semantic expansion strategies. We sought to propose an innovative method that could automatically evaluate these strategies, based on the three main metrics used in information science (precision, recall, and F-measure). Methods Three semantic expansion strategies were assessed. They differed by the synonyms used to build the queries as follows: MeSH synonyms, Unified Medical Language System (UMLS) mappings, and custom mappings (Catalogue et Index des Sites Médicaux de langue Française [CISMeF]). The precision, recall, and F-measure metrics were automatically computed for the three strategies and for the standard automatic term mapping (ATM) of PubMed. The method to automatically compute the metrics involved computing the number of all relevant citations (A), using National Library of Medicine indexing as the gold standard (“preferred term”[MH]), the number of citations retrieved by the added terms (”synonym 1“[TIAB] OR ”synonym 2“[TIAB] OR …) (B), and the number of relevant citations retrieved by the added terms (combining the previous two queries with an “AND” operator) (C). It was possible to programmatically compute the metrics for each strategy using each of the 28,313 MeSH descriptors as a “preferred term,” corresponding to 239,724 different queries built and sent to the PubMed application program interface. The four search strategies were ranked and compared for each metric. Results ATM had the worst performance for all three metrics among the four strategies. The MeSH strategy had the best mean precision (51%, SD 23%). The UMLS strategy had the best recall and F-measure (41%, SD 31% and 36%, SD 24%, respectively). CISMeF had the second best recall and F-measure (40%, SD 31% and 35%, SD 24%, respectively). However, considering a cutoff of 5%, CISMeF had better precision than UMLS for 1180 descriptors, better recall for 793 descriptors, and better F-measure for 678 descriptors. Conclusions This study highlights the importance of using semantic expansion strategies to improve information retrieval. However, the performances of a given strategy, relatively to another, varied greatly depending on the MeSH descriptor. These results confirm there is no ideal search strategy for all descriptors. Different semantic expansions should be used depending on the descriptor and the user’s objectives. Thus, we developed an interface that allows users to input a descriptor and then proposes the best semantic expansion to maximize the three main metrics (precision, recall, and F-measure).
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Affiliation(s)
- Clément R Massonnaud
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, U1142, INSERM, Sorbonne Université, Paris, France
| | - Gaétan Kerdelhué
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, U1142, INSERM, Sorbonne Université, Paris, France
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, U1142, INSERM, Sorbonne Université, Paris, France
| | - Romain Lelong
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, U1142, INSERM, Sorbonne Université, Paris, France
| | - Nicolas Griffon
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, U1142, INSERM, Sorbonne Université, Paris, France
| | - Stefan J Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
- Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, U1142, INSERM, Sorbonne Université, Paris, France
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Lelong R, Soualmia LF, Grosjean J, Taalba M, Darmoni SJ. Building a Semantic Health Data Warehouse in the Context of Clinical Trials: Development and Usability Study. JMIR Med Inform 2019; 7:e13917. [PMID: 31859675 PMCID: PMC6942180 DOI: 10.2196/13917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/02/2019] [Accepted: 08/19/2019] [Indexed: 01/08/2023] Open
Abstract
Background The huge amount of clinical, administrative, and demographic data recorded and maintained by hospitals can be consistently aggregated into health data warehouses with a uniform data model. In 2017, Rouen University Hospital (RUH) initiated the design of a semantic health data warehouse enabling both semantic description and retrieval of health information. Objective This study aimed to present a proof of concept of this semantic health data warehouse, based on the data of 250,000 patients from RUH, and to assess its ability to assist health professionals in prescreening eligible patients in a clinical trials context. Methods The semantic health data warehouse relies on 3 distinct semantic layers: (1) a terminology and ontology portal, (2) a semantic annotator, and (3) a semantic search engine and NoSQL (not only structured query language) layer to enhance data access performances. The system adopts an entity-centered vision that provides generic search capabilities able to express data requirements in terms of the whole set of interconnected conceptual entities that compose health information. Results We assessed the ability of the system to assist the search for 95 inclusion and exclusion criteria originating from 5 randomly chosen clinical trials from RUH. The system succeeded in fully automating 39% (29/74) of the criteria and was efficiently used as a prescreening tool for 73% (54/74) of them. Furthermore, the targeted sources of information and the search engine–related or data-related limitations that could explain the results for each criterion were also observed. Conclusions The entity-centered vision contrasts with the usual patient-centered vision adopted by existing systems. It enables more genericity in the information retrieval process. It also allows to fully exploit the semantic description of health information. Despite their semantic annotation, searching within clinical narratives remained the major challenge of the system. A finer annotation of the clinical texts and the addition of specific functionalities would significantly improve the results. The semantic aspect of the system combined with its generic entity-centered vision enables the processing of a large range of clinical questions. However, an important part of health information remains in clinical narratives, and we are currently investigating novel approaches (deep learning) to enhance the semantic annotation of those unstructured data.
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Affiliation(s)
- Romain Lelong
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France.,LITIS EA 4108, TIBS, Normandy University, Rouen, France
| | - Lina F Soualmia
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France.,LITIS EA 4108, TIBS, Normandy University, Rouen, France.,LIMICS U1142, Inserm, Sorbonne University, Paris, France
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France.,LIMICS U1142, Inserm, Sorbonne University, Paris, France
| | - Mehdi Taalba
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
| | - Stéfan J Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France.,LIMICS U1142, Inserm, Sorbonne University, Paris, France
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41
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Massonnaud C, Lelong R, Kerdelhué G, Lejeune E, Grosjean J, Griffon N, Darmoni SJ. Performance evaluation of three semantic expansions to query PubMed. Health Info Libr J 2019; 38:113-124. [DOI: 10.1111/hir.12291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 11/22/2019] [Indexed: 01/29/2023]
Affiliation(s)
- Clément Massonnaud
- Department of Biomedical Informatics Rouen University Hospital Normandy France
- LIMICS U1142 Sorbonne Université Paris France
| | - Romain Lelong
- Department of Biomedical Informatics Rouen University Hospital Normandy France
- LIMICS U1142 Sorbonne Université Paris France
| | - Gaétan Kerdelhué
- Department of Biomedical Informatics Rouen University Hospital Normandy France
- LIMICS U1142 Sorbonne Université Paris France
| | - Emeline Lejeune
- Department of Biomedical Informatics Rouen University Hospital Normandy France
- LIMICS U1142 Sorbonne Université Paris France
| | - Julien Grosjean
- Department of Biomedical Informatics Rouen University Hospital Normandy France
- LIMICS U1142 Sorbonne Université Paris France
| | - Nicolas Griffon
- Department of Biomedical Informatics Rouen University Hospital Normandy France
- LIMICS U1142 Sorbonne Université Paris France
| | - Stefan J. Darmoni
- Department of Biomedical Informatics Rouen University Hospital Normandy France
- LIMICS U1142 Sorbonne Université Paris France
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Siefridt C, Grosjean J, Lefebvre T, Rollin L, Darmoni S, Schuers M. Evaluation of automatic annotation by a multi-terminological concepts extractor within a corpus of data from family medicine consultations. Int J Med Inform 2019; 133:104009. [PMID: 31715451 DOI: 10.1016/j.ijmedinf.2019.104009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/03/2019] [Accepted: 10/14/2019] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Research in family medicine is necessary to improve the quality of care. The number of publications in general medicine remains low. Databases from Electronic Medical Records can increase the number of these publications. These data must be coded to be used pertinently. The objective of this study was to assess the quality of semantic annotation by a multi-terminological concept extractor within a corpus of family medicine consultations. METHOD Consultation data in French from 25 general practitioners were automatically annotated using 28 different terminologies. The data extracted were classified into three groups: reasons for consulting, observations and consultation results. The first evaluation led to a correction phase of the tool which led to a second evaluation. For each evaluation, the precision, recall and F-measure were quantified. Then, the inter- and intra-terminological coverage of each terminology was assessed. RESULTS Nearly 15,000 automatic annotations were manually evaluated. The mean values for the second evaluation of precision, recall and F-measure were 0.85, 0.83 and 0.84 respectively. The most common terminologies used were SNOMED CT, SNOMED 3.5 and NClt. The terminologies with the best intra-terminological coverage were ICPC-2, DRC and CISMeF Meta-Terms. CONCLUSION A multi-terminological concepts extractor can be used for the automatic annotation of consultation data in family medicine. Integrating such a tool into general practitioners' business software would be a solution to the lack of routine coding. Developing the use of a single terminology specific to family medicine could improve coding, facilitate semantic interoperability and the communication of relevant information.
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Affiliation(s)
- Charlotte Siefridt
- Department of General Medicine, Rouen University Hospital, Rouen, France; Department of Biomedical Informatics, Rouen University Hospital, Rouen, France.
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France; INSERM, U1142, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, LIMICS, Sorbonne Université, Paris, France
| | - Tatiana Lefebvre
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France
| | - Laetitia Rollin
- INSERM, U1142, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, LIMICS, Sorbonne Université, Paris, France; Department of Occupational and Environmental Medicine, Rouen University Hospital, Rouen, France
| | - Stefan Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France; INSERM, U1142, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, LIMICS, Sorbonne Université, Paris, France
| | - Matthieu Schuers
- Department of General Medicine, Rouen University Hospital, Rouen, France; INSERM, U1142, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, LIMICS, Sorbonne Université, Paris, France
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Dufour JC, Grosjean J, Darmoni S, Yasini M, Marchand G, Simon C, Sarradon-Eck A, Préau M, Darmon D, Schuers M, Hassanaly P, Giorgi R. ApiAppS: A Project to Study and Help Practitioners in Recommending mHealth Apps and Devices to Their Patients. Stud Health Technol Inform 2019; 264:1919-1920. [PMID: 31438407 DOI: 10.3233/shti190713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The ApiAppS ongoing project aims to provide physicians with a decision support system for the prescription / recommendation of mHealth technologies. We describe the context and the components of the project which includes: 1) a technical part on modelling and implementing the decision support system, and 2) a psychosocial investigation part designed to have a better knowledge of general practitioners (GPs) and patients' expectations, beliefs and practices.
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Affiliation(s)
- Jean-Charles Dufour
- Aix Marseille Univ, APHM, INSERM, IRD, SESSTIM, Hop Timone, BioSTIC, Marseille, France
| | - Julien Grosjean
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France.,Sorbonne Université, UMR_S 1142, LIMICS, Paris, France
| | - Stefan Darmoni
- Department of Biomedical Informatics, Rouen University Hospital, Rouen, France.,Sorbonne Université, UMR_S 1142, LIMICS, Paris, France
| | - Mobin Yasini
- Department of Research and Development, DMD Santé, Paris, France
| | | | | | - Aline Sarradon-Eck
- Aix Marseille Univ, Institut Paoli-Calmettes, INSERM, IRD, SESSTIM, CanBios, Marseille, France
| | - Marie Préau
- Social Psychology Research Group (GRePS), Lyon 2 University, Lyon, France
| | - David Darmon
- Université Côte d'Azur, Département d'enseignement et de recherche en médecine générale, Nice, France.,Aix Marseille Univ, INSERM, IRD, SESSTIM, Marseille, France
| | - Matthieu Schuers
- Department of General Practice, Department of Biomedical Informatics, Rouen University, Rouen University Hospital, LITIS EA 4108, Normandie University, Rouen, France
| | | | - Roch Giorgi
- Aix Marseille Univ, APHM, INSERM, IRD, SESSTIM, Hop Timone, BioSTIC, Marseille, France
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Dynomant E, Lelong R, Dahamna B, Massonnaud C, Kerdelhué G, Grosjean J, Canu S, Darmoni S. Word Embedding for French Natural Language in Healthcare: A Comparative Study. Stud Health Technol Inform 2019; 264:118-122. [PMID: 31437897 DOI: 10.3233/shti190195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Structuring raw medical documents with ontology mapping is now the next step for medical intelligence. Deep learning models take as input mathematically embedded information, such as encoded texts. To do so, word embedding methods can represent every word from a text as a fixed-length vector. A formal evaluation of three word embedding methods has been performed on raw medical documents. The data corresponds to more than 12M diverse documents produced in the Rouen hospital (drug prescriptions, discharge and surgery summaries, inter-services letters, etc.). Automatic and manual validation demonstrates that Word2Vec based on the skip-gram architecture had the best rate on three out of four accuracy tests. This model will now be used as the first layer of an AI-based semantic annotator.
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Affiliation(s)
- Emeric Dynomant
- OmicX, 72 Rue de la République, 76140, Le Petit Quevilly, Normandie, France.,Department of Biomedical Informatics, Cour Leschevin, CHU de Rouen, 1 Rue de Germont, 76031 Rouen, Normandie, France.,LITIS, Université de Rouen Normandie, Avenue de l'Université, 76800, Saint-Étienne-du-Rouvray, Normandie, France
| | - Romain Lelong
- Department of Biomedical Informatics, Cour Leschevin, CHU de Rouen, 1 Rue de Germont, 76031 Rouen, Normandie, France.,LITIS, Université de Rouen Normandie, Avenue de l'Université, 76800, Saint-Étienne-du-Rouvray, Normandie, France
| | - Badisse Dahamna
- Department of Biomedical Informatics, Cour Leschevin, CHU de Rouen, 1 Rue de Germont, 76031 Rouen, Normandie, France.,LIMICS, Campus des Cordeliers, INSERM U1142, 15 Rue de l'École de Médecine, 75006, Paris, France
| | - Clément Massonnaud
- Department of Biomedical Informatics, Cour Leschevin, CHU de Rouen, 1 Rue de Germont, 76031 Rouen, Normandie, France
| | - Gaëtan Kerdelhué
- Department of Biomedical Informatics, Cour Leschevin, CHU de Rouen, 1 Rue de Germont, 76031 Rouen, Normandie, France.,LIMICS, Campus des Cordeliers, INSERM U1142, 15 Rue de l'École de Médecine, 75006, Paris, France
| | - Julien Grosjean
- Department of Biomedical Informatics, Cour Leschevin, CHU de Rouen, 1 Rue de Germont, 76031 Rouen, Normandie, France.,LIMICS, Campus des Cordeliers, INSERM U1142, 15 Rue de l'École de Médecine, 75006, Paris, France
| | - Stéphane Canu
- LITIS, Université de Rouen Normandie, Avenue de l'Université, 76800, Saint-Étienne-du-Rouvray, Normandie, France
| | - Stéfan Darmoni
- Department of Biomedical Informatics, Cour Leschevin, CHU de Rouen, 1 Rue de Germont, 76031 Rouen, Normandie, France.,LIMICS, Campus des Cordeliers, INSERM U1142, 15 Rue de l'École de Médecine, 75006, Paris, France
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Dynomant E, Lelong R, Dahamna B, Massonnaud C, Kerdelhué G, Grosjean J, Canu S, Darmoni SJ. Word Embedding for the French Natural Language in Health Care: Comparative Study. JMIR Med Inform 2019; 7:e12310. [PMID: 31359873 PMCID: PMC6690161 DOI: 10.2196/12310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/13/2018] [Accepted: 04/21/2019] [Indexed: 12/05/2022] Open
Abstract
Background Word embedding technologies, a set of language modeling and feature learning techniques in natural language processing (NLP), are now used in a wide range of applications. However, no formal evaluation and comparison have been made on the ability of each of the 3 current most famous unsupervised implementations (Word2Vec, GloVe, and FastText) to keep track of the semantic similarities existing between words, when trained on the same dataset. Objective The aim of this study was to compare embedding methods trained on a corpus of French health-related documents produced in a professional context. The best method will then help us develop a new semantic annotator. Methods Unsupervised embedding models have been trained on 641,279 documents originating from the Rouen University Hospital. These data are not structured and cover a wide range of documents produced in a clinical setting (discharge summary, procedure reports, and prescriptions). In total, 4 rated evaluation tasks were defined (cosine similarity, odd one, analogy-based operations, and human formal evaluation) and applied on each model, as well as embedding visualization. Results Word2Vec had the highest score on 3 out of 4 rated tasks (analogy-based operations, odd one similarity, and human validation), particularly regarding the skip-gram architecture. Conclusions Although this implementation had the best rate for semantic properties conservation, each model has its own qualities and defects, such as the training time, which is very short for GloVe, or morphological similarity conservation observed with FastText. Models and test sets produced by this study will be the first to be publicly available through a graphical interface to help advance the French biomedical research.
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Affiliation(s)
- Emeric Dynomant
- OmicX, Le Petit Quevilly, France.,Rouen University Hospital, Department of Biomedical Informatics, D2IM, Rouen, France.,Rouen University, LITIS Laboratory, National Institute of Applied Sciences, Saint-Étienne-du-Rouvray, France
| | - Romain Lelong
- Rouen University Hospital, Department of Biomedical Informatics, D2IM, Rouen, France.,Rouen University, LITIS Laboratory, National Institute of Applied Sciences, Saint-Étienne-du-Rouvray, France
| | - Badisse Dahamna
- Rouen University Hospital, Department of Biomedical Informatics, D2IM, Rouen, France.,LIMICS, Sorbonne Universités, Paris, France
| | - Clément Massonnaud
- Rouen University Hospital, Department of Biomedical Informatics, D2IM, Rouen, France
| | - Gaétan Kerdelhué
- Rouen University Hospital, Department of Biomedical Informatics, D2IM, Rouen, France.,LIMICS, Sorbonne Universités, Paris, France
| | - Julien Grosjean
- Rouen University Hospital, Department of Biomedical Informatics, D2IM, Rouen, France.,LIMICS, Sorbonne Universités, Paris, France
| | - Stéphane Canu
- Rouen University, LITIS Laboratory, National Institute of Applied Sciences, Saint-Étienne-du-Rouvray, France
| | - Stefan J Darmoni
- Rouen University Hospital, Department of Biomedical Informatics, D2IM, Rouen, France.,LIMICS, Sorbonne Universités, Paris, France
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Salles A, Dufour J, Hassanaly P, Michel P, Cabot C, Grosjean J. Analyse du discours médical sur Twitter®. Étude d’un corpus de tweets émis par des médecins généralistes entre juin 2012 et mars 2017 et contenant le hashtag #DocTocToc. Rev Epidemiol Sante Publique 2019. [DOI: 10.1016/j.respe.2019.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Ndangang M, Aussy K, Grosjean J, Tanguy L. Intérêt d’une base d’associations exhaustives d’actes de la classification commune des actes médicaux et de dispositifs médicaux : un projet en cours au CHU de Rouen, France. Rev Epidemiol Sante Publique 2019. [DOI: 10.1016/j.respe.2019.01.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Jamoulle M, Augusto DK, Pizzanelli M, Tavares ADO, Resnick M, Grosjean J, Darmoni S. [An online dynamic knowledge base in multiple languages on general medicine and primary care]. Pan Afr Med J 2019; 32:66. [PMID: 31223358 PMCID: PMC6560960 DOI: 10.11604/pamj.2019.32.66.15952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION The International Classification of Primary Care, Second version (ICPC-2) aligned with the 10th Revision of the International Classification of Disease (ICD-10) is a standard for primary care epidemiology compendium. ICPC-2 has been also intended to identify the clinical topics in family medicine. Contextual field-specific knowledge in family medicine and primary care such as health structures, management, categories of patients, research methods, ethical or environmental features are not standardized and reflect, more often, the views of experts. METHODS A qualitative research method, applied to the analysis of several Family Medicine congresses, has helped identify, in addition to clinical items, a spectrum of contextual concepts addressed by family doctors during their exchanges at the congresses. Assembled in a hierarchical manner, these concepts were given expression, together with ICPC-2, under the name of Q-codes Version 2.5, in the multilingual multi-terminology semantic server of the Department of Information and medical informatics (D2Im) at the University of Rouen, France. The two classifications are edited under the acronym 3 CGP for Core Content classification of General Practice. This free access server allows you to consult the ICPC-2 in 22 languages and the Q-codes in ten languages. RESULTS The result of the joint use of these two classifications, as descriptors in congress to identify the concepts in texts or index the gray literature for family medicine and primary care is presented here in its various pilot uses. The validity and generalizability of 3CGP appears to be good in the light of the translations already carried out by colleagues around the world and of the applicability of the method in the two sides of the Atlantic. However the reproducibility and the inter-coder variations still remain to be tested for Q-codes. Maintenance remains an issue. CONCLUSION This method highlights the conceptual extension, the complexity and the dynamics of the role of general practitioner and family doctor as well as of primary care physician.
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Affiliation(s)
- Marc Jamoulle
- Département de Médecine Générale, Université de Liège, Belgique
- Département d'Information et d'Informatique Médicale, Université de Rouen, France
| | - Daniel Knupp Augusto
- Société Brésilienne de Médecine de Famille et Communautaire (SBMFC), Curutiba, Brésil
| | - Miguel Pizzanelli
- Département de Médecine de Famille, Université de la République (UDELAR), Montevideo, Uruguay
| | | | - Melissa Resnick
- Medical Librarian, Terminologist, Houston, Texas, United States of America
| | - Julien Grosjean
- Département d'Information et d'Informatique Médicale, Université de Rouen, France
| | - Stefan Darmoni
- Département d'Information et d'Informatique Médicale, Université de Rouen, France
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Jamoulle M, Resnick M, Grosjean J, Ittoo A, Cardillo E, Vander Stichele R, Darmoni S, Vanmeerbeek M. Development, dissemination, and applications of a new terminological resource, the Q-Code taxonomy for professional aspects of general practice/family medicine. Eur J Gen Pract 2018; 24:68-73. [PMID: 29243572 PMCID: PMC5795790 DOI: 10.1080/13814788.2017.1404986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 10/09/2017] [Accepted: 10/15/2017] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND While documentation of clinical aspects of General Practice/Family Medicine (GP/FM) is assured by the International Classification of Primary Care (ICPC), there is no taxonomy for the professional aspects (context and management) of GP/FM. OBJECTIVES To present the development, dissemination, applications, and resulting face validity of the Q-Codes taxonomy specifically designed to describe contextual features of GP/FM, proposed as an extension to the ICPC. DEVELOPMENT The Q-Codes taxonomy was developed from Lamberts' seminal idea for indexing contextual content (1987) by a multi-disciplinary team of knowledge engineers, linguists and general practitioners, through a qualitative and iterative analysis of 1702 abstracts from six GP/FM conferences using Atlas.ti software. A total of 182 concepts, called Q-Codes, representing professional aspects of GP/FM were identified and organized in a taxonomy. Dissemination: The taxonomy is published as an online terminological resource, using semantic web techniques and web ontology language (OWL) ( http://www.hetop.eu/Q ). Each Q-Code is identified with a unique resource identifier (URI), and provided with preferred terms, and scope notes in ten languages (Portuguese, Spanish, English, French, Dutch, Korean, Vietnamese, Turkish, Georgian, German) and search filters for MEDLINE and web searches. APPLICATIONS This taxonomy has already been used to support queries in bibliographic databases (e.g., MEDLINE), to facilitate indexing of grey literature in GP/FM as congress abstracts, master theses, websites and as an educational tool in vocational teaching, Conclusions: The rapidly growing list of practical applications provides face-validity for the usefulness of this freely available new terminological resource.
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Affiliation(s)
- Marc Jamoulle
- Department of General Practice, University of LiègeLiègeBelgium
| | | | - Julien Grosjean
- Department of Information and Medical Informatics (D2IM), University of RouenRouenFrance
| | - Ashwin Ittoo
- HEC School of Management, University of LiègeLiègeBelgium
| | - Elena Cardillo
- Italian Institute of Informatics and Telematics, National Research CouncilCosenzaItaly
| | | | - Stefan Darmoni
- Department of Information and Medical Informatics (D2IM), University of RouenRouenFrance
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Guerin C, Maynard C, Philit J, Dumollard C, Grosjean J, Fourcade J. Hémorragie intra-alvéolaire chez des consommateurs de cocaïne, ne pas s’arrêter aux apparences : deux cas cliniques. Rev Med Interne 2018. [DOI: 10.1016/j.revmed.2018.10.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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