A semi-automatic semantic method for mapping SNOMED CT concepts to VCM Icons

VCM (Visualization of Concept in Medicine) is an iconic language for representing key medical concepts by icons. However, the use of this language with reference terminologies, such as SNOMED CT, will require the mapping of its icons to the terms of these terminologies. Here, we present and evaluate a semi-automatic semantic method for the mapping of SNOMED CT concepts to VCM icons. Both SNOMED CT and VCM are compositional in nature; SNOMED CT is expressed in description logic and VCM semantics are formalized in an OWL ontology. The proposed method involves the manual mapping of a limited number of underlying concepts from the VCM ontology, followed by automatic generation of the rest of the mapping. We applied this method to the clinical findings of the SNOMED CT CORE subset, and 100 randomly-selected mappings were evaluated by three experts. The results obtained were promising, with 82 of the SNOMED CT concepts correctly linked to VCM icons according to the experts. Most of the errors were easy to fix

Ontology-Based Clinical Information Extraction Using SNOMED CT

Extracting and encoding clinical information captured in unstructured clinical documents with standard medical terminologies is vital to enable secondary use of clinical data from practice. SNOMED CT is the most comprehensive medical ontology with broad types of concepts and detailed relationships and it has been widely used for many clinical applications. However, few studies have investigated the use of SNOMED CT in clinical information extraction. In this dissertation research, we developed a fine-grained information model based on the SNOMED CT and built novel information extraction systems to recognize clinical entities and identify their relations, as well as to encode them to SNOMED CT concepts. Our evaluation shows that such ontology-based information extraction systems using SNOMED CT could achieve state-of-the-art performance, indicating its potential in clinical natural language processing

Front-Line Physicians' Satisfaction with Information Systems in Hospitals

Day-to-day operations management in hospital units is difficult due to continuously varying situations, several actors involved and a vast number of information systems in use. The aim of this study was to describe front-line physicians' satisfaction with existing information systems needed to support the day-to-day operations management in hospitals. A cross-sectional survey was used and data chosen with stratified random sampling were collected in nine hospitals. Data were analyzed with descriptive and inferential statistical methods. The response rate was 65 % (n = 111). The physicians reported that information systems support their decision making to some extent, but they do not improve access to information nor are they tailored for physicians. The respondents also reported that they need to use several information systems to support decision making and that they would prefer one information system to access important information. Improved information access would better support physicians' decision making and has the potential to improve the quality of decisions and speed up the decision making process.Peer reviewe

A semi-automatic semantic method for mapping SNOMED CT concepts to VCM Icons.

International audienceVCM (Visualization of Concept in Medicine) is an iconic language for representing key medical concepts by icons. However, the use of this language with reference terminologies, such as SNOMED CT, will require the mapping of its icons to the terms of these terminologies. Here, we present and evaluate a semi-automatic semantic method for the mapping of SNOMED CT concepts to VCM icons. Both SNOMED CT and VCM are compositional in nature; SNOMED CT is expressed in description logic and VCM semantics are formalized in an OWL ontology. The proposed method involves the manual mapping of a limited number of underlying concepts from the VCM ontology, followed by automatic generation of the rest of the mapping. We applied this method to the clinical findings of the SNOMED CT CORE subset, and 100 randomly-selected mappings were evaluated by three experts. The results obtained were promising, with 82 of the SNOMED CT concepts correctly linked to VCM icons according to the experts. Most of the errors were easy to fix

Medical Informatics

Information technology has been revolutionizing the everyday life of the common man, while medical science has been making rapid strides in understanding disease mechanisms, developing diagnostic techniques and effecting successful treatment regimen, even for those cases which would have been classified as a poor prognosis a decade earlier. The confluence of information technology and biomedicine has brought into its ambit additional dimensions of computerized databases for patient conditions, revolutionizing the way health care and patient information is recorded, processed, interpreted and utilized for improving the quality of life. This book consists of seven chapters dealing with the three primary issues of medical information acquisition from a patient's and health care professional's perspective, translational approaches from a researcher's point of view, and finally the application potential as required by the clinicians/physician. The book covers modern issues in Information Technology, Bioinformatics Methods and Clinical Applications. The chapters describe the basic process of acquisition of information in a health system, recent technological developments in biomedicine and the realistic evaluation of medical informatics

Actes des 25es journées francophones d'Ingénierie des Connaissances (IC 2014)

National audienceLes Journées Francophones d'Ingénierie des Connaissances fêtent cette année leurs 25 ans. Cette conférence est le rendez-vous annuel de la communauté française et francophone qui se retrouve pour échanger et réfléchir sur des problèmes de recherche qui se posent en acquisition, représentation et gestion des connaissances. Parmi les vingt et un articles sélectionnés pour publication et présentation à la conférence, un thème fondateur de l'ingénierie des connaissances domine : celui de la modélisation de domaines. Six articles traitent de la conception d'ontologies, trois articles de l'annotation sémantique et du peuplement d'ontologies et deux articles de l'exploitation d'ontologies dans des systèmes à base de connaissances. L'informatique médicale est le domaine d'application privilégié des travaux présentés, que l'on retrouve dans sept articles. L'ingénierie des connaissances accompagne l'essor des technologies du web sémantique, en inventant les modèles, méthodes et outils permettant l'intégration de connaissances et le raisonnement dans des systèmes à base de connaissances sur le web. Ainsi, on retrouve les thèmes de la représentation des connaissances et du raisonnement dans six articles abordant les problématiques du web de données : le liage des données, leur transformation et leur interrogation ; la représentation et la réutilisation de règles sur le web de données ; la programmation d'applications exploitant le web de données. L'essor des sciences et technologies de l'information et de la communication, et notamment des technologies du web, dans l'ensemble de la société engendre des mutations dans les pratiques individuelles et collectives. L'ingénierie des connaissances accompagne cette évolution en plaçant l'utilisateur au cœur des systèmes informatiques, pour l'assister dans le traitement de la masse de données disponibles. Quatre articles sont dédiés aux problématiques du web social : analyse de réseaux sociaux, détection de communautés, folksonomies, personnalisation de recommandations, représentation et prise en compte de points de vue dans la recherche d'information. Deux articles traitent de l'adaptation des systèmes aux utilisateurs et de l'assistance aux utilisateurs et deux autres de l'aide à la prise de décision. Le taux de sélection de cette édition de la conférence est de 50%, avec dix-neuf articles longs et deux articles courts acceptés parmi quarante-deux soumissions. S'y ajoutent une sélection de neuf posters et démonstrations parmi douze soumissions, présentés dans une session dédiée et inclus dans les actes. Enfin, une innovation de cette édition 2014 de la conférence est la programmation d'une session spéciale " Projets et Industrie ", animée par Frédérique Segond (Viseo), à laquelle participeront Laurent Pierre (EDF), Alain Berger (Ardans) et Mylène Leitzelman (Mnemotix). Trois conférencières invitées ouvriront chacune des journées de la conférence que je remercie chaleureusement de leur participation. Nathalie Aussenac-Gilles (IRIT) retracera l'évolution de l'ingénierie des connaissances en France depuis 25 ans, de la pénurie à la surabondance. A sa suite, Frédérique Segond (Viseo) abordera le problème de " l'assouvissement " de la faim de connaissances dans la nouvelle ère des connaissances dans laquelle nous sommes entrés. Enfin, Marie-Laure Mugnier (LIRMM) présentera un nouveau cadre pour l'interrogation de données basée sur une ontologie, fondé sur des règles existentielles

Towards a system of concepts for Family Medicine. Multilingual indexing in General Practice/ Family Medicine in the era of Semantic Web

UNIVERSITY OF LIÈGE, BELGIUM Executive Summary Faculty of Medicine Département Universitaire de Médecine Générale. Unité de recherche Soins Primaires et Santé Doctor in biomedical sciences Towards a system of concepts for Family Medicine. Multilingual indexing in General Practice/ Family Medicine in the era of SemanticWeb by Dr. Marc JAMOULLE Introduction This thesis is about giving visibility to the often overlooked work of family physicians and consequently, is about grey literature in General Practice and Family Medicine (GP/FM). It often seems that conference organizers do not think of GP/FM as a knowledge-producing discipline that deserves active dissemination. A conference is organized, but not much is done with the knowledge shared at these meetings. In turn, the knowledge cannot be reused or reapplied. This these is also about indexing. To find knowledge back, indexing is mandatory. We must prepare tools that will automatically index the thousands of abstracts that family doctors produce each year in various languages. And finally this work is about semantics1. It is an introduction to health terminologies, ontologies, semantic data, and linked open data. All are expressions of the next step: Semantic Web for health care data. Concepts, units of thought expressed by terms, will be our target and must have the ability to be expressed in multiple languages. In turn, three areas of knowledge are at stake in this study: (i) Family Medicine as a pillar of primary health care, (ii) computational linguistics, and (iii) health information systems. Aim • To identify knowledge produced by General practitioners (GPs) by improving annotation of grey literature in Primary Health Care • To propose an experimental indexing system, acting as draft for a standardized table of content of GP/GM • To improve the searchability of repositories for grey literature in GP/GM. 1For specific terms, see the Glossary page 257 x Methods The first step aimed to design the taxonomy by identifying relevant concepts in a compiled corpus of GP/FM texts. We have studied the concepts identified in nearly two thousand communications of GPs during conferences. The relevant concepts belong to the fields that are focusing on GP/FM activities (e.g. teaching, ethics, management or environmental hazard issues). The second step was the development of an on-line, multilingual, terminological resource for each category of the resulting taxonomy, named Q-Codes. We have designed this terminology in the form of a lightweight ontology, accessible on-line for readers and ready for use by computers of the semantic web. It is also fit for the Linked Open Data universe. Results We propose 182 Q-Codes in an on-line multilingual database (10 languages) (www.hetop.eu/Q) acting each as a filter for Medline. Q-Codes are also available under the form of Unique Resource Identifiers (URIs) and are exportable in Web Ontology Language (OWL). The International Classification of Primary Care (ICPC) is linked to Q-Codes in order to form the Core Content Classification in General Practice/Family Medicine (3CGP). So far, 3CGP is in use by humans in pedagogy, in bibliographic studies, in indexing congresses, master theses and other forms of grey literature in GP/FM. Use by computers is experimented in automatic classifiers, annotators and natural language processing. Discussion To the best of our knowledge, this is the first attempt to expand the ICPC coding system with an extension for family physician contextual issues, thus covering non-clinical content of practice. It remains to be proven that our proposed terminology will help in dealing with more complex systems, such as MeSH, to support information storage and retrieval activities. However, this exercise is proposed as a first step in the creation of an ontology of GP/FM and as an opening to the complex world of Semantic Web technologies. Conclusion We expect that the creation of this terminological resource for indexing abstracts and for facilitating Medline searches for general practitioners, researchers and students in medicine will reduce loss of knowledge in the domain of GP/FM. In addition, through better indexing of the grey literature (congress abstracts, master’s and doctoral theses), we hope to enhance the accessibility of research results and give visibility to the invisible work of family physicians