Stefan J Darmoni

• MD, PhD
• Department of Biomedical Informatics, Rouen University Hospital, France & LIMICS INSERM U1142 & TIBS, LITIS EA 4108 at Université de Rouen Normandie

The compliance of health terminology servers with the FAIR principles is crucial for establishing an interoperable digital health ecosystem that facilitates health data exchange. These servers must maintain high-quality standards while providing persistent, multilingual, and cross-lingual management of health terminologies. Implementing the FAIR pr...

BACKGROUND Off-label drug prescribing is prevalent in medicine, including psychiatry, often due to unmet therapeutic needs and failures of standard treatments. The PSYHAMM project, funded by the French Research Agency, investigates these practices. To support this research, a clinical data warehouse with advanced data analysis tools has been develo...

To evaluate clinical prognosis following the introduction of a first targeted therapy (TT) according to the serological profile of rheumatoid arthritis (RA) and to analyze differences in efficacy of TT. This single-center retrospective study included patients with RA who received a first TT between 2000 and 2020. Patients were seropositive (IgM and...

Objective: A comprehensive understanding of professional and technical terms is essential to achieving practical results in multidisciplinary projects dealing with health informatics and digital health. The medical informatics multilingual ontology (MIMO) initiative has been created through international cooperation. MIMO is continuously updated an...

Background: Medication review is a structured interview of the patient, performed by the pharmacist and aimed at optimizing drug treatments. In practice, medication review is a long and cognitively-demanding task that requires specific knowledge. Clinical practice guidelines have been proposed, but their application is tedious. Methods: We designed...

One Digital Health (ODH) merges the Digital Health and One Health approaches to create a comprehensive framework for future health ecosystems. In this rapidly evolving field, a standardized vocabulary is not just a convenience, but a necessity to ensure efficient communication. This research proposes the development of a "One Digital Health-Unified...

Aims The global older population is growing rapidly, and the rise in polypharmacy has increased potentially inappropriate medication (PIM) encounters. PIMs pose health risks, but detecting them automatically in large medical databases is complex. This review aimed to uncover PIM prevalence in individuals aged 65 years or older using health database...

Santé Numérique Rouen-Nice (SaNuRN; “Digital Health Rouen-Nice” in English) is a 5-year project by the University of Rouen Normandy (URN) and 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,...

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 He...

Background The enzymatic system of cytochrome P450 ( CYP450 ) is a group of enzymes involved in the metabolism of drugs present in the liver. Literature records instances of underdosing of drugs due to the concurrent administration of another drug that strongly induces the same cytochrome for which the first drug is a substrate and overdosing due t...

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 Informatic...

BACKGROUND 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 health-related students, professionals, and administrators. The project includes a skills framework, training modules, and teaching resources. SaNuRN is expected to train a signi...

Clopidogrel is one of the most prescribed antiplatelet drugs for cardiovascular diseases prevention. Clopidogrel is a prodrug metabolised by CYP2C19 in active metabolites with anti-aggregant effect. Pharmacogenetic variants such as CYP2C19*2 variant can alter the anti-aggregant effect of clopidogrel leading to a higher risk of cardiovascular diseas...

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 p...

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...

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 a...

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 resource...

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...

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 and methods: Therefore, the European Federation for Medical Infor...

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,...

This article presents a research funded by the French National Research Agency (ANR) on the design of a prescription decision aid for mobile health applications for French general practitioners. This research, proposed by an inter-university consortium, has become an interdisciplinary development in partnership with patients. The article sheds ligh...

Understanding statistical results is crucial in order to spread right conclusions. In observational studies, statistical results are often reported as associations without going further. However, each association comes from causal relations. Causal diagrams are visual representations enabling to understand causal mechanisms behind the association f...

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...

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 perceptio...

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...

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...

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, sev...

Background 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, t...

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 sem...

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 he...

Background Many drugs are still being prescribed in a “off-label mode” and especially in psychiatry. Off-label prescription situations may vary depending on several factors and such practice is not well identifiable in the literature. Methods: A new public academic drug database has been recently created and is able to contain off-label indications...

In the context of the IA.TROMED project we intend to develop and evaluate original algorithmic methods that will rely on semantic enrichment of embeddings by combining new deep learning algorithms, such as models founded on transformers, and symbolic artificial intelligence. The documents’ embeddings, the graphs’ embeddings of biomedical concepts,...

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...

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 neces...

Background: PubMed is one of the most important basic tools to access medical literature. Semantic query expansion using synonyms can improve retrieval efficacy. Objective: The objective was to evaluate the performance of three semantic query expansion strategies. Methods: Queries were built for forty MeSH descriptors using three semantic expa...

PubMed is the biggest and most used bibliographic database worldwide, hosting more than 26M biomedical publications. One of its useful features is the "similar articles" section, allowing the end-user to find scientific articles linked to the consulted document in term of context. The aim of this study is to analyze whether it is possible to replac...

PubMed is the biggest and most used bibliographic database worldwide, hosting more than 26M biomedical publications. One of its useful features is the "similar articles" section, allowing the end-user to find scientific articles linked to the consulted document in term of context. The aim of this study is to analyze whether it is possible to replac...

il n'existe pas de standard universellement accepté pour nommer les médicaments. L'identification du médicament a fait l'objet de nombreux travaux de normalisation. Notre objectif est de définir un modèle formel du médicament en français pour lier les différentes entités manipulables autour du médicament. Ce modèle formel vise un double sous-object...

BACKGROUND The huge amount of clinical, administrative and demographic data recorded and maintained by hospitals can be consistently aggregated into Health Data Warehouses (HDWs) with a uniform data model. In 2017, Rouen University Hospital (RUH) initiated the design of a Semantic Health Data Warehouse (SHDW) enabling both semantic description and...

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...

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...

BACKGROUND With the continuous expansion of available biomedical data, efficient and effective information retrieval has become of utmost importance. Semantic expansions of queries using synonyms may improve information retrieval. OBJECTIVE The aim of this study was to propose an innovative method that could estimate automatically the three main m...

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 "pr...

BACKGROUND Word embedding technologies are now used in a wide range of applications. However, no formal evaluation and comparison have been made on models produced by the three most famous implementations (Word2Vec, GloVe and FastText). OBJECTIVE The goal of this study is to compare embedding implementations on a corpus of documents produced in a...

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 Fa...

Introduction The pharmaceutical record system (PRS) is a French nationwide centralized electronic database shared among all community pharmacists listing all drugs dispensed by community pharmacists in the last four months. The objective of this study, the Medication Assessment Through Real time Information eXchange - Distributed Pharmaceutical Rec...

Objective: There is a growing interest in using natural language processing (NLP) for healthcare-associated infections (HAIs) monitoring. A French project consortium, SYNODOS, developed a NLP solution for detecting medical events in electronic medical records for epidemiological purposes. The objective of this study was to evaluate the performance...

Background: Unstructured health documents (e.g. discharge summaries) represent an important and unavoidable source of information. Methods: A semantic annotator identified all the concepts present in the health documents from the clinical data warehouse of the Rouen University Hospital. Results: 2,087,784,055 annotations were generated from a...

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 o...

Résumé Introduction Les publications scientifiques en français sont de plus en plus éclipsées par les publications en langue anglaise, notamment dans les bases de données bibliographiques Internationales. Il s’agit pourtant de ressources potentiellement utiles pour beaucoup de professionnels médicaux et paramédicaux. Objectifs L’objectif de cet a...

Background: Adverse drug reactions (ADRs) are an important cause of morbidity and mortality. Classical Pharmacovigilance process is limited by underreporting which justifies the current interest in new knowledge sources such as social media. The Adverse Drug Reactions from Patient Reports in Social Media (ADR-PRISM) project aims to extract ADRs re...

With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational biology, in order to maximize the potential of their data. OMICtools is designed to meet this need with its open-acce...

Background MEDLINE is the most widely used medical bibliographic database in the world. Most of its citations are in English and this can be an obstacle for some researchers to access the information the database contains. We created a multilingual query builder to facilitate access to the PubMed subset using a language other than English. The aim...

Introduction In January 2015, Rouen University Hospital’s information system experienced serious issues. It was necessary to rapidly switch from the computerized provider order entry (CPOE) system towards a paper-based order entry (PBOE) system. This was an opportunity to evaluate prescriber opinion on the two provider order entry (POE) systems. M...

The hereby proposed terminology called "Q-Codes" can be defined as an extension of the International Classification of Primary Care (ICPC-2). It deals with non-clinical concepts that are relevant in General Practice/Family Medicine (GP/FM). This terminology is a good way to put an emphasis on underestimated topics such as Teaching, Patient issues o...

Extracting concepts from medical texts is a key to support many advanced applications in medical information retrieval. Entity recognition in French texts is moreover challenged by the availability of many resources originally developed for English texts. This paper proposes an evaluation of the terminology coverage in a corpus of 50,000 French art...

While the digitization of medical documents has greatly expanded during the past decade, health information retrieval has become a great challenge to address many issues in medical research. Information retrieval in electronic health records (EHR) should also reduce the difficult tasks of manual information retrieval from records in paper format or...

This paper presents SIBM's participation in the Multilingual Information Extraction task 2 of the CLEF eHealth 2016 evaluation initiative which focuses on named entity recognition in French written text. We report on the indexing of the provided QUAERO dataset with multiple knowledge organization systems (KOS) partially or totally translated in Fre...

Background: Despite international initiatives like Orphanet, it remains difficult to find up-to-date information about rare diseases. The aim of this study is to propose an exhaustive set of queries for PubMed based on terminological knowledge and to evaluate it versus the queries based on expertise provided by the most frequently used resource in...

BACKGROUND To evaluate the impact of the pharmaceutical patient record use in emergency, geriatric and anaesthesia and intensive care departments, an experimentation was launched in 2013 in 55 hospitals. The purpose of the study was to assess the opinions of physicians and pharmacists about the benefits and usability of the patient pharmaceutical r...

In this article, we propose a new approach for indexing biomedical documents based on a possibilistic network that carries out partial matching between documents and biomedical vocabulary. The main contribution of our approach is to deal with the imprecision and uncertainty of the indexing task using possibility theory. We enhance estimation of the...

Introduction The electronic health record (EHR) is a very important potential source of data for various areas, such as medical decision support tools, evidence-based medicine or epidemiological surveillance. Much of this data is available in text format. Methods of natural language processing can be used to perform data mining and facilitate inter...

Background: Reliability and credibility of research conducted by industry have been questioned, including in the field of occupational health. Methods: Cohort studies on occupational cancer published between 2000 and 2010 were compared according to their results, their conclusions, their funding, and the affiliation of their authors. Results:...

[en] Abstract New tools in data management have emerged in the last decade, which are going to revolutionize electronic health records and health information systems. Family practitioners are the first, main and continuous contact with the patient. They are the source and endpoint of the circle of information, generated by judicious medical documen...

In this paper, we report on our participation in the clinical named entity recognition task of the CLEF eHealth 2015 evaluation initiative i.e. to fully automatically identify clinically relevant enti ties in medical text in French. We address the task by using several biomedical knowledge organization systems(KOS) containing terms and their varia...

To summarize the best papers in the field of Knowledge Representation and Management (KRM). A comprehensive review of medical informatics literature was performed to select some of the most interesting papers of KRM published in 2014. Four articles were selected, two focused on annotation and information retrieval using an ontology. The two others...

The objective of the SYNODOS collaborative project was to develop a generic IT solution, combining a medical terminology server, a semantic analyser and a knowledge base. The goal of the project was to generate meaningful epidemiological data for various medical domains from the textual content of French medical records. In the context of this proj...

To translate the 11th edition of the International Classification of Diseases (ICD-11) into French, we proposed a lexical approach using Natural Language Processing techniques. This method relies on the 56 biomedical terminologies and ontologies included in the Cross-lingual Health Multiple Terminologies and Ontologies Portal. From a sample of 336...

Studies on the impact of a Health Information Technology seldom consider socio-technical characteristics of the work system in which the technology is implemented. Yet those dimensions may act as hidden variables that could explain the inconsistency of impact studies' results in terms of performance, quality and satisfaction. This paper reports on...

Objective: The aim of this paper was to present a practical InfoRoute algorithm and applications developed by CISMeF to perform a contextual information retrieval across multiple medical websites in different health domains. Methods: The algorithm was developed to treat multiple types of queries: natural, Boolean and advanced. The algorithm also...

Consequences of the computerization of laboratory and radiology information system (LIS and RIS) are not well documented. The aim of this study was to evaluate the impact of computerization of LIS and RIS of four hospitals on performance and quality of care. The study was divided into three phases. First, the subprocesses and information flows of L...

This paper proposes a new approach for indexing biomedical documents based on the combination of a Possibilistic Network and a Vector Space Model. This later carries out partial matching between documents and biomedical vocabularies. The main contribution of the proposed approach is to combine the cosine similarity and the two measures of possibili...

Objective: This part II article about the ‘words of prevention’ presents in a terminological way the content of ten current concepts used in the prevention domain which are closely linked to quaternary prevention: (1) overinformation, (2) overdiagnosis, (3) medically unexplained symptoms, (4) overmedicalisation, (5) incidentaloma, (6) overscreening...