R. Duvauferrier

Roogle: an information retrieval engine for clinical data warehouse.

High amount of relevant information is contained in reports stored in the electronic patient records and associated metadata. R-oogle is a project aiming at developing information retrieval engines adapted to these reports and designed for clinicians. The system consists in a data warehouse (full-text reports and structured data) imported from two different hospital information systems. Information retrieval is performed using metadata-based semantic and full-text search methods (as Google). Applications may be biomarkers identification in a translational approach, search of specific cases, and constitution of cohorts, professional practice evaluation, and quality control assessment.

Technique et évaluation du guidage échographique pour la réalisation de biopsies synoviales.

Resume Objectif Decrire et evaluer la technique des biopsies synoviales sous guidage echographique pour l’ensemble des articulations peripheriques. Materiel et methodes De janvier 2002 a janvier 2005, nous avons realise 83 biopsies synoviales echoguidees pour des patients souffrant d’une monoarthrite non etiquetee. Apres verification echographique de la presence d’un epaississement synovial, l’abord articulaire etait decide en fonction de la zone d’epaississement synovial maximal et des structures anatomiques a eviter. Un controle echographique au cours et au decours de l’examen verifiait l’absence de complications. Les performances techniques de la methode echoguidee sont evaluees en considerant comme critere de reussite la presence de tissu synovial a l’examen anatomopathologique. Elles sont comparees aux resultats des autres techniques de biopsies synoviales publies dans la litterature. Resultats La presence de tissu synovial a l’examen histologique est retrouvee dans 78 cas (94 %). Le taux de reussite est de 100 % pour les prelevements realises sur l’epaule (13 prelevements), 75 % pour le coude (3 sur 4 prelevements), 85,7 % pour le poignet (6 sur 7 prelevements), 88,2 % pour la hanche (15 sur 17 prelevements), 97 % pour le genou (34 sur 35 prelevements) et 100 % pour la cheville (7 prelevements). Aucune complication n’a ete observee. Pour chaque articulation, les performances des biopsies echoguidees sont superieures aux resultats des biopsies sous guidage radioscopique publies dans la litterature. Conclusion Le guidage echographique des biopsies synoviales des articulations peripheriques est une technique simple, sure et efficace qui apporte de nombreux avantages en comparaison des biopsies synoviales realisees sous controle radioscopique.

A unified representation of findings in clinical radiology using the UMLS and DICOM

PURPOSEnCollecting and analyzing findings constitute the basis of medical activity. Computer assisted medical activity raises the problem of modelling findings. We propose a unified representation of findings integrating the representations of findings in the GAMUTS in Radiology [M.M. Reeder, B. Felson, GAMUTS in radiology Comprehensive lists of roentgen differential diagnosis, fourth ed., 2003], the Unified Medical Language System (UMLS), and the Digital Imaging and Communication in Medicine Structured Report (DICOM-SR).nnnMATERIALS AND METHODSnStarting from a corpus of findings in bone and joint radiology [M.M. Reeder, B. Felson, GAMUTS in Radiology comprehensive lists of roentgen differential diagnosis, fourth ed., 2003] (3481 words), an automated mapping to the UMLS was performed with the Metamap Program. The resulting UMLS terms and Semantic Types were analyzed in order to find a generic template in accordance with DICOM-SR structure.nnnRESULTSnUMLS Concepts were missing for 45% of the GAMUTS findings. Three kinds of regularities were observed in the way the Semantic Types were combined: pathological findings, physiological findings and anatomical findings. A generic and original DICOM-SR template modelling finding was proposed. It was evaluated for representing GAMUTS jaws findings. 21% missing terms had to be picked up from Radlex (5%) or created (16%).nnnDISCUSSION-CONCLUSIONnThis article shows that it is possible to represent findings using the UMLS and the DICOM SR formalism with a semi-automated method. The Metamap program helped to find a model to represent the semantic structure of free texts with standardized terms (UMLS Concepts). Nevertheless, the coverage of the UMLS is not comprehensive. This study shows that the UMLS should include more technical concepts and more concepts regarding findings, signs and symptoms to be suitable for radiology representation. The semi-automated translation of the whole GAMUTS using the UMLS concepts and the DICOM SR relations could help to create or supplement the DCMR Templates and Context Groups pertaining to the description of imaging findings.

The value of using verbs in Medline searches.

New findings are continuously identified thanks to novel diagnostic procedures, among others in medical imaging. It would be useful to retrieve these new findings from literature. The aim of this work is to investigate if using verbs in MEDLINE queries can improve the retrieval of findings. Verbs used in the field of findings were selected: ‘to show’ (an examination shows a finding) and ‘to confirm’ (a finding confirms a diagnosis). For each of these verbs, semantically close verbs were researched on the WordNet website. Then, the extent to which adding these verbs to a query about various radiological pathologies can improve findings retrieval in Medline citations was studied. This method has been tested on two sets of MEDLINE citations regarding the diagnostic imaging of musculo-skeletal disorders. Using appropriate verbs in Medline queries enhances the precision from 53% to 61% and from 53% to 74%, respectively, in our first and second test set. A recall of 74% and 83% was reached in our two experiments. Using relevant verbs can be a rather simple way to improve the retrieval of findings related to diseases and diagnostic procedures from Medline citations.

L’informatisation du signe radiologique

The goal of this article is to present to the radiologist the different theories of the sign and their consequences for sign representation in computer systems. All the theories of the sign are presented, but the most relevant are highlighted in order to explain the great modeling systems currently in use (such as DICOM-SR or the UMLS). The constructivist approach of the notion of disease, the semiosis process, which starting from signs produces new signs, and the structuralist analysis of sign through language are emphasized. The purpose of this analysis is to end up with a consensual representation of the sign that can be understood by human beings and processed by machines. Such a representation, also known as an ontology, is based on a semantic organization of language, thus allowing medicine to become a truly scientific discipline. It aims at disambiguating the symbols given to machines, which will help us in our reasoning.

Représentation formelle des critères d’éligibilité aux essais cliniques: Exigences sémantiques de représentation des relations

Reference terminologies based and computable knowledge representations for eligibility criteria are needed to provide computer-based decision support for automated screening, and other purposes. RuleEd and ERGO, a tool and an ad-hoc language for encoding CT, are recent initiatives to achieve this goal. RuleEd defines a collection of connectors that aims at connecting domain concepts to represent criteria in a formal way. Our study is focused on these connectors. Method: We assessed the RuleEd native collection (Ci) of connectors and we proposed an improved new version (Co). Then, from two samples of Ci and Co, we evaluated how SNOMED CT and NCIT could encode and represent the RuleEd connectors. Results: RuleEd provides 362 connectors organized in 10 categories. These categories are confusing. Many Ci connectors are redundant and we reduced Ci into 133 Co connectors (−64%). SNOMED CT has the best coverage rate for encoding Ci and Co connectors (47% up to 61%). Nevertheless, both terminologies have still open issues, especially a lack of formal representation and need to be improved, to be used for an automatic reasoning purpose.

« Méta-analyse » : un outil de recherche et d’analyse d’articles de radiologie sur le web

Meta-analyse: a web-based tool for research and analysis of radiology papers. Finding articles providing answers to specific clinical questions is greatly facilitated by the availability of indexed Medline abstracts using the Pubmed search engine. Nonetheless, the large number of references sometimes requires a time-consuming review of multiple abstracts. In order to streamline the search process, we have created a tool facilitating the search and review of these abstracts. We present here this tool named «xa0Meta-analysexa0».

Apport de l’IRM 3 Tesla dans l’exploration du cartilage du genou

Resume Le probleme actuel de l’IRM du cartilage articulaire est la resolution, en sachant qu’ avec une IRM 1.5 Tesla et une antenne monocanal, la resolution est en routine de environ 0,5 x 0,5 x 3 mm. Le but de cette etude est d’evaluer les performances de l’IRM 3 tesla et des nouvelles antennes. Cinquante cinq patients se presentant pour une pathologie mecanique ou traumatique du genou ont ete inclus. La machine utilisee est une IRM Philips 3 Tesla Achieva avec une antenne genou sense 8 canaux. Les sequences utilisees sont : une sequence 3D ponderee en densite de proton avec une epaisseur de coupe de 0,8 mm, une FOV de 150 mm et une matrice de 512 ; une sequence 3D WATS F avec une epaisseur de coupe a 0,8 une matrice a 512 et une FOV a 150 mm. La resolution obtenue est 0,29 x 0,29 x 0,8 mm. Ces sequences necessitent 2 a 4 excitations, ce qui donne des temps d’acquisition de 7 a 11 mn. L’epaisseur de coupe se trouve a la limite des possibilites machines. L’absence d’isotropisme interdit les reconstructions multiplanaires sous peine d’une degradation de l’image. L’imagerie IRM haute resolution obtenue grâce au 3 Tesla et a l’antenne 8 canaux ameliore l’exploration du cartilage au niveau du genou.

Methode de creation de bases de connaissances radiologiques utilisant le test de concordance des scripts

Objectifs Proposer et evaluer une methode de creation d’une base de connaissances radiologiques centree sur les plaintes des patients utilisant le test de concordance des scripts. Materiels et methodes Nous utilisons la methode d’elaboration des scripts pour interroger des experts sur les scapulalgies. Ils creent des items : indications (si je pense faire – et qu’alors je trouve – l’effet sur la necessite de demander cet examen est) et diagnostics (si je pense a – et qu’alors je trouve – l’effet sur l’hypothese diagnostique est). Les items obtenus sont ensuite relies comme suit : signe d’appel (indique) examen (montre) signe radiologique (diagnostique) maladie. L’analyse globale des relations a ensuite ete effectuee. Resultats Le reseau semantique est constitue de 131 chainons diagnostics et 89 chainons indications. Les chainons indications sont constitues de 20 examens et de 59 signes d’appel. Les chainons diagnostics sont constitues de 55 diagnostics et 72 signes radiologiques. Le reseau se replie car maladies, signes d’appel et signes radiologiques peuvent partager les memes concepts. Conclusion Le test de concordance des scripts permet d’interroger les experts en suivant leur logique hypotheticodeductive. Le reseau semantique obtenu est une modelisation du processus d’indication et de diagnostic radiologique. Il est utilisable pour des tâches automatisees d’evaluation ou d’expertise.