Rémy Choquet

This article deals with the problematic of biomedical information sharing in the study of antibioresistance growth in Europe. Our general working hypothesis is: how can we share biomedical information in Europe in a non ambiguous way, in a fast way, and on demand? Many issues are raised by this working hypothesis: the issue of the quality of the data, the issue of the representation of data through structure, vocabulary, and semantics. We also address the problem of alignment of data with… Voir plus

This article deals with the problematic of biomedical information sharing in the study of antibioresistance growth in Europe. Our general working hypothesis is: how can we share biomedical information in Europe in a non ambiguous way, in a fast way, and on demand? Many issues are raised by this working hypothesis: the issue of the quality of the data, the issue of the representation of data through structure, vocabulary, and semantics. We also address the problem of alignment of data with domain ontologies and the problem of data mediation using domain ontologies. We then present a system of semantic interoperability based on rules addressing the problem of semantic alignment of heterogeneous systems applied to our domain. Finally we discuss how semantics can contribute to the improvement of information sharing and we also discuss the limits of the current tools and methods. Voir moins

OBJECTIVES : To summarize advances of excellent current research in the new emerging field of Clinical Research Informatics.
METHOD:
Synopsis of four key articles selected for the IMIA Yearbook 2013. The selection was performed by querying PubMed and Web of Science with predefined keywords. From the original set of 590 papers, a first subset of 461 articles which was in the scope of Clinical Research Informatics was refined into a second subset of 79 relevant articles from which 15… Voir plus

OBJECTIVES : To summarize advances of excellent current research in the new emerging field of Clinical Research Informatics.
METHOD:
Synopsis of four key articles selected for the IMIA Yearbook 2013. The selection was performed by querying PubMed and Web of Science with predefined keywords. From the original set of 590 papers, a first subset of 461 articles which was in the scope of Clinical Research Informatics was refined into a second subset of 79 relevant articles from which 15 articles were retained for peer-review.
RESULTS:
The four selected articles exemplify current research efforts conducted in the areas of data representation and management in clinical trials, secondary use of EHR data for clinical research, information technology platforms for translational and comparative effectiveness research and implementation of privacy control.
CONCLUSIONS:
The selected articles not only illustrate how innovative information technology supports classically organized randomized controlled trials but also demonstrate that the long promised benefits of electronic health care data for research are becoming a reality through concrete platforms and projects. Voir moins

Clinical data captured in hospital information systems may be unusable in their original format due to missing information or knowledge. The use of external resources (e.g. domain ontology) could be a way of dealing with this lack of knowledge. Our study thus aimed to develop a framework allowing a user to perform medical queries in the context of infectious diseases. By creating an interaction between a knowledge source and clinical data, using semantic and semantic web tools and methods, the… Voir plus

Clinical data captured in hospital information systems may be unusable in their original format due to missing information or knowledge. The use of external resources (e.g. domain ontology) could be a way of dealing with this lack of knowledge. Our study thus aimed to develop a framework allowing a user to perform medical queries in the context of infectious diseases. By creating an interaction between a knowledge source and clinical data, using semantic and semantic web tools and methods, the users are able to perform queries on a database to obtain results about antibiotic resistance. This work has been performed in the context of the DebugIT European project that aims to control and monitor the antibioresistance growth via a semantic interoperability platform. The results obtained by the use of different semantic web tools were quantitatively evaluated by comparison of the number of results and the query execution time. We have compared our approach with classic business intelligence approaches in terms of usability and functionality.
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This thesis deals with the problematics of biomedical information sharing in the study of antibiotics resistance evolution to bacteries in Europe. Our general working hypothesis is : how can we share biomedical information in Europe in a non ambi- guous way, in a fast way, and on demand ? Many issues are raised by this working hypothesis. We will deal with the issue of the quality of the data, the issue of the representation of data through their structure, their vocabulary, their semantics. We… Voir plus

This thesis deals with the problematics of biomedical information sharing in the study of antibiotics resistance evolution to bacteries in Europe. Our general working hypothesis is : how can we share biomedical information in Europe in a non ambi- guous way, in a fast way, and on demand ? Many issues are raised by this working hypothesis. We will deal with the issue of the quality of the data, the issue of the representation of data through their structure, their vocabulary, their semantics. We will also address the problems of alignment of data with domain ontologies. And the problem of data mediation helped with domain ontologies. We will then present a system of semantic interoperability based on rules which addresses the problem of semantic alignment of heterogeneous systems applied to our domain. Finally we will discuss how semantics can contribute to the improvement of infor- mation sharing and we will also discuss the limits of the current tools and methods. Voir moins

In this paper, we introduce a data integration methodology that promotes technical, syntactic and semantic interoperability for operational healthcare data sources. ETL processes provide access to different operational databases at the technical level. Furthermore, data instances have they syntax aligned according to biomedical terminologies using natural language processing. Finally, semantic web technologies are used to ensure common meaning and to provide ubiquitous access to the data. The… Voir plus

In this paper, we introduce a data integration methodology that promotes technical, syntactic and semantic interoperability for operational healthcare data sources. ETL processes provide access to different operational databases at the technical level. Furthermore, data instances have they syntax aligned according to biomedical terminologies using natural language processing. Finally, semantic web technologies are used to ensure common meaning and to provide ubiquitous access to the data. The system's performance and solvability assessments were carried out using clinical questions against seven healthcare institutions distributed across Europe. The architecture managed to provide interoperability within the limited heterogeneous grid of hospitals. Preliminary scalability result tests are provided. Voir moins

Building qualitative clinical decision support or monitoring based on information stored in clinical information (or EHR) systems cannot be done without assessing and controlling information quality. Numerous works have introduced methods and measures to qualify and enhance data, information models and terminologies quality. This paper introduces an approach based on an Information Quality Triangle that aims at providing a generic framework to help in characterizing quality measures and methods… Voir plus

Building qualitative clinical decision support or monitoring based on information stored in clinical information (or EHR) systems cannot be done without assessing and controlling information quality. Numerous works have introduced methods and measures to qualify and enhance data, information models and terminologies quality. This paper introduces an approach based on an Information Quality Triangle that aims at providing a generic framework to help in characterizing quality measures and methods in the context of the integration of EHR data in a clinical datawarehouse. We have successfully experimented the proposed approach at the HEGP hospital in France, as part of the DebugIT EU FP7 project. Voir moins