Biomedical subjects

Pierre Le Beux

Publications and source records attributed to Pierre Le Beux.

At least 19 recordsLinked to original sources

PubMed2006

A model for a regional health information network sharing clinical information between professionals in Britanny.

The purpose of this paper is to present a generic model of information system supporting healthcare networks for health professionals in Brittany. This model is aimed to develop cooperation between hospital professionals, primary care and practitioners whatever the specific pathology, by providing tools for exchanging and sharing medical-related data. The model is designed based on the heterogeneity factors revealed by a prospective survey. It includes secured exchange of nominative medical data, all other information and activities being accessible by a Web portal. Other associated tools are a synchronous collaborative platform, and a e-learning module. The first implementation, currently in use by the professionals, is presented for the existing neurology healthcare networks.

France↗

PubMed2006

Multimedia and physiology: a new way to ensure the quality of medical education and medical knowledge.

BACKGROUND: since the eighties and the existence of virtual campuses, the value of computers in distance education has been acknowledged. The development of information and communication technologies is driving at discriminating distance education and on-line education. PURPOSE: the aim of the "Campus Numérique de Physiologie" is not to reproduce an on-line copy of classical textbooks but to put at students' and physicians' disposal the huge possibilities of multimedia resources for an active and easier understanding of complex physiopathological phenomena. METHODS: the on-line course materials were created using both original IBC-made and registered trade-mark software tools. Multiscale modelling and corresponding knowledge bases were implemented by mathematicians, biologists and software engineers from Rennes. The website, which is accessible through a server of the French Virtual Medical University, was developed in the language HTML/PHP connected to a MySQL database. RESULTS: the content managing system is consistent with classical home page facilities and multicriteria browser. Interactive resources are freely available for the site's users. Two- and three-dimensional simulations born out of mathematical qualitative and quantitative models at the molecular, cellular or organic level keep students active with regards to fundamental mechanisms by interactively manipulating the simulation environment. CONCLUSION: authors comment the already available course materials which should stimulate the creation of new documents following a validation by a qualified commission of the "Société de Physiologie". Providing evaluation tests, teachers anticipate that the increasing content of this virtual campus will allow users to gain a complete understanding and an integrative view of many physiopathological mechanisms.

Education, Distance↗

PubMed2005

Indexing method of digital audiovisual medical resources with semantic Web integration.

Digitalization of audiovisual resources and network capability offer many possibilities which are the subject of intensive work in scientific and industrial sectors. Indexing such resources is a major challenge. Recently, the Motion Pictures Expert Group (MPEG) has developed MPEG-7, a standard for describing multimedia content. The goal of this standard is to develop a rich set of standardized tools to enable efficient retrieval from digital archives or the filtering of audiovisual broadcasts on the Internet. How could this kind of technology be used in the medical context? In this paper, we propose a simpler indexing system, based on the Dublin Core standard and compliant to MPEG-7. We use MeSH and the UMLS to introduce conceptual navigation. We also present a video-platform which enables encoding and gives access to audiovisual resources in streaming mode.

Abstracting and Indexing↗

PubMed2004

MeSH and specialized terminologies: coverage in the field of molecular biology.

There is real need among researchers for data in molecular biology, due to the explosive development in this field. Information extraction techniques have been developed in this specific domain, to extract structured information from the literature. The National Library of Medicine provides access to 12 million MEDLINE citations, accessible via PubMed. Information retrieval techniques which are used to select documents that are relevant according to user request. As other domains in medicine, biomolecular scientific literature is indexed by MeSH terms. Automatic identification of protein and gene names in scientific articles is an important step in the indexing process, since proteins and genes are often associated with multiple names, and authors alternate between these synonyms. In this article we assess the contribution of specialized terminologies in the field of molecular biology compared to MeSH.

Abstracting and Indexing↗

PubMed2004

Towards the automatic generation of biomedical sources schema.

Biologists and physicians need to access biological and medical data for their experimentations and researches. This information is available on the Internet and is scattered over many heterogeneous data sources. Collecting information is consequently tedious, time consuming and must be improved. To cope with this difficulty, our overall objective is to realize a mediator-based system to integrate heterogeneous biomedical data sources. This requires first an automatic generation of source schema, which is the goal of this work. For that, we describe an algorithm which is based on information extraction. It consists of the extraction of meta-information from each source to infer their schema. Our system enables users to access relevant and specific data, which are up-to-date. To solve the semantic heterogeneity of data sources, we are considering the creation of an ontology. Finally, the management of source evolution is discussed

Algorithms↗

PubMed2004

Experiments in cross-language medical information retrieval using a mixing translation module.

Given the ever-increasing scale and diversity of medical literature widely published in English on the Internet, improving the performance of information retrieval by cross-language is an urgent research objective. Cross-language medical information retrieval (CLMIR) consists of providing a query in one language and searching medical document collections in one or more different languages. Our users of CLMIR are users who are able to read biomedical texts in English, but have difficulty formulating English queries. This paper proposes a French/English CLMIR system as a mixing model for supporting the retrieval of English medical documents. Methods fall into the category of query translation approach in which we use a hybrid machine translation that combines a pattern-based module with a rule-based translator and includes three steps from pre- to- post-translation. In parallel to this hybrid machine translation, we use multilingual UMLS Methasaurus as a complementary translator. The results show that using a mixing translation module outperforms machine translation-based method and thesaurus-based method used separately.

Information Storage and Retrieval↗

PubMed2003

Collaborative environment for clinical reasoning and distance learning sessions.

BACKGROUND: The medical curriculum has changed with the adoption of the student-centered learning paradigm. Clinical reasoning learning (CRL) is used in order to develop and improve students' clinical reasoning and problem-solving skills. PURPOSE: We have observed that, in complement to traditional CRL sessions, students commonly consult resources available on the internet. Based on this observation, our objective is to create computer tools to coordinate CRL sessions at distance, integrating these electronic resources at every step of the reasoning process. MATERIAL AND METHODS: In order to create the system, we elaborated an object-oriented model of a computer-supported collaborative learning environment. The proposed system includes a local web-server to store electronic resources and a relational database to store their electronic addresses (urls). JAVA was used as the programming language. RESULTS: We developed a set of cooperative platform-independent tools. This environment includes a communication tool. Multimedia data exchange is possible. Information is shared thanks to an electronic notepad and whiteboard tools. PERSPECTIVES: This learning environment will be integrated in the French Virtual Medical University project, and is intended to be used for undergraduate, internships, residency or continuing medical education.

Computers, Handheld↗

PubMed2003

Developing the ontological foundations of a terminological system for end-stage diseases, organ failure, dialysis and transplantation.

The Etablissement français des Greffes (EfG) is a state agency dealing with Public Health issues related to organ, tissue and cell transplantation in France. The evaluation of organ retrieval and transplantation activities, one of its missions, is supported by a national information system (EfG-IS). The EfG-IS is moving towards a new n-tier architecture comprising a terminology server for end-stage diseases, organ failure, dialysis and transplantation (EfG-TS). Following a preliminary audit of the existing coding system and in order to facilitate data recording, to improve the quality of information, to assume compatibility with terminological existing standards and to allow semantic interoperability with other local, national or international registries, a specific work has been conducted on the thesauri to integrate within the EfG-TS. In this paper focusing on the server's content rather than the container, we report first the functional and cognitive requirements that resulted from the preliminary audit. We then describe the methodological approach used to build the terminological server on "sound ontological foundations". We performed the semantic analysis of existing medical terms to set up disease description frame-like structures. These diseases description frames consist of a limited set of nosological discriminating slots such as etiology, semiology, pathology, evolution and associated diseases. Each relevant medical term is thus associated to a concept defined and inserted within a hierarchy according to disease description frame resulting from the semantic analysis. Last, because this terminological server is shared by various transplant and dialysis centers to record patient data at different time point, contextualization of terms appeared as one of the functional requirements. We will also point out various contexts for medical terms and how they have been taken into account.

Automation↗

PubMed2003

Automatic concept extraction from spoken medical reports.

OBJECTIVE: The objective of this project is to investigate methods whereby a combination of speech recognition and automated indexing methods substitute for current transcription and indexing practices. METHODS: We based our study on existing speech recognition software programs and on NOMINDEX, a tool that extracts MeSH concepts from medical text in natural language and that is mainly based on a French medical lexicon and on the UMLS. For each document, the process consists of three steps: (1) dictation and digital audio recording, (2) speech recognition, (3) automatic indexing. The evaluation consisted of a comparison between the set of concepts extracted by NOMINDEX after the speech recognition phase and the set of keywords manually extracted from the initial document. The method was evaluated on a set of 28 patient discharge summaries extracted from the MENELAS corpus in French, corresponding to in-patients admitted for coronarography. RESULTS: The overall precision was 73% and the overall recall was 90%. Indexing errors were mainly due to word sense ambiguity and abbreviations. A specific issue was the fact that the standard French translation of MeSH terms lacks diacritics. A preliminary evaluation of speech recognition tools showed that the rate of accurate recognition was higher than 98%. Only 3% of the indexing errors were generated by inadequate speech recognition. DISCUSSION: We discuss several areas to focus on to improve this prototype. However, the very low rate of indexing errors due to speech recognition errors highlights the potential benefits of combining speech recognition techniques and automatic indexing.

Abstracting and Indexing↗

PubMed2003

Computer-assisted diagnosis system in digestive endoscopy.

The purpose of this paper is to present an intelligent atlas of indexed endoscopic lesions that could be used in computer-assisted diagnosis as reference data. The development of such a system requires a mix of medical and engineering skills for analyzing and reproducing the cognitive processes that underlie the medical decision-making process. The analysis of both endoscopists experience and endoscopic terminologies developed by professional associations shows that diagnostic reasoning in digestive endoscopy uses a scene-object approach. The objects correspond to the endoscopic findings and the medical context of examination and the scene to the endoscopic diagnosis. According to expert assessment, the classes of endoscopic findings and diagnoses, their primitive characteristics (or indices), and their relationships have been listed. Each class describes an endoscopic finding or diagnosis in an intensive way. The retrieval method is based on a similarity metric that estimates the membership value of the case under investigation and the prototype of the class. A simulation test with randomized objects demonstrates a good classification of endoscopic findings. The correct class is the unique response in 68% of the tested objects, the first of multiple responses in 28%. Four descriptors are shown to be of major importance in the classification algorithm: anatomic location, shape, color, and relief. At the present time, the application database contains approximately 150 endoscopic images and is accessible via Internet. Experiments are in progress with endoscopists for the validation of the system and for the understanding of the similarity between images. The next step will integrate the system in a learning tool for junior endoscopists.

Algorithms↗

PubMed2003

Beds Simulator 1.0: a software for the modelisation of the number of beds required for a hospital department.

The determination of the number of beds needed for a hospital department is a complex problem that try to take into account efficiency, forecasting of needs, appropriateness of stays. Health authority used methods based on ratios that do not take into account local specificities and use rather to support an economic decision. On the other side, the models developed are too specific to be applied to all type of hospital department. Moreover, all the solutions depend on the LoS (Length of Stay). We have developed a non parametric method to solve this problem. This modelisation was successfully tested in teaching and non teaching hospitals, for an Intensive Care Unit, two Internal Medicine and a surgical departments. A software easy to use was developed, working on Windows available on our website www.sante.univ-nantes.fr/med/stat/.

Bed Occupancy↗

PubMed2003

A frame-based representation of ICD-10.

UNLABELLED: Physicians are required to code information concerning a patient's stay in order to measure the medical activity in hospitals. They use the International Statistical Classification of Diseases and Related Health Problems, Tenth Revision (ICD-10). Coding is usually performed manually and computerized tools may be useful in speeding up and facilitating the tedious task of coding patient information. The aim of this work is to build a surface semantic model of ICD-10 in order to ameliorate a coding help system. METHODS: This work was focused on chapter XI of the ICD-10, Diseases of the Digestive System. Each term from both analytical and alphabetical indexes about this chapter were submitted to a morphological analysis in order to extract the medical concepts within. After a statistical analysis of these concepts and the way they connect themselves, a semantic model based on a "semantic frame" approach was built. RESULTS: Although this model could represent a reasonable amount of medical knowledge within chapter XI of the ICD-10 in a quite satisfactory way, it shows lack of efficiency for some other chapters. CONCLUSION: Difficulties have to be overcome when modelling a classification meant for manual utilisation, and a lot of work still has to be done to obtain an effective coding help system using the ICD-10.

Forms and Records Control↗

PubMed2003

A contextual coding system for transplantation and end stage diseases.

The Establissement français des Greffes (EfG) is a state agency dealing with Public Health issues related to organ, tissue and cell transplantation in France. EfG maintains a national information system (EfG-IS) for the evaluation of organ transplantation activities. The EfG-IS is moving toward a new n-tier architecture comprising a terminological server. Because this terminological server is shared by various kind of transplant teams and dialysis centers to record patients data at different time point, contextualisation of terms appeared as a functional requirement. We report in this paper various contexts for medical terms and how they have been taken into account.

Cell Transplantation↗

PubMed2003

Method for automatic management of the semantic network ambiguity in the UMLS: possible application for information retrieval on the Web.

The Unified Medical Language System (UMLS) is an extensive collection of terms and concepts. The UMLS includes biomedical terms from standard classifications. The semantic network (SN) links the concepts, sometimes ambiguously. In this paper we try, on one hand to describe the relationship between concepts more efficiently and on the other hand to find new relationships. Assuming that re-usability and automatic extraction of knowledge from existing thesaurus enables an improvement of the metatheasaurus, we cross the SN with linked concepts from the ADM (Assisted Medical Diagnosis). Results are presented and our discussion concerns firstly the use of the SN only; secondly the improvement that allows pre-selection of linked concepts, and thirdly the possibility to coincide with other developments that improve the metathesaurus.

Electronic Data Processing↗

PubMed2003

Medical pedagogical resources management.

The main objective of this work is to help the management of training resources for students using a pedagogical network available at the Medical School of Rennes. With the increase of the number of connections and the number of medical documents available on this network, the management of new contents requires a lot of efforts for the webmaster. In order to improve the management of the resources, we implemented an automatic web engine for teachers, able to manage the links for the most interesting resources for their practice.

Computer-Assisted Instruction↗

PubMed2003

Indexing method of digital audiovisual medical resources with semantic Web integration.

Digitalization of audio-visual resources combined with the performances of the networks offer many possibilities which are the subject of intensive work in the scientific and industrial sectors. Indexing such resources is a major challenge. Recently, the Motion Pictures Expert Group (MPEG) has been developing MPEG-7, a standard for describing multimedia content. The good of this standard is to develop a rich set of standardized tools to enable fast efficient retrieval from digital archives or filtering audiovisual broadcasts on the internet. How this kind of technologies could be used in the medical context? In this paper, we propose a simpler indexing system, based on Dublin Core standard and complaint to MPEG-7. We use MeSH and UMLS to introduce conceptual navigation. We also present a video-platform with enables to encode and give access to audio-visual resources in streaming mode.

Abstracting and Indexing↗

PubMed2003

Development of an indexing search engine for the UMVF: proposal for an indexing method based on Dublin Core and XML.

The UMVF (French Virtual Medical University) has many heterogeneous resources hosted by the servers of university partners of the project. One of its objectives is to develop an efficient tool to perform a single search on these resources. We first defined a standardized and interoperable indexing method. For each document, an XML file containing information on the fifteen elements of Dublin Core was created. We checked its structure and content with a DTD. If the XML file was valid, its data were then integrated into a central database from which the engine carried out a search. We tested our tool successfully with the resources hosted by the Rennes Laboratory of Medical Informatics in cooperation with the Radiology Medical Campus [1]. Our method allows the standardization of the production of information by the various servers and it conforms to the constraints of the semantic Web owing to the technologies chosen.

Abstracting and Indexing↗

PubMed2003

Health data management and strategic management in Brittany: some practical problems.

Recent changes in the organisation of the French health system include 1996's ordinances, and more recently (4th Law march 2002). The general tendency of all these reforms is the management of the health system at the regional level in France. In This paper we try to find how health data management systems could be concerned by this changes. In the first part we will explain why the health data management systems are implicated in theses changes. After that we specify the kind of information needed for strategic management of health at the regional level in Brittany. Then we discuss what information is available from all health data management systems at the regional level as far as decision making in health is concerned.

Database Management Systems↗