Papers by Badisse Dahamna
Studies in health technology and informatics
The Health Terminology/Ontology Portal (HeTOP) was developed to provide easy access to health ter... more The Health Terminology/Ontology Portal (HeTOP) was developed to provide easy access to health terminologies and ontologie. The repository is not only dedicated to professionals but is also a valuable teaching tool. Currently, it provides access to thirty two health terminologies and ontologies available mainly in French or in English, but also in German, Italian, Chinese, etc. HeTOP can be used by both humans and computers via Web services. To integrate new resources into HeTOP, three steps are necessary: (1) designing a meta-model into which each terminology (or ontology) can be integrated, (2) developing a process to include terminologies into HeTOP, (3) building and integrating existing and new inter & intra-terminology semantic harmonization into HeTOP. Currently, 600 unique machines use the MeSH version of HeTOP every day and restricted terminologies/ontologies are used for teaching purposes in several medical schools in France. The multilingual version of HeTOP is available (U...
Studies in health technology and informatics
Following a recent change in the indexing policy for French quality controlled health gateway CIS... more Following a recent change in the indexing policy for French quality controlled health gateway CISMeF, multiple terminologies are now being used for indexing in addition to MeSH®. To evaluate precision and recall of super-concepts for information retrieval in a multi-terminology paradigm compared to MeSH-only. We evaluate the relevance of resources retrieved by multi-terminology super-concepts and MeSH-only super-concepts queries. Recall was 8-14% higher for multi-terminology super-concepts compared to MeSH only super-concepts. Precision decreased from 0.66 for MeSH only super-concepts to 0.61 for multi-terminology super-concepts. Retrieval performance was found to vary significantly depending on the super-concepts (p<10-4) and indexing methods (manual vs automatic; p<0.004). A multi-terminology paradigm contributes to increase recall but lowers precision. Automated tools for indexing are not accurate enough to allow a very precise information retrieval.
When searching the medical literature, health professionals and lay people strongly prefer to use... more When searching the medical literature, health professionals and lay people strongly prefer to use their native language. Therefore, Medical Subject Headings (MeSH ® ) translations would be helpful to those who are not fluent in English to ac- cess scientific papers indexed in the MEDLINE ® bibliographic database. Furthermore, medical terminologies such as MeSH are challenging in any language (1).
Informatique et Santé, 2009
Abstract In the health sector, there exist practically as many different terminologies as there a... more Abstract In the health sector, there exist practically as many different terminologies as there are fields of application. Hence, and given the growing need for cooperation between health players, a new “interoperable” terminology base is now required featuring a shared semantic frame of reference to enable the various terminologies to interact effectively. Three groups (LERTIM, CISMeF, and MONDECA) have set
Studies in health technology and informatics, 2008
The present work aims at discovering new associations between medical concepts to be exploited as... more The present work aims at discovering new associations between medical concepts to be exploited as input in retrieval and indexing. Association rules method is applied to documents. The process is carried out on three major document categories referring to e-health information consumers: health professionals, students and lay people. Association rules evaluation is founded on statistical measures combined with domain knowledge. Association rules represent existing relations between medical concepts (60.62%) and new knowledge (54.21%). Based on observations, 463 expert rules are defined by medical librarians for retrieval and indexing. Association rules bear out existing relations, produce new knowledge and support users and indexers in document retrieval and indexing.
Studies in health technology and informatics, 2008
The aim of this study is to provide to indexers MeSH terms to be considered as major ones in a li... more The aim of this study is to provide to indexers MeSH terms to be considered as major ones in a list of terms automatically extracted from a document. We propose a method combining symbolic knowledge - the UMLS Metathesaurus and Semantic Network - and statistical knowledge drawn from co-occurrences of terms in the CISMeF database (a French-language quality-controlled health gateway) using data mining measures. The method was tested on CISMeF corpus of 293 resources. There was a proportion of 0.37+/-0.26 major terms in the processed records. The method produced lists of terms with a proportion of terms initially pointed out as major of 0.54+/-0.31. The method we propose reduces the number of terms, which seem not useful for content description of resources, such as "check tags", but retains the most descriptive ones. Discarding these terms is accounted for by: 1) the removal by using semantic knowledge of associations of concepts bearing no real medical significance, 2) the ...
Studies in health technology and informatics, 2008
Among the numerous new functionalities of the Internet, commonly called Web 2.0, Web syndication ... more Among the numerous new functionalities of the Internet, commonly called Web 2.0, Web syndication illustrates the trend for better and faster information sharing. Web feeds (a.k.a RSS feeds), which were used mostly on weblogs at first, are now also widely used in academic, scientific and institutional websites such as PubMed. As very few French language feeds were listed or catalogued in the Health field by the year of 2007, it was decided to implement them in the quality-controlled health gateway CISMeF ([French] acronym for Catalogue and Index of French Language Health Resources on the Internet). Furthermore, making full use of the nature of Web syndication, a Web feed aggregator was put online in to provide a dynamic news gateway called "CISMeF actualités" (http://www.chu-rouen.fr/actualites/). This article describes the process to retrieve and implement the Web feeds in the catalogue and how its terminology was adjusted to describe this new content. It also describes ho...
Studies in health technology and informatics, 2006
The amount of health data accessible on the Web is increasing and Internet has become a major sou... more The amount of health data accessible on the Web is increasing and Internet has become a major source of health information. Many tools and search engines are available but medical information retrieval remains difficult for both the health professional and the patients. In this paper we describe heuristics that aim at matching as much as possible queries with the content of the documents in the context of the CISMeF catalogue (Catalogue and Index of Health Resources in French) and its Doc'CISMeF search tool. The queries are represented by terms and the content of the documents is indexed by a terminology based on the MeSH thesaurus. Several operations are performed to match the terms of the terminology: natural language processing techniques on multi-words queries, phonemisation, spelling correction, plain text search with adjacency etc.. Each one is tested to evaluate its contribution in matching the terminology and the indexed documents. The implemented heuristics contribute s...
Studies in health technology and informatics, 2007
The growing number of resources to be indexed in the catalogue of online health resources in Fren... more The growing number of resources to be indexed in the catalogue of online health resources in French (CISMeF) calls for curating strategies involving automatic indexing tools while maintaining the catalogue's high indexing quality standards. To develop a simple automatic tool that retrieves MeSH descriptors from documents titles. In parallel to research on advanced indexing methods, a bag-of-words tool was developed for timely inclusion in CISMeF's maintenance system. An evaluation was carried out on a corpus of 99 documents. The indexing sets retrieved by the automatic tool were compared to manual indexing based on the title and on the full text of resources. 58% of the major main headings were retrieved by the bag-of-words algorithm and the precision on main heading retrieval was 69%. Bag-of-words indexing has effectively been used on selected resources to be included in CISMeF since August 2006. Meanwhile, on going work aims at improving the current version of the tool.
Studies in health technology and informatics, 2008
The neighbors of a document are those documents in a corpus that are most similar to it. The obje... more The neighbors of a document are those documents in a corpus that are most similar to it. The objective of this paper is to develop and evaluate the related resources algorithm (CISMeF-RRA) in the context of a quality-controlled health gateway on the Internet CISMeF. CISMeF-RRA is inspired by the PubMed Related Citations Articles. CISMeF-RRA combines statistical distances with a semantic distance using MeSH terms/qualifiers. In this feasibility study an evaluation was performed using 50 CISMeF resources randomly chosen. Overall, 49% of the related documents were ranked as relevant. if this feasibility study is confirmed by another evaluation of more resources, CISMeF-RRA will be implemented in the CISMeF catalog.
Studies in health technology and informatics, 2009
The objective of this work is the creation of a bilingual (French/English) drug information porta... more The objective of this work is the creation of a bilingual (French/English) drug information portal (DIP), in a multi-terminological context. The development of the DIP was based on the CISMeF portal, which catalogues and indexes the most important and quality-controlled sources of institutional health information in French. DIP has created specific functionalities related to drug and used specific drugs terminologies and classifications: the ATC classification, the CAS numbers, the French codes CIS, and CIP, as well as trade names and the International Nonproprietary Names of the drugs. DIP is the result of collaboration between the CISMeF team and the VIDAL private Company, specialized in drug information. DIP is conceived to facilitate the user information retrieval using several health terminologies. In the framework of the drug field, using multi-terminological context, indexing drugs with the appropriate codes or/and terms revealed to be very important to have the appropriate i...
Document numérique, 2003
PSI, FRE CNRS 2645. RÉSUMÉ. Le nombre de ressources disponibles sur l'Internet concernant l'ensei... more PSI, FRE CNRS 2645. RÉSUMÉ. Le nombre de ressources disponibles sur l'Internet concernant l'enseignement de la médecine sont en croissance permanente. Il devient de plus en plus difficile, pour l'étudiant comme pour l'enseignant, de repérer des documents de qualité et répondant à une question précise. CISMeF et son outil de recherche associé Doc'CISMeF, permettent de répondre à cette attente. Ils sont fondés sur un modèle d'information qui intègre les mots clés et les qualificatifs du thesaurus MeSH et y adjoint deux concepts supplémentaires avec les métatermes et les types de ressources. La réalisation du catalogue s'appuie sur une sélection rigoureuse des ressources notamment au regard de critères de qualité stricts (grille de critères du NetScoring et langage de métadonnées HIDDEL). Plusieurs modes de recherche sont proposés. La recherche «avancée» permet des requêtes élaborées, pouvant combiner plusieurs champs grâce aux opérateurs booléens ET, OU, SAUF. Doc'CISMeF a été choisi pour être un des outils de recherche de l'Université Médicale Virtuelle Francophone (UMVF).
Informatique et Santé, 2011
The Script Concordance test (SC) test is an assessment tool that measures the capacity to solve i... more The Script Concordance test (SC) test is an assessment tool that measures the capacity to solve ill-defined problems, that is, reasoning in a context of uncertainty. This study assesses the feasibility, reliability and validity of the SC test made available on the Web to French urologists.
The Catalogue and index of French-language medical sites (CISMeF) is a medical portal that provid... more The Catalogue and index of French-language medical sites (CISMeF) is a medical portal that provides users with results as pertinent as possible according to their requirements, expectations, and context of use. Indexing and single-term research are based on theMedical subject headings(MeSH) thesaurus. The integration of new medical terminology for indexing the catalogue&amp;amp;amp;amp;#39;s resources is intended to minimize false-negatives during searches and to contextualize the users&amp;amp;amp;amp;#39; needs. The creation of a drug information portal makes more targeted research possible, with numerous entries according to user (physicians, pharmacists, chemists, and pharmacologists). For simplicity&amp;amp;amp;amp;#39;s sake, the catalogue&amp;amp;amp;amp;#39;s index of resources by different nomenclatures is not entirely displayed. The choice of display is left to the user, with MeSH only as the default. These multi-nomenclature tools should be applicable as well to electronic patient records. In this case, the objective is to improve patient care by better searches and identification of the information required during consultations and hospitalization.
Background: Categorization is designed to enhance resource description by organizing content desc... more Background: Categorization is designed to enhance resource description by organizing content description so as to enable the reader to grasp quickly and easily what are the main topics discussed in it. The objective of this work is to propose a categorization algorithm to classify a set of scientific articles indexed with the MeSH thesaurus, and in particular those of the MEDLINE bibliographic database. In a large bibliographic database such as MEDLINE, finding materials of particular interest to a specialty group, or relevant to a particular audience, can be difficult. The categorization refines the retrieval of indexed material. In the CISMeF terminology, metaterms can be considered as super-concepts. They were primarily conceived to improve recall in the CISMeF quality-controlled health gateway.
Artificial Intelligence in Medicine, 2007
The present work aims at refining and expanding user's queries thanks to association rules. We ad... more The present work aims at refining and expanding user's queries thanks to association rules. We adapted the A-Close algorithm to a medical corpus indexed by MeSH descriptors. The originality of our approach lies in the use of the association rules in the information retrieval process and the exploitation of the structure of the domain knowledge to evaluate the association rules. The results show the usefulness of this query expansion approach. Based on observations, new knowledge is modelled as expert rules.
Medical Teacher, 2006
Access to accurate and quality-controlled health information on the Internet for medical students... more Access to accurate and quality-controlled health information on the Internet for medical students is not an easy task. CISMeF is the search tool of a MeSH-indexed directory of medical Internet resources in French. Since 2004, a new French Pre-Residency Examination (PRE) is compulsory for all medical students in the 6th year of the curriculum. The goal of this study is to evaluate CISMeF as a tool to provide teaching resources available on the Internet covering PRE material. The CISMeF terminology and the PRE CISMeF module are described. To assess the CISMeF performance in covering PRE program, its precision (number of relevant resources/number of overall resources extracted by CISMeF) and coverage (number of PRE questions covered by at least one resource in the CISMeF gateway) were computed. The CISMeF module for the new French Pre-Residency Examination is efficient as it already covers 95.7% of the program with a precision of 82.2%. Our data demonstrates that CISMeF is acceptable to guide students&amp;amp;amp;amp;amp;amp;#39; learning and should be a useful teaching resource for the preparation of the French Pre-Residency Examination.
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Papers by Badisse Dahamna