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2016 001 ACL-int Bouvry, C.; Tvardik, N.; Kergourlay, I.; Bittar, A.; Arnod-Prin, P.; Segond, F.; Dini, L.; Darmoni, S. & Metzger, M.H.. The SYNODOS Project: System for the Normalization and Organization of Textual Medical Data for Observation in Healthcare. IRBM , April, Volume 37, Number 2, Pages 109-115, 2016.
BibTeX: @article{Bouvry2016, author = {Bouvry, C. and Tvardik, N. and Kergourlay, I. and Bittar, A. and Arnod-Prin, P. and Segond, F. and Dini, L. and Darmoni, S. and Metzger, M.H.}, title = {The {SYNODOS} {Project}: {System} for the {Normalization} and {Organization} of {Textual} {Medical} {Data} for {Observation} in {Healthcare}}, month = {April}, journal = {IRBM}, year = {2016}, volume = {37}, number = {2}, pages = {109--115}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1959031816300045}, doi = {10.1016/j.irbm.2016.03.002} }
001 ACL-int Chebil, Wiem; Soualmia, Lina Fatima; Omri, Mohamed Nazih & Darmoni, Stéfan Jacques. Indexing biomedical documents with a possibilistic network. Journal of the Association for Information Science and Technology , April, Volume 67, Number 4, Pages 928-941, 2016.
Abstract: In this article, we propose a new approach for indexing biomedical documents based on a possibilistic network that carries out partial matching between documents and biomedical vocabulary. The main contribution of our approach is to deal with the imprecision and uncertainty of the indexing task using possibility theory. We enhance estimation of the similarity between a document and a given concept using the two measures of possibility and necessity. Possibility estimates the extent to which a document is not similar to the concept. The second measure can provide confirmation that the document is similar to the concept. Our contribution also reduces the limitation of partial matching. Although the latter allows extracting from the document other variants of terms than those in dictionaries, it also generates irrelevant information. Our objective is to filter the index using the knowledge provided by the Unified Medical Language System®. Experiments were carried out on different corpora, showing encouraging results (the improvement rate is +26.37% in terms of main average precision when compared with the baseline).
BibTeX: @article{Chebil2014, author = {Chebil, Wiem and Soualmia, Lina Fatima and Omri, Mohamed Nazih and Darmoni, Stéfan Jacques}, title = {Indexing biomedical documents with a possibilistic network}, month = {April}, journal = {Journal of the Association for Information Science and Technology}, year = {2016}, volume = {67}, number = {4}, pages = {928-941}, url = {http://onlinelibrary.wiley.com/doi/10.1002/asi.23435/abstract}, doi = {10.1002/asi.23435} }
001 ACL-int Daykin, J; Groukt, R; Guesnet, Y; Lecroq, T; Lefebvre, A; Léonard, M & Prieur-Gaston, E. Binary Block Order Rouen Transform. Theoretical Computer Science , 2016. Accepted.
BibTeX: @article{Daykin2016, author = {Daykin, J and Groukt, R and Guesnet, Y and Lecroq, T and Lefebvre, A and Léonard, M and Prieur-Gaston, E}, title = {Binary Block Order Rouen Transform}, journal = {Theoretical Computer Science}, year = {2016}, note = {Accepted} }
001 ACL-int Fici, G; Kociumaka, T; Lecroq, T; Lefebvre, A & Prieur-Gaston, E. Fast Computation of Abelian Runs. Theoretical Computer Science , 2016. accepted.
BibTeX: @article{Ficia, author = {Fici, G and Kociumaka, T and Lecroq, T and Lefebvre, A and Prieur-Gaston, E}, title = {Fast Computation of Abelian Runs}, journal = {Theoretical Computer Science}, year = {2016}, note = {accepted} }
001 ACL-int Gabriele Fici; Alessio Langiu; Thierry Lecroq; Arnaud Lefebvre; Filippo Mignosi; Jarkko Peltomäki & Élise Prieur-Gaston. Abelian powers and repetitions in Sturmian words. Theor. Comput. Sci. , Volume 635, Pages 16-34, 2016.
BibTeX: @article{Fici2016, author = {Gabriele Fici and Alessio Langiu and Thierry Lecroq and Arnaud Lefebvre and Filippo Mignosi and Jarkko Peltom{\"{a}}ki and {\'{E}}lise Prieur{-}Gaston}, title = {Abelian powers and repetitions in Sturmian words}, journal = {Theor. Comput. Sci.}, year = {2016}, volume = {635}, pages = {16--34}, url = {http://dx.doi.org/10.1016/j.tcs.2016.04.039}, doi = {10.1016/j.tcs.2016.04.039} }
001 ACL-int Fici, G; Lecroq, T; Lefebvre, A; Prieur-Gaston, E & Smyth, WF. A Note on Easy and Efficient Computation of Full Abelian Periods of a Word. Discrete Applied Mathematics , 2016. to appear.
BibTeX: @article{Fici2016a, author = {Fici, G and Lecroq, T and Lefebvre, A and Prieur-Gaston, E and Smyth, WF}, title = {A Note on Easy and Efficient Computation of Full Abelian Periods of a Word}, journal = {Discrete Applied Mathematics}, year = {2016}, note = {to appear} }
001 ACL-int Fici, Gabriele; Lecroq, Thierry; Lefebvre, Arnaud; Prieur-Gaston, Élise & Smyth, William F.. A note on easy and efficient computation of full abelian periods of a word. Discrete Applied Mathematics , 2016.
Abstract: Constantinescu and Ilie (2006) introduced the idea of an Abelian period with head and tail of a finite word. An Abelian period is called full if both the head and the tail are empty. We present a simple and easy-to-implement O ( n log log n ) -time algorithm for computing all the full Abelian periods of a word of length n over a constant-size alphabet. Experiments show that our algorithm significantly outperforms the O ( n ) algorithm proposed by Kociumaka et al. (2013) for the same problem.
BibTeX: @article{Fici, author = {Fici, Gabriele and Lecroq, Thierry and Lefebvre, Arnaud and Prieur-Gaston, Élise and Smyth, William F.}, title = {A note on easy and efficient computation of full abelian periods of a word}, journal = {Discrete Applied Mathematics}, year = {2016}, url = {http://www.sciencedirect.com/science/article/pii/S0166218X15004850}, doi = {10.1016/j.dam.2015.09.024} }
001 ACL-int Griffon, N.; Schuers, M.; Dhombres, F.; Merabti, T.; Kerdelhué, G.; Rollin, L. & Darmoni, S. J.. Searching for rare diseases in PubMed: a blind comparison of Orphanet expert query and query based on terminological knowledge.. BMC Med Inform Decis Mak , Volume 16, Number 1, Pages 101, 2016.
Abstract: Despite international initiatives like Orphanet, it remains difficult to find up-to-date information about rare diseases. The aim of this study is to propose an exhaustive set of queries for PubMed based on terminological knowledge and to evaluate it versus the queries based on expertise provided by the most frequently used resource in Europe: Orphanet.Four rare disease terminologies (MeSH, OMIM, HPO and HRDO) were manually mapped to each other permitting the automatic creation of expended terminological queries for rare diseases. For 30 rare diseases, 30 citations retrieved by Orphanet expert query and/or query based on terminological knowledge were assessed for relevance by two independent reviewers unaware of the query's origin. An adjudication procedure was used to resolve any discrepancy. Precision, relative recall and F-measure were all computed.For each Orphanet rare disease (n = 8982), there was a corresponding terminological query, in contrast with only 2284 queries provided by Orphanet. Only 553 citations were evaluated due to queries with 0 or only a few hits. There were no significant differences between the Orpha query and terminological query in terms of precision, respectively 0.61 vs 0.52 (p = 0.13). Nevertheless, terminological queries retrieved more citations more often than Orpha queries (0.57 vs. 0.33; p = 0.01). Interestingly, Orpha queries seemed to retrieve older citations than terminological queries (p < 0.0001).The terminological queries proposed in this study are now currently available for all rare diseases. They may be a useful tool for both precision or recall oriented literature search.
BibTeX: @article{Griffon2016a, author = {Griffon, N. and Schuers, M. and Dhombres, F. and Merabti, T. and Kerdelhué, G. and Rollin, L. and Darmoni, S. J.}, title = {Searching for rare diseases in PubMed: a blind comparison of Orphanet expert query and query based on terminological knowledge.}, journal = {BMC Med Inform Decis Mak}, year = {2016}, volume = {16}, number = {1}, pages = {101}, url = {http://dx.doi.org/10.1186/s12911-016-0333-0}, doi = {10.1186/s12911-016-0333-0} }
001 ACL-int Haddoud, M; Mokhtari, A; Lecroq, T & Abdeddaïm, S. Combining supervised term weighting metrics for SVM text classification with extended term representation Knowledge and Information Systems. , 2016.
BibTeX: @article{Haddoud, author = {Haddoud, M and Mokhtari, A and Lecroq, T and Abdeddaïm, S}, title = {Combining supervised term weighting metrics for SVM text classification with extended term representation Knowledge and Information Systems}, year = {2016} }
001 ACL-int Mareschal, Sylvain; Dubois, Sydney; Viailly, Pierre-Julien; Bertrand, Philippe; Bohers, Elodie; Maingonnat, Catherine; Jaïs, Jean-Philippe; Tesson, Bruno; Ruminy, Philippe; Peyrouze, Pauline; Copie-Bergman, Christiane; Fest, Thierry; Jo Molina, Thierry; Haioun, Corinne; Salles, Gilles; Tilly, Hervé; Lecroq, Thierry; Leroy, Karen & Jardin, Fabrice. Whole exome sequencing of relapsed/refractory patients expands the repertoire of somatic mutations in diffuse large B-cell lymphoma.. Genes Chromosomes Cancer , Mar, Volume 55, Number 3, Pages 251-267, 2016.
Abstract: Despite the many efforts already spent to enumerate somatic mutations in diffuse large B-cell lymphoma (DLBCL), previous whole-genome and whole-exome studies conducted on patients of mixed outcomes failed at characterizing the 30% of patients who will relapse or resist current immunochemotherapies. To address this issue, we performed whole-exome sequencing of normal/tumoral DNA pairs in 14 relapsed/refractory (R/R) patients subclassified by full-transcriptome arrays (six activated B-cell like, three germinal center B-cell like, and five primary mediastinal B-cell lymphomas), from the LNH-03 LYSA clinical trial program. Aside from well-known DLBCL features, gene and pathway level recurrence analyses proposed several interesting leads including TBL1XR1 and activating mutations in IRF4 or in the insulin regulation pathway. Sequencing-based copy number analysis defined 23 short recurrently altered regions involving genes such as REL, CDKN2A, HYAL2, and TP53. Moreover, it highlighted mutations in genes such as GNA13, CARD11, MFHAS1, and PCLO as associated with secondary variant allele amplification events. The five primary mediastinal B-cell lymphomas (PMBL), while unexpected in a R/R cohort, showed a significantly higher mutation rate (P = 0.003) and provided many insights on this classical Hodgkin lymphoma related subtype. Novel genes such as XPO1, MFHAS1, and ITPKB were found particularly mutated, along with various cytokine-based signaling pathways. Among these analyses, somatic events in the NF-κB pathway were found preponderant in the three DLBCL subtypes, confirming its major implication in DLBCL aggressiveness and pinpointing several new candidate genes.
BibTeX: @article{Mareschal2016, author = {Mareschal, Sylvain and Dubois, Sydney and Viailly, Pierre-Julien and Bertrand, Philippe and Bohers, Elodie and Maingonnat, Catherine and Jaïs, Jean-Philippe and Tesson, Bruno and Ruminy, Philippe and Peyrouze, Pauline and Copie-Bergman, Christiane and Fest, Thierry and {Jo Molina}, Thierry and Haioun, Corinne and Salles, Gilles and Tilly, Hervé and Lecroq, Thierry and Leroy, Karen and Jardin, Fabrice}, title = {Whole exome sequencing of relapsed/refractory patients expands the repertoire of somatic mutations in diffuse large B-cell lymphoma.}, month = {Mar}, journal = {Genes Chromosomes Cancer}, year = {2016}, volume = {55}, number = {3}, pages = {251--267}, url = {http://dx.doi.org/10.1002/gcc.22328}, doi = {10.1002/gcc.22328} }
001 ACL-int Na, Joong Chae; Kim, Hyunjoon; Park, Heejin; Lecroq, Thierry; Léonard, Martine; Mouchard, Laurent & Park, Kunsoo. FM-index of alignment: A compressed index for similar strings. Theoretical Computer Science , 2016.
Abstract: In this paper we propose the FM-index of alignment, a compressed index for similar strings with the functionalities of pattern search and random access. For this, we first design a new and improved version of the suffix array of alignment. The FM-index of alignment is an FM-index of this suffix array of alignment. The FM-index of alignment supports the LF-mapping and backward search, the key functionalities of the FM-index, but the LF-mapping and backward search of our index is significantly more involved than the original FM-index. We implemented the FM-index of alignment and did experiments on 100 genome sequences from the 1000 Genomes Project. The index size of the FM-index of alignment is about a half of that of RLCSA due to Mäkinen et al.
BibTeX: @article{Na, author = {Na, Joong Chae and Kim, Hyunjoon and Park, Heejin and Lecroq, Thierry and Léonard, Martine and Mouchard, Laurent and Park, Kunsoo}, title = {{FM}-index of alignment: {A} compressed index for similar strings}, journal = {Theoretical Computer Science}, year = {2016}, url = {http://www.sciencedirect.com/science/article/pii/S0304397515007288}, doi = {10.1016/j.tcs.2015.08.008} }
001 ACL-int N. Ben Nsira; T. Lecroq & M. Elloumi. On-line string matching in highly similar DNA sequences. Mathematics in Computer Science , 2016.
BibTeX: @article{Bennsira2015b, author = {N. Ben Nsira and T. Lecroq and M. Elloumi}, title = {On-line string matching in highly similar {DNA} sequences}, journal = {Mathematics in Computer Science}, year = {2016} }
001 ACL-int Schuers, Matthieu; Griffon, Nicolas; Kerdelhue, Gaëtan; Foubert, Quentin; Mercier, Alain & Darmoni, Stéfan J.. Behavior and attitudes of residents and general practitioners in searching for health information: From intention to practice. International Journal of Medical Informatics , May, Volume 89, Pages 9-14, 2016.
Abstract: Background Physicians are increasingly encouraged to practice evidence-based medicine (EBM), and their decisions require evidence based on valid research. Existing literature shows a mismatch between general practitioners’ (GPs) information needs and evidence available online. The aim of this study was to explore the attitudes and behavior of residents in general medicine and GPs when seeking medical information online. Methods Five focus groups (FGs) involving residents in general medicine and GPs were conducted between October 2013 and January 2014. The overall number of participants recruited was 35. The focus group discussion guide focused on participants’ experiences in searching for health information on the Internet, perceived barriers and possible solutions for improving the quality of their own search processes. Descriptive analysis was performed by three researchers. Results Participants described a wide range of research topics, covering all general medicine core competencies, and especially patient-oriented topics. They used a limited list of websites. Participants were not confident about their ability to assess the quality of the information they found. Their assessment of data quality was based on intuition, and they mainly sought concordance with their existing knowledge. The way the data were exposed was considered very important. Participants were looking for information that was directly linked to their clinical practice. Information seeking processes varied among participants. They felt they had not mastered query building for conducting searches, and were aware of the impact this shortcoming had on the quality of their search for information. Conclusions Residents in general medicine and GPs understood the importance of EBM and the need for objective and reliable information. The present study highlights the difficulties in identifying this kind of information, and suggests ideas for improvement. Available search tools should change in order to fill the gap with real-world clinical practice, for example by integrating a patient-centred approach.
BibTeX: @article{Schuers2016, author = {Schuers, Matthieu and Griffon, Nicolas and Kerdelhue, Gaëtan and Foubert, Quentin and Mercier, Alain and Darmoni, Stéfan J.}, title = {Behavior and attitudes of residents and general practitioners in searching for health information: {From} intention to practice}, month = {May}, journal = {International Journal of Medical Informatics}, year = {2016}, volume = {89}, pages = {9--14}, url = {http://www.sciencedirect.com/science/article/pii/S1386505616300235}, doi = {10.1016/j.ijmedinf.2016.02.003} }
001 ACL-int Soualmia, LF & Charlet, J. Efficient Results in Semantic Interoperability for Health Care. IMIA Yearbook of Medical Informatics , Pages 134-137, 2016. in press..
BibTeX: @article{Soualmia2016, author = {Soualmia, LF and Charlet, J}, title = {Efficient Results in Semantic Interoperability for Health Care}, journal = {IMIA Yearbook of Medical Informatics}, year = {2016}, pages = {134-137}, note = {in press.} }
002 ACL-nat Griffon, Nicolas; Schuers, Matthieu & Darmoni, Stefan J.. Littérature Scientifique en Santé (LiSSa) : une alternative à l’anglais ?. La Presse Médicale , November, Volume 45, Number 11, Pages 955-956, 2016.
BibTeX: @article{Griffon2016b, author = {Griffon, Nicolas and Schuers, Matthieu and Darmoni, Stefan J.}, title = {Littérature {Scientifique} en {Santé} ({LiSSa}) : une alternative à l’anglais ?}, month = {November}, journal = {La Presse Médicale}, year = {2016}, volume = {45}, number = {11}, pages = {955--956}, url = {http://www.sciencedirect.com/science/article/pii/S0755498216303505}, doi = {10.1016/j.lpm.2016.11.001} }
002 ACL-nat Griffon, Nicolas; Schuers, Matthieu; Kerdelhué, Gaétan; Grosjean, Julien & Darmoni, Stéfan. Littérature scientifique en santé (LiSSa) : une base de données bibliographiques en français. La Revue Du Praticien , 2016.
BibTeX: @article{Griffon2016c, author = {Griffon, Nicolas and Schuers, Matthieu and Kerdelhué, Gaétan and Grosjean, Julien and Darmoni, Stéfan}, title = {Littérature scientifique en santé ({LiSSa}) : une base de données bibliographiques en français}, journal = {La Revue Du Praticien}, year = {2016} }
002 ACL-nat Lamy, JB; Soualmia, LF; Duclos, C & Venot, A. Formalisation de la Sémantique des Langages Iconiques : Méthode à base d’Ontologie et Applications. Revue d’Intelligence Artificielle , 2016. in press..
BibTeX: @article{Lamy2016, author = {Lamy, JB and Soualmia, LF and Duclos, C and Venot, A}, title = {Formalisation de la Sémantique des Langages Iconiques : Méthode à base d’Ontologie et Applications}, journal = {Revue d’Intelligence Artificielle}, year = {2016}, note = {in press.} }
002 ACL-nat Mary, M; Soualmia, LF & Gansel, X. Interopérabilité sémantique entre vocabulaires contrôlés : Évaluation de la qualité des alignements sur des données de standards du diagnostic in vitro. Revue Ingénierie des Systèmes d’Information (ISI) , 2016. in press..
BibTeX: @article{Mary2016c, author = {Mary, M and Soualmia, LF and Gansel, X}, title = {Interopérabilité sémantique entre vocabulaires contrôlés : Évaluation de la qualité des alignements sur des données de standards du diagnostic in vitro}, journal = {Revue Ingénierie des Systèmes d’Information (ISI)}, year = {2016}, note = {in press.} }
002 ACL-nat Schuers, M.; Timsit, M.; Gillibert, A.; Fred, A.; Griffon, N.; Bénichou, J.; Darmoni, S.J. & Staccini, P.. Intérêt et utilisabilité du dossier pharmaceutique en pratique médicale. Enquête auprès de médecins et pharmaciens hospitaliers (étude MATRIX). Revue d'Épidémiologie et de Santé Publique , September, Volume 64, Number 4, Pages 229-236, 2016.
Abstract: Position du problème Une expérimentation a été lancée en 2013 pour évaluer l’impact de la consultation du dossier pharmaceutique dans les services d’urgences, de gériatrie et d’anesthésie-réanimation de 55 établissements hospitaliers. L’objectif de cette étude était d’évaluer l’intérêt et l’utilisabilité du dossier pharmaceutique auprès des médecins et pharmaciens utilisateurs. Méthodes Un auto-questionnaire électronique a été envoyé à tous les pharmaciens, anesthésistes-réanimateurs, gériatres et urgentistes des 55 établissements expérimentateurs du dossier pharmaceutique. Ce questionnaire évaluait l’utilisabilité du dossier pharmaceutique via la traduction française de l’échelle d’utilisabilité des systèmes, ainsi que l’usage du dossier pharmaceutique, son intérêt et ses limites perçues dans la pratique clinique et la satisfaction générale vis-à-vis de l’outil. Les questionnaires ont été collectés de novembre 2014 à janvier 2015. Résultats Quatre-vingt-seize questionnaires ont été recueillis. Ils concernaient 47 centres hospitaliers, soit 86 % des 55 établissements expérimentateurs du dossier pharmaceutique. Le recoupement des réponses a permis d’identifier 36 établissements au sein desquels le dossier pharmaceutique était actif. Soixante-treize questionnaires remplis par des praticiens ayant pu expérimenter le dossier pharmaceutique ont pu être exploités. Parmi les répondants, on comptait 57 % de pharmaciens (n = 42) et 43 % de médecins (n = 31), dont 13 gériatres, 11 urgentistes et 7 anesthésistes-réanimateurs. Le score moyen d’utilisabilité du dossier pharmaceutique était de 62,5 sur 100. Il ne variait ni selon la profession du répondant, ni selon son ancienneté d’exercice. Il était positivement corrélé à la fréquence d’utilisation. Plus de la moitié des répondants déclaraient utiliser rarement, ou jamais, le dossier pharmaceutique. La durée de la période d’accès aux données du dossier était considérée comme insuffisante. L’absence de mention des posologies des médicaments délivrés, le faible nombre de patients disposant de leur carte d’assurance maladie et le faible nombre de patients ayant un dossier pharmaceutique ouvert constituaient les principaux obstacles à une plus grande utilisation du dossier pharmaceutique. Conclusion Deux ans après le début de l’expérimentation visant à élargir l’accès au dossier pharmaceutique à des professionnels médicaux, les premiers éléments d’évaluation sont encourageants. Il reste nécessaire d’évaluer les conséquences de l’accès au dossier pharmaceutique pour les médecins.
BibTeX: @article{Schuers2016a, author = {Schuers, M. and Timsit, M. and Gillibert, A. and Fred, A. and Griffon, N. and Bénichou, J. and Darmoni, S.J. and Staccini, P.}, title = {Intérêt et utilisabilité du dossier pharmaceutique en pratique médicale. {Enquête} auprès de médecins et pharmaciens hospitaliers (étude {MATRIX})}, month = {September}, journal = {Revue d'Épidémiologie et de Santé Publique}, year = {2016}, volume = {64}, number = {4}, pages = {229--236}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0398762016302905}, doi = {10.1016/j.respe.2016.05.001} }
004 ACTI Cabot, Chloé; Lelong, Romain; Grosjean, Julien; Soualmia, Lina F. & Darmoni, Stéfan J.. Retrieving Clinical and Omic Data from Electronic Health Records.. Stud Health Technol Inform , Volume 221, Pages 115, 2016.
BibTeX: @article{Cabot2016, author = {Cabot, Chloé and Lelong, Romain and Grosjean, Julien and Soualmia, Lina F. and Darmoni, Stéfan J.}, title = {Retrieving Clinical and Omic Data from Electronic Health Records.}, journal = {Stud Health Technol Inform}, year = {2016}, volume = {221}, pages = {115} }
004 ACTI Cabot, C; Soualmia, LF; Dahamna, B & Darmoni, SJ. SIBM at CLEF eHealth Evaluation Lab 2016: Extracting Concepts in French Medical Texts with ECMT and CIMIND. CLEF2016 Working Notes, Pages 47-60, 2016.
BibTeX: @inproceedings{Cabot2016a, author = {Cabot, C and Soualmia, LF and Dahamna, B and Darmoni, SJ}, title = {SIBM at CLEF eHealth Evaluation Lab 2016: Extracting Concepts in French Medical Texts with ECMT and CIMIND}, booktitle = {CLEF2016 Working Notes}, year = {2016}, pages = {47-60}, url = {http://ceur-ws.org/Vol-1609/16090047.pdf} }
004 ACTI Gómez-Sánchez, AF; González-Cantalejo, M; Kerdelhué, G; Iriarte, P & Isabel-Gómez, R. Evaluating the information retrieval quality and methodological accuracy of Systematic Reviews and Meta-analysis on congenital malformations (2004-2014). EAHIL, 2016.
BibTeX: @inproceedings{Gomez-Sanchez2016, author = {Gómez-Sánchez, AF and González-Cantalejo, M and Kerdelhué, G and Iriarte, P and Isabel-Gómez, R}, title = {Evaluating the information retrieval quality and methodological accuracy of Systematic Reviews and Meta-analysis on congenital malformations (2004-2014)}, booktitle = {EAHIL}, year = {2016} }
004 ACTI Lelong, R; Cabot, C; Soualmia, LF & Darmoni, SJ. Semantic Search Engine to Query into Electronic Health Records with a Multiple-Layer Query Language. MEDIR workshop, 2016. Accepted.
BibTeX: @inproceedings{Lelong2016, author = {Lelong, R and Cabot, C and Soualmia, LF and Darmoni, SJ}, title = {Semantic Search Engine to Query into Electronic Health Records with a Multiple-Layer Query Language}, booktitle = {MEDIR workshop}, year = {2016}, note = {Accepted} }
004 ACTI Mary, M; Soualmia, LF & Gansel, X. Usability and Improvement of Existing Alignments: the LOINC-SNOMED CT Case Study. 20th International Conference on Knowledge Engineering and Knowledge Management, EKAW, Bologna, Italy, 2016. in press..
BibTeX: @inproceedings{Mary2016e, author = {Mary, M and Soualmia, LF and Gansel, X}, title = {Usability and Improvement of Existing Alignments: the LOINC-SNOMED CT Case Study}, booktitle = {20th International Conference on Knowledge Engineering and Knowledge Management, EKAW}, address = {Bologna, Italy}, year = {2016}, note = {in press.} }
005 ACTN Henry, V; Soualmia, LF; Grosjean, J; Desfeux, A; Darmoni, SJ & Gonzalez, B. OMIConto : une Ressource Termino-Ontologique pour la Qualification et l’Indexation des Outils d’Analyse en Sciences Omiques. Actes du 2ème Atelier Intelligence Artificielle & Santé@Ingénierie des Connaissances, Montpellier, France, 2016. In press.
BibTeX: @inproceedings{Henry2016, author = {Henry, V and Soualmia, LF and Grosjean, J and Desfeux, A and Darmoni, SJ and Gonzalez, B}, title = {OMIConto : une Ressource Termino-Ontologique pour la Qualification et l’Indexation des Outils d’Analyse en Sciences Omiques}, booktitle = {Actes du 2ème Atelier Intelligence Artificielle \& Santé@Ingénierie des Connaissances}, address = {Montpellier, France}, year = {2016}, note = {In press} }
005 ACTN Mary, M; Soualmia, LF & Gan. Évaluation de la Qualité des Liens Sémantiques entre Vocabulaires Contrôlés. Actes de l'Atelier SoWeDo (des Sources Ouvertes au Web de Données)@Ingénierie des Connaissances, Montpellier, France, 2016. In press.
BibTeX: @inproceedings{Mary2016a, author = {Mary, M and Soualmia, LF and Gan}, title = {Évaluation de la Qualité des Liens Sémantiques entre Vocabulaires Contrôlés}, booktitle = {Actes de l'Atelier SoWeDo (des Sources Ouvertes au Web de Données)@Ingénierie des Connaissances}, address = {Montpellier, France}, year = {2016}, note = {In press} }
005 ACTN Mary, M; Soualmia, LF & Gans. Interopérabilité Sémantique dans le Domaine du Diagnostic in vitro : Évaluation d’Algorithmes sur LOINC et l’Ontologie SNOMED CT. Actes des 27èmes Journées Francophones d'Ingénierie des Connaissances (IC), Montpellier, France, 2016. In press.
BibTeX: @inproceedings{Mary2016b, author = {Mary, M and Soualmia, LF and Gans}, title = {Interopérabilité Sémantique dans le Domaine du Diagnostic in vitro : Évaluation d’Algorithmes sur LOINC et l’Ontologie SNOMED CT}, booktitle = {Actes des 27èmes Journées Francophones d'Ingénierie des Connaissances (IC)}, address = {Montpellier, France}, year = {2016}, note = {In press} }
005 ACTN Mary, M; Soualmia, LF & Gansel, X. Interopérabilité Sémantique dans le Domaine du Diagnostic in vitro. Actes du 2ème Atelier Intelligence Artificielle & Santé@Ingénierie des Connaissances, Montpellier, France, 2016. In press.
BibTeX: @inproceedings{Mary2016, author = {Mary, M and Soualmia, LF and Gansel, X}, title = {Interopérabilité Sémantique dans le Domaine du Diagnostic in vitro}, booktitle = {Actes du 2ème Atelier Intelligence Artificielle \& Santé@Ingénierie des Connaissances}, address = {Montpellier, France}, year = {2016}, note = {In press} }
005 ACTN Mary, M; Soualmia, LF & Gansel X. Projection des Propriétés d’une Ontologie pour la Classification d’une Ressource Terminologique. Actes des 6èmes Journées Francophones sur les Ontologies (JFO), Bordeaux, France, 2016. in press..
BibTeX: @inproceedings{Mary2016d, author = {Mary, M and Soualmia, LF and Gansel X}, title = {Projection des Propriétés d’une Ontologie pour la Classification d’une Ressource Terminologique}, booktitle = {Actes des 6èmes Journées Francophones sur les Ontologies (JFO)}, address = {Bordeaux, France}, year = {2016}, note = {in press.} }
007 AFF Griffon, N; Rollin, L; Schuers, M; Dhombres, F; Loiseau, S; Douze, L; Marcilly, R; Chabot, O; Delerue, D; Dutoit, D; Dahamna, B; Kerdelhué, G; Grosjean, J; Gehanno, JF & Darmoni, SJ. Une base de données bibliographiques en français pour la Littérature Scientifique en Santé : LiSSa. JFIM, 2016.
BibTeX: @inproceedings{Griffon2016, author = {Griffon, N and Rollin, L and Schuers, M and Dhombres, F and Loiseau, S and Douze, L and Marcilly, R and Chabot, O and Delerue, D and Dutoit, D and Dahamna, B and Kerdelhué, G and Grosjean, J and Gehanno, JF and Darmoni, SJ}, title = {Une base de données bibliographiques en français pour la Littérature Scientifique en Santé : LiSSa}, booktitle = {JFIM}, year = {2016} }
007 AFF Kerdelhué, G & Grosjean, J. A tool to design complex bibliographic queries in your own language. EAHIL, 2016.
BibTeX: @inproceedings{Kerdelhue2016, author = {Kerdelhué, G and Grosjean, J}, title = {A tool to design complex bibliographic queries in your own language}, booktitle = {EAHIL}, year = {2016} }
008 OS Maxime Crochemore & Thierry Lecroq. Multiple String Matching. Encyclopedia of Algorithms, Pages 1378-1382, 2016.
BibTeX: @incollection{Crochemore2016, author = {Maxime Crochemore and Thierry Lecroq}, title = {Multiple String Matching}, booktitle = {Encyclopedia of Algorithms}, year = {2016}, pages = {1378--1382}, url = {http://dx.doi.org/10.1007/978-1-4939-2864-4_366}, doi = {10.1007/978-1-4939-2864-4_366} }
008 OS Maxime Crochemore & Thierry Lecroq. String Matching. Encyclopedia of Algorithms, Pages 2113-2117, 2016.
BibTeX: @incollection{Crochemore2016a, author = {Maxime Crochemore and Thierry Lecroq}, title = {String Matching}, booktitle = {Encyclopedia of Algorithms}, year = {2016}, pages = {2113--2117}, url = {http://dx.doi.org/10.1007/978-1-4939-2864-4_365}, doi = {10.1007/978-1-4939-2864-4_365} }
2015 001 ACL-int Aimé, X; Traore, L; Chniti, A; Sadou, E; Ouagne, D; Charlet, J; Jaulent, MC; Darmoni, SJ; Griffon, N; Amardeilh, F; Bascarane, L; Lepage, E & Daniel, C. Semantic interoperability platform for Healthcare Information Exchange. IRBM - Innovation and Research in BioMedical , 2015. Accepted.
BibTeX: @article{Aime2015, author = {Aimé, X and Traore, L and Chniti, A and Sadou, E and Ouagne, D and Charlet, J and Jaulent, MC and Darmoni, SJ and Griffon, N and Amardeilh, F and Bascarane, L and Lepage, E and Daniel, C}, title = {Semantic interoperability platform for Healthcare Information Exchange}, journal = {IRBM - Innovation and Research in BioMedical}, year = {2015}, note = {Accepted} }
001 ACL-int H. Bouhamed; A. Masmoudi; T. Lecroq & A. Rebai. Structure space of Bayesian networks is dramatically reduced by subdividing it in sub-networks. Journal of Computational and Applied Mathematics , Volume 287, Pages 48-62, 2015.
BibTeX: @article{bouhamed2015, author = {H. Bouhamed and A. Masmoudi and T. Lecroq and A. Rebai}, title = {Structure space of Bayesian networks is dramatically reduced by subdividing it in sub-networks}, journal = {Journal of Computational and Applied Mathematics}, year = {2015}, volume = {287}, pages = {48--62} }
001 ACL-int H. Bouhamed; A. Masmoudi; T. Lecroq & A. Rebai. Reducing the structure space of Bayesian classifiers using some general algorithms. Journal of Mathematical Modelling and Algorithms in Operations Research , June, Volume 14, Number 2, Pages 197-237, 2015.
BibTeX: @article{bouhamed2015a, author = {H. Bouhamed and A. Masmoudi and T. Lecroq and A. Rebai}, title = {Reducing the structure space of Bayesian classifiers using some general algorithms}, month = {June}, journal = {Journal of Mathematical Modelling and Algorithms in Operations Research}, year = {2015}, volume = {14}, number = {2}, pages = {197-237} }
001 ACL-int Jamoulle, Marc; Gavilan, Enrique; Cardoso, Raquel Val; Mariño, Maria Ana; Pizzanelli, Miguel; Grosjean, Julien & Darmoni, Stefan. The words of prevention, part II: ten terms in the realm of quaternary prevention. Revista Brasileira de Medicina de Família e Comunidade , April, 2015.
Abstract: Objective: This part II article about the ‘words of prevention’ presents in a terminological way the content of ten current concepts used in the prevention domain which are closely linked to quaternary prevention: (1) overinformation, (2) overdiagnosis, (3) medically unexplained symptoms, (4) overmedicalisation, (5) incidentaloma, (6) overscreening, (7) overtreatment, (8) shared decision making, (9) deprescribing, and (10) disease mongering. Methods: with the support of the laboratory team of the University of Rouen, France, which is dedicated to medical terminology and semantic relationships, it was possible to utilize a graphic user interface (called DBGUI) allowing the construction of links for each of chosen terms, and making automatic links to MeSH, if any. Those concepts are analyzed in their environment in current literature, as well as in their MeSH counterparts, if any, and related semantic online terminologies. Results and Discussion: The rules in terminological development aspire to cover the whole field of a concept and in the meantime, it helps to avoid the noise due to proxy and not exactly related issues. This refers to exhaustivity and specificity in information retrieval. Our finds show that referring to MeSH only in information retrieval in General Practice/Family medicine can induce much noise and poor adequacy to the subject investigated. Conclusion: Gathering concepts in specially prepared terminologies for further development of ontologies is a necessity to enter in the semantic web area and the era of distributed data.
BibTeX: @article{Jamoulle2015, author = {Jamoulle, Marc and Gavilan, Enrique and Cardoso, Raquel Val and Mariño, Maria Ana and Pizzanelli, Miguel and Grosjean, Julien and Darmoni, Stefan}, title = {The words of prevention, part {II}: ten terms in the realm of quaternary prevention}, month = {April}, journal = {Revista Brasileira de Medicina de Família e Comunidade}, year = {2015}, url = {http://orbi.ulg.ac.be/handle/2268/176757} }
001 ACL-int Jamoulle, Marc; Stichele, Vander; H, Robert; Cardillo, Elena; Roumier, Joseph; Grosjean, Julien & Darmoni, Stefan. Semantic Web and the Future of Health Care Data in Family Practice. Merit Research Journal of Medicine and Medical Sciences , December, Volume 3, Number 12, 2015.
BibTeX: @article{Jamoulle2015b, author = {Jamoulle, Marc and Stichele, Vander and H, Robert and Cardillo, Elena and Roumier, Joseph and Grosjean, Julien and Darmoni, Stefan}, title = {Semantic {Web} and the {Future} of {Health} {Care} {Data} in {Family} {Practice}}, month = {December}, journal = {Merit Research Journal of Medicine and Medical Sciences}, year = {2015}, volume = {3}, number = {12}, url = {http://orbi.ulg.ac.be/handle/2268/189292} }
001 ACL-int N. Ben Nsira; T. Lecroq & M. Elloumi. A fast Boyer-Moore type pattern matching algorithm for highly similar sequences. International Journal of Data Mining and Bioinformatics , Volume 13, Number 3, Pages 266-288, 2015.
BibTeX: @article{Nsira2015, author = {N. Ben Nsira and T. Lecroq and M. Elloumi}, title = {A fast {B}oyer-{M}oore type pattern matching algorithm for highly similar sequences}, journal = {International Journal of Data Mining and Bioinformatics}, year = {2015}, volume = {13}, number = {3}, pages = {266-288} }
001 ACL-int Rollin, L; Griffon, N; Darmoni, SJ & Gehanno, JF. Influence of author's affiliation and funding sources on the results of cohort studies on occupational cancer. American Journal of Industrial Medicine , 2015.
BibTeX: @article{Rollin2015, author = {Rollin, L and Griffon, N and Darmoni, SJ and Gehanno, JF}, title = {Influence of author's affiliation and funding sources on the results of cohort studies on occupational cancer}, journal = {American Journal of Industrial Medicine}, year = {2015}, doi = {10.1002/ajim.22549} }
001 ACL-int Soualmia, L. F. & Lecroq, T.. Bioinformatics Methods and Tools to Advance Clinical Care. Findings from the Yearbook 2015 Section on Bioinformatics and Translational Informatics.. Yearb Med Inform , Aug, Volume 10, Number 1, Pages 170-173, 2015.
Abstract: To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care.We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review.The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival.The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and development efforts contribute to the challenge of impacting clinically the obtained results towards a personalized medicine.
BibTeX: @article{Soualmia2015b, author = {Soualmia, L. F. and Lecroq, T.}, title = {Bioinformatics Methods and Tools to Advance Clinical Care. Findings from the Yearbook 2015 Section on Bioinformatics and Translational Informatics.}, month = {Aug}, journal = {Yearb Med Inform}, year = {2015}, volume = {10}, number = {1}, pages = {170--173}, url = {http://dx.doi.org/10.15265/IY-2015-026}, doi = {10.15265/IY-2015-026} }
001 ACL-int Toubiana, L. & Griffon, N.. Modelling, Simulation and Social Network Data: What's New for Public Health and Epidemiology Informatics?. Yearb Med Inform , Aug, Volume 10, Number 1, Pages 216-219, 2015.
BibTeX: @article{Toubiana2015, author = {Toubiana, L. and Griffon, N.}, title = {Modelling, Simulation and Social Network Data: What's New for Public Health and Epidemiology Informatics?}, month = {Aug}, journal = {Yearb Med Inform}, year = {2015}, volume = {10}, number = {1}, pages = {216--219}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587051/pdf/ymi-10-0216.pdf}, doi = {10.15265/IY-2015-031} }
004 ACTI H. Bannai; S. Inenaga; T. Kociumaka; A. Lefebvre; J. Radoszewski; W. Rytter; S. Sugimoto & T. Waleń. Efficient Algorithms for Longest Closed Factor Array. Proceedings of the 22th Symposium on String Processing and Information Retrieval (SPIRE), London, UK, 2015. accepted.
BibTeX: @inproceedings{Bannai2015, author = {H. Bannai and S. Inenaga and T. Kociumaka and A. Lefebvre and J. Radoszewski and W. Rytter and S. Sugimoto and T. Wale\'n}, title = {Efficient Algorithms for Longest Closed Factor Array}, booktitle = {Proceedings of the 22th Symposium on String Processing and Information Retrieval (SPIRE)}, address = {London, UK}, year = {2015}, note = {accepted} }
004 ACTI Hideo Bannai; Shunsuke Inenaga; Tomasz Kociumaka; Arnaud Lefebvre; Jakub Radoszewski; Wojciech Rytter; Shiho Sugimoto & Tomasz Walen. Efficient Algorithms for Longest Closed Factor Array. String Processing and Information Retrieval - 22nd International Symposium, SPIRE 2015, London, UK, September 1-4, 2015, Proceedings, Pages 95-102, 2015.
BibTeX: @inproceedings{Bannai2015a, author = {Hideo Bannai and Shunsuke Inenaga and Tomasz Kociumaka and Arnaud Lefebvre and Jakub Radoszewski and Wojciech Rytter and Shiho Sugimoto and Tomasz Walen}, title = {Efficient Algorithms for Longest Closed Factor Array}, booktitle = {String Processing and Information Retrieval - 22nd International Symposium, {SPIRE} 2015, London, UK, September 1-4, 2015, Proceedings}, year = {2015}, pages = {95--102}, url = {http://dx.doi.org/10.1007/978-3-319-23826-5_10}, doi = {10.1007/978-3-319-23826-5_10} }
004 ACTI C. Barton; A. Heliou; L. Mouchard & S. Pissis. Engineering the Computation of Minimal Absent Words. 11th International Conference on Parallel Processing and Applied Mathematic, Krakow, Poland, 2015. accepted.
BibTeX: @inproceedings{ppam2015, author = {C. Barton and A. Heliou and L. Mouchard and S. Pissis}, title = {Engineering the Computation of Minimal Absent Words}, booktitle = {11th International Conference on Parallel Processing and Applied Mathematic}, address = {Krakow, Poland}, year = {2015}, note = {accepted} }
004 ACTI Carl Barton; Alice Heliou; Laurent Mouchard & Solon P. Pissis. Parallelising the Computation of Minimal Absent Words. Parallel Processing and Applied Mathematics - 11th International Conference, PPAM 2015, Krakow, Poland, September 6-9, 2015. Revised Selected Papers, Part II, Pages 243-253, 2015.
BibTeX: @inproceedings{Barton2015, author = {Carl Barton and Alice Heliou and Laurent Mouchard and Solon P. Pissis}, title = {Parallelising the Computation of Minimal Absent Words}, booktitle = {Parallel Processing and Applied Mathematics - 11th International Conference, {PPAM} 2015, Krakow, Poland, September 6-9, 2015. Revised Selected Papers, Part {II}}, year = {2015}, pages = {243--253}, url = {http://dx.doi.org/10.1007/978-3-319-32152-3_23}, doi = {10.1007/978-3-319-32152-3_23} }
004 ACTI Chebil, W; Soualmia, LF; Omri, MN & Darmoni, SJ. Biomedical Concepts Extraction with a Possibilistic Network and a Vector Space Model. 15th Conference on Artificial Intelligence in MEdicine, AIME'15, Lecture Notes in Artificial Intelligence, Volume 9105, Pages 227-231, 2015.
BibTeX: @inproceedings{Chebil2015, author = {Chebil, W and Soualmia, LF and Omri, MN and Darmoni, SJ}, title = {Biomedical Concepts Extraction with a Possibilistic Network and a Vector Space Model}, booktitle = {15th Conference on Artificial Intelligence in MEdicine, AIME'15}, year = {2015}, series = {Lecture Notes in Artificial Intelligence}, volume = {9105}, pages = {227-231} }
004 ACTI G. Fici; T. Lecroq; A. Lefebvre & É. Prieur-Gaston. Online Computation of Abelian Runs. Proceedings of the 9th International Conference on Language and Automata Theory and Applications (LATA 2015), Nice, France, Lecture Notes in Computer Science, Number 8977, Pages 391-401, Springer-Verlag, Berlin, 2015.
BibTeX: @inproceedings{Fici2015, author = {G. Fici and T. Lecroq and A. Lefebvre and \'E. Prieur-Gaston}, title = {Online Computation of Abelian Runs}, booktitle = {Proceedings of the 9th International Conference on Language and Automata Theory and Applications (LATA 2015)}, address = {Nice, France}, publisher = {Springer-Verlag, Berlin}, year = {2015}, series = {Lecture Notes in Computer Science}, number = {8977}, pages = {391--401} }
004 ACTI Franco-Contreras, Javier; Coatrieux, Gouenou; Massari, Philippe; Darmoni, Stefan; Cuppens-Boulahia, Nora; Cuppens, Frédéric & Roux, Christian. Data quality evaluation in medical database watermarking.. Stud Health Technol Inform MIE 2015, Volume 210, Pages 276-280, 2015.
Abstract: The use of watermarking in the protection of medical relational databases requires that the introduced distortion does not hinder records interpretation. In this paper, we present the preliminary results of a watermarked data quality evaluation protocol developed so as to analyze the perception the practitioner has of the watermark. These results show that some attributes are more appropriate for watermarking than others and also that incoherent or unlikely records resulting from careless watermarking are easily identified by an expert.
BibTeX: @inproceedings{Franco-Contreras2015, author = {Franco-Contreras, Javier and Coatrieux, Gouenou and Massari, Philippe and Darmoni, Stefan and Cuppens-Boulahia, Nora and Cuppens, Frédéric and Roux, Christian}, title = {Data quality evaluation in medical database watermarking.}, booktitle = {MIE 2015}, journal = {Stud Health Technol Inform}, year = {2015}, volume = {210}, pages = {276--280} }
004 ACTI Grouin, C; Griffon, N & Névéol, A. Is it possible to recover personal health information from an automatically de-identified corpus of French EHRs?. Proc of LOUHI - the Sixth International Workshop on Health Text Mining and Information Analysis, Lisbon, Portugal, 2015.
BibTeX: @inproceedings{Grouin2015a, author = {Grouin, C and Griffon, N and Névéol, A}, title = {Is it possible to recover personal health information from an automatically de-identified corpus of French EHRs?}, booktitle = {Proc of LOUHI - the Sixth International Workshop on Health Text Mining and Information Analysis}, address = {Lisbon, Portugal}, year = {2015} }
004 ACTI M. Haddoud; A. Mokhtari; T. Lecroq & S. Abdeddaïm. Accurate Keyphrase Extraction from Scientific Papers by Mining Linguistic Information. Proceedings of the First Workshop on Mining Scientific Papers: Computational Linguistics and Bibliometrics (CLBib 2015), Istanbul, Turkey, CEUR Workshop Proceedings, Volume 1384, Pages 12-17, CEUR-WS.org, 2015.
BibTeX: @inproceedings{Haddoud2015, author = {M. Haddoud and A. Mokhtari and T. Lecroq and S. Abdeddaïm}, title = {Accurate Keyphrase Extraction from Scientific Papers by Mining Linguistic Information}, booktitle = {Proceedings of the First Workshop on Mining Scientific Papers: Computational Linguistics and Bibliometrics (CLBib 2015)}, address = {Istanbul, Turkey}, publisher = {CEUR-WS.org}, year = {2015}, series = {CEUR Workshop Proceedings}, volume = {1384}, pages = {12--17} }
004 ACTI M. Haddoud; A. Mokhtari; T. Lecroq & S. Abdeddaïm. Supervised term weights for biomedical text classification. Proceedings of the 12th International meeting on Computational Intelligence methods for Bioinformatics and Biostatistics, CNR Research Area, Naples (Italy), 2015. accepted.
BibTeX: @inproceedings{Haddoud2015b, author = {M. Haddoud and A. Mokhtari and T. Lecroq and S. Abdeddaïm}, title = {Supervised term weights for biomedical text classification}, booktitle = {Proceedings of the 12th International meeting on Computational Intelligence methods for Bioinformatics and Biostatistics}, address = {CNR Research Area, Naples (Italy)}, year = {2015}, note = {accepted} }
004 ACTI Katsahian, Sandrine; Simond Moreau, Erica; Leprovost, Damien; Lardon, Jeremy; Bousquet, Cedric; Kerdelhué, Gaétan; Abdellaoui, Redhouane; Texier, Nathalie; Burgun, Anita; Boussadi, Abdelali & Faviez, Carole. Evaluation of Internet Social Networks using Net scoring Tool: A Case Study in Adverse Drug Reaction Mining.. Stud Health Technol Inform MIE 2015, Volume 210, Pages 526-530, 2015.
Abstract: Suspected adverse drug reactions (ADR) reported by patients through social media can be a complementary tool to already existing ADRs signal detection processes. However, several studies have shown that the quality of medical information published online varies drastically whatever the health topic addressed. The aim of this study is to use an existing rating tool on a set of social network web sites in order to assess the capabilities of these tools to guide experts for selecting the most adapted social network web site to mine ADRs.First, we reviewed and rated 132 Internet forums and social networks according to three major criteria: the number of visits, the notoriety of the forum and the number of messages posted in relation with health and drug therapy. Second, the pharmacist reviewed the topic-oriented message boards with a small number of drug names to ensure that they were not off topic. Six experts have been chosen to assess the selected internet forums using a French scoring tool: Net scoring. Three different scores and the agreement between experts according to each set of scores using weighted kappa pooled using mean have been computed.Three internet forums were chosen at the end of the selection step. Some criteria get high score (scores 3-4) no matter the website evaluated like accessibility (45-46) or design (34-36), at the opposite some criteria always have bad scores like quantitative (40-42) and ethical aspect (43-44), hyperlinks actualization (30-33). Kappa were positives but very small which corresponds to a weak agreement between experts.The personal opinion of the expert seems to have a major impact, undermining the relevance of the criterion. Our future work is to collect results given by this evaluation grid and proposes a new scoring tool for Internet social networks assessment.
BibTeX: @inproceedings{Katsahian2015, author = {Katsahian, Sandrine and {Simond Moreau}, Erica and Leprovost, Damien and Lardon, Jeremy and Bousquet, Cedric and Kerdelhué, Gaétan and Abdellaoui, Redhouane and Texier, Nathalie and Burgun, Anita and Boussadi, Abdelali and Faviez, Carole}, title = {Evaluation of Internet Social Networks using Net scoring Tool: A Case Study in Adverse Drug Reaction Mining.}, booktitle = {MIE 2015}, journal = {Stud Health Technol Inform}, year = {2015}, volume = {210}, pages = {526--530} }
004 ACTI Merabti, T; Lelong, R & Darmoni, SJ. InfoRoute: the CISMeF Context-specific Search Algorithm. Studies in Health Technology and Informatics MEDINFO, Volume 216, Pages 544-8, 2015. accepted.
BibTeX: @inproceedings{Merabti2015, author = {Merabti, T and Lelong, R and Darmoni, SJ}, title = {InfoRoute: the CISMeF Context-specific Search Algorithm}, booktitle = {Studies in Health Technology and Informatics MEDINFO}, year = {2015}, volume = {216}, pages = {544-8}, note = {accepted} }
004 ACTI Schuers, M; Joulakian, M; Griffon, N; Pachéco, J; Périgard, C; Lepage, E; Watbled, L; Massari, P & Darmoni, SJ. Quality indicators from laboratory and radiology information systems. Studies in Health Technology and Informatics MEDINFO, Volume 216, Pages 212-6, 2015. PREPS EVAL-SI.
Abstract: Consequences of the computerization of laboratory and radiology information system (LIS and RIS) are not well documented. The aim of this study was to evaluate the impact of computerization of LIS and RIS of four hospitals on performance and quality of care. The study was divided into three phases. First, the subprocesses and information flows of LIS and RIS were described. Then, a literature review was performed in order to identify the indicators used to assess the impact of computerization. Finally, comparisons were made between 2 hospitals. Using the initial framework, each partner described its process mapping concerning LIS and RIS. The review identified a wide panel of indicators. Only 41 were useful to assess the impact of information systems. For each two by two comparison, lists of relevant indicators have been selected from the identified indicators and according to the process mapping comparison. Two by two comparisons have to be completed. Eventually, these indicators may be integrated in the quality process of hospital information systems.
BibTeX: @inproceedings{Schuers2015a, author = {Schuers, M and Joulakian, M and Griffon, N and Pachéco, J and Périgard, C and Lepage, E and Watbled, L and Massari, P and Darmoni, SJ}, title = {Quality indicators from laboratory and radiology information systems}, booktitle = {MEDINFO}, journal = {Studies in Health Technology and Informatics}, year = {2015}, volume = {216}, pages = {212-6}, note = {PREPS EVAL-SI}, doi = {10.3233/978-1-61499-564-7-212} }
004 ACTI Soualmia, LF; Cabot, C; Dahamna, B & Darmoni, SJ. SIBM at CLEF e-Health Evaluation Lab 2015. proceedings of CLEF 2015 - Conference and Labs of the Evaluation Forum, CEUR Workshop Proceedings, Volume 1391, 2015.
BibTeX: @inproceedings{Soualmia2015a, author = {Soualmia, LF and Cabot, C and Dahamna, B and Darmoni, SJ}, title = {SIBM at CLEF e-Health Evaluation Lab 2015}, booktitle = {proceedings of CLEF 2015 - Conference and Labs of the Evaluation Forum}, year = {2015}, series = {CEUR Workshop Proceedings}, volume = {1391}, url = {http://ceur-ws.org/Vol-1391/125-CR.pdf} }
004 ACTI Soualmia, LF; Lelong, R; Dahamna, B & Darmoni, SJ. Rewriting Natural Language Queries Using Patterns. proceedings of MRMD, Lecture Notes in Computer Science, Volume 9059, Pages 1-14, Springer-Verlag, 2015.
BibTeX: @inproceedings{Soualmia2015, author = {Soualmia, LF and Lelong, R and Dahamna, B and Darmoni, SJ}, title = {Rewriting Natural Language Queries Using Patterns}, booktitle = {proceedings of MRMD}, publisher = {Springer-Verlag}, year = {2015}, series = {Lecture Notes in Computer Science}, volume = {9059}, pages = {1-14} }
004 ACTI String Processing and Information Retrieval - 22nd International Symposium, SPIRE 2015, London, UK, September 1-4, 2015, Proceedings. , Lecture Notes in Computer Science, Volume 9309, Springer, 2015.
BibTeX: @proceedings{Iliopoulos2015,, title = {String Processing and Information Retrieval - 22nd International Symposium, {SPIRE} 2015, London, UK, September 1-4, 2015, Proceedings}, publisher = {Springer}, year = {2015}, series = {Lecture Notes in Computer Science}, volume = {9309}, url = {http://dx.doi.org/10.1007/978-3-319-23826-5}, doi = {10.1007/978-3-319-23826-5} }
005 ACTN Cabot, C; Soualmia, LF & Darmoni, SJ. Intégration de données cliniques et omiques pour la recherche d’information dans le Dossier Patient Informatisé. IC2015, 2015. Accepted.
BibTeX: @inproceedings{Cabot2015, author = {Cabot, C and Soualmia, LF and Darmoni, SJ}, title = {Intégration de données cliniques et omiques pour la recherche d’information dans le Dossier Patient Informatisé}, booktitle = {IC2015}, year = {2015}, note = {Accepted}, url = {https://hal.archives-ouvertes.fr/hal-01179292/document} }
005 ACTN B. Cazaux; T. Lecroq & E. Rivals. Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree. Proceedings of the 9th International Conference on Language and Automata Theory and Applications (LATA 2015), Nice, France, Lecture Notes in Computer Science, Number 8977, Pages 109-120, Springer-Verlag, Berlin, 2015.
BibTeX: @inproceedings{Cazaux2015, author = {B. Cazaux and T. Lecroq and E. Rivals}, title = {Construction of a de {B}ruijn Graph for Assembly from a Truncated Suffix Tree}, booktitle = {Proceedings of the 9th International Conference on Language and Automata Theory and Applications (LATA 2015)}, address = {Nice, France}, publisher = {Springer-Verlag, Berlin}, year = {2015}, series = {Lecture Notes in Computer Science}, number = {8977}, pages = {109--120} }
005 ACTN Grouin, C; Griffon, N & Névéol, A. Étude des risques de réidentification des patients à partir d'un corpus désidentifié de comptes-rendus cliniques en français. Atelier ETeRNAL Ethique et TRaitemeNt Automatique des Langues, Caen, France, Juin, 2015. Accepté.
BibTeX: @inproceedings{Grouin2015, author = {Grouin, C and Griffon, N and Névéol, A}, title = {Étude des risques de réidentification des patients à partir d'un corpus désidentifié de comptes-rendus cliniques en français}, booktitle = {Atelier ETeRNAL Ethique et TRaitemeNt Automatique des Langues}, address = {Caen, France}, month = {Juin}, year = {2015}, note = {Accepté} }
005 ACTN Lelong, R; Cabot, C; Merabti, T; Grosjean, J; Joulakian, M; Griffon, N; Dahamna, B; Massari, P & Darmoni, SJ. Information Retrieval in Electronic Health Records Using a Multiple Layer Query Language. RITS, 2015. projet RAVEL ANR TecSan.
BibTeX: @inproceedings{Lelong2015a, author = {Lelong, R and Cabot, C and Merabti, T and Grosjean, J and Joulakian, M and Griffon, N and Dahamna, B and Massari, P and Darmoni, SJ}, title = {Information Retrieval in Electronic Health Records Using a Multiple Layer Query Language}, booktitle = {RITS}, year = {2015}, note = {projet RAVEL ANR TecSan} }
006 COM Carl Barton; Alice Heliou; Laurent Mouchard & Solon Pissis. Linear-time Computation of Minimal Absent Words Using Suffix Array. , 2015. Londres, Royaume-Uni.
BibTeX: @misc{lsd2015c, author = {Carl Barton and Alice Heliou and Laurent Mouchard and Solon Pissis}, title = {Linear-time Computation of Minimal Absent Words Using Suffix Array}, year = {2015}, note = {Londres, Royaume-Uni} }
006 COM Bastien Cazaux; Thierry Lecroq & Eric Rivals. From Indexing Data Structures to de Bruijn Graphs. , 2015. Londres, Royaume-Uni.
BibTeX: @misc{lsd2015b, author = {Bastien Cazaux and Thierry Lecroq and Eric Rivals}, title = {From Indexing Data Structures to de Bruijn Graphs}, year = {2015}, note = {Londres, Royaume-Uni} }
006 COM Maxime Crochemore & Thierry Lecroq. Multiple String Matching. Encyclopedia of Algorithms, Springer, 2015.
BibTeX: @incollection{Crochemore2015, author = {Maxime Crochemore and Thierry Lecroq}, title = {Multiple String Matching}, booktitle = {Encyclopedia of Algorithms}, publisher = {Springer}, year = {2015} }
006 COM G. Fici; T. Lecroq; A. Lefebvre & É. Prieur-Gaston. Online computation of Abelian runs. , 2015. Londres, Royaume-Uni.
BibTeX: @misc{lsd2015, author = {G. Fici and T. Lecroq and A. Lefebvre and \'E. Prieur-Gaston}, title = {Online computation of Abelian runs}, year = {2015}, note = {Londres, Royaume-Uni} }
006 COM Lelong, R; Soualmia, LF; Dahamna, B; Grosjean, J & Darmoni, SJ. Rewriting Natural Language Queries using Patterns in an Electronic Health Records System. European Conference on Information Retrieval; Workshop on Multimodal Retrieval in the Medical Domain, Vienna, Austria, March, 2015.
BibTeX: @inproceedings{Lelong2015, author = {Lelong, R and Soualmia, LF and Dahamna, B and Grosjean, J and Darmoni, SJ}, title = {Rewriting Natural Language Queries using Patterns in an Electronic Health Records System}, booktitle = {European Conference on Information Retrieval; Workshop on Multimodal Retrieval in the Medical Domain}, address = {Vienna, Austria}, month = {March}, year = {2015} }
006 COM C. Ovide; M.-C. Kiefer-Meyer; C. Bérard; N. Vergne; T. Lecroq; P. Lerouge; I. Tournier; H. Dauchel & M. Bardor. RNA sequencing technology will help deciphering the morphogenesis mechanisms in the model diatom Phaeodactylum tricornutum. 4ème Journée de l'IRIB, 2015.
BibTeX: @inproceedings{Ovide2015, author = {C. Ovide and M.-C. Kiefer-Meyer and C. Bérard and N. Vergne and T. Lecroq and P. Lerouge and I. Tournier and H. Dauchel and M. Bardor}, title = {RNA sequencing technology will help deciphering the morphogenesis mechanisms in the model diatom \textit{Phaeodactylum tricornutum}}, booktitle = {4ème Journée de l'IRIB}, year = {2015} }
007 AFF Gicquel, Q; Tvardik, N; Bouvry, C; Kergourlay, I; Bittar, A; Segond, F; Darmoni, SJ & Metzger, MH. Annotation methods to develop and evaluate an expert system based on natural langage processing in electronic medical records. Studies in Health Technology and Informatics MEDINFO, Volume 216, Pages 1067, 2015.
BibTeX: @inproceedings{Gicquel2015, author = {Gicquel, Q and Tvardik, N and Bouvry, C and Kergourlay, I and Bittar, A and Segond, F and Darmoni, SJ and Metzger, MH}, title = {Annotation methods to develop and evaluate an expert system based on natural langage processing in electronic medical records}, booktitle = {Studies in Health Technology and Informatics MEDINFO}, year = {2015}, volume = {216}, pages = {1067}, doi = {10.3233/978-1-61499-564-7-1067} }
007 AFF Henry, V; Grosjean, J; Soualmia, LF; Bandrowski, A; Gonzalez, B; Darmoni, SJ & Desfeux, A. OMIC-Onto : une ressource pour l'indexation et la recherche d'outils omiques. JOBIM, Clermont-Ferrand, France, Juillet, 2015. Accepted.
BibTeX: @inproceedings{Henry2015, author = {Henry, V and Grosjean, J and Soualmia, LF and Bandrowski, A and Gonzalez, B and Darmoni, SJ and Desfeux, A}, title = {OMIC-Onto : une ressource pour l'indexation et la recherche d'outils omiques}, booktitle = {JOBIM}, address = {Clermont-Ferrand, France}, month = {Juillet}, year = {2015}, note = {Accepted} }
007 AFF Jamoulle, Marc; Pizzanelli, Miguel; Grosjean, Julien; Kerdelhue, Gaetan & Darmoni, Stefan. International Classification of Primary Care in a cross-lingual terminology portal. , March, 2015. Best Poster Award.
Abstract: ICPC is available in the HeTOP cross-lingual terminology portal (URL: www.hetop.eu) [1] in 19 languages, mostly European (e.g. Spanish, Portuguese) but also in Japanese or Mandarin. The HeTOP interface has been also translated in 10 languages, including by Wonca colleagues (in Turkish, Vietnamese and Romanian). This is very important for non-English speakers to access a health Web site in his/her native language. Thanks to a partial manual mapping between ICPC2 and MeSH, it is now also possible to query PubMed from 20% of ICPC2 codes. This task is time consuming as in lot of cases, the mapping is 1 to N (one ICPC code generates several MeSH terms; e.g. the ICPC term "diverticular disease" is mapped to two MeSH terms " diverticulosis, colonic" and " diverticulitis". HeTOP currently contains 56 health terminologies and ontologies (only 17 are included in UMLS as most of them are French terminologies), 1,951,834 concepts, 6,636,000 terms, 8,023,181 relations and 1,340,855 relations. Overall, HeTOP contains 108 millions of SPARQL triplets. These figures underlines the possible application of the so called "health big data". Overall, the number of distinct UMLS concepts with at least one French translation in UMLS (MeSH, MedDRA, WHOART, ICPC) is 45,405 vs. 317,539 in HeTOP. 1. Grosjean, J; Merabti, T; Griffon, N; Dahamna, B & Darmoni, SJ. Teaching medicine with a terminology/ontology portal. Stud Health Technol Inform 2012:180;949-53.
BibTeX: @inproceedings{Jamoulle2015a, author = {Jamoulle, Marc and Pizzanelli, Miguel and Grosjean, Julien and Kerdelhue, Gaetan and Darmoni, Stefan}, title = {International {Classification} of {Primary} {Care} in a cross-lingual terminology portal}, month = {March}, year = {2015}, note = {Best Poster Award}, url = {http://orbi.ulg.ac.be/handle/2268/179499} }
007 AFF Kerdelhué, G; Grosjean, J & Darmoni, SJ & le consortium du projet BDBfr. LiSSa : Une nouvelle base de données de la littérature Scientifique en Santé en langue française. 7ème journée ITS / 2ème journée innovation, Montpellier, France, Décembre, 2015.
BibTeX: @inproceedings{Kerdelhue2015, author = {Kerdelhué, G and Grosjean, J and Darmoni, SJ \& le consortium du projet BDBfr}, title = {LiSSa : Une nouvelle base de données de la littérature Scientifique en Santé en langue française}, booktitle = {7ème journée ITS / 2ème journée innovation}, address = {Montpellier, France}, month = {Décembre}, year = {2015}, url = {http://www.chu-rouen.fr/cismef/wp/wp-content/uploads/2015/12/ITS_poster_2015_lissa.pdf} }
007 AFF Merabti, T; Grosjean, J; Rodrigues, JM & Darmoni, SJ. Translating ICD-11 into French using lexical-based approach: a preliminary study. Studies in Health Technology and Informatics MEDINFO, Volume 216, Pages 1036, 2015.
BibTeX: @inproceedings{Merabti2015a, author = {Merabti, T and Grosjean, J and Rodrigues, JM and Darmoni, SJ}, title = {Translating ICD-11 into French using lexical-based approach: a preliminary study}, booktitle = {Studies in Health Technology and Informatics MEDINFO}, year = {2015}, volume = {216}, pages = {1036} }
007 AFF A. Quillet; C. Saad; G. Ferry; Y. Anouar; N. Vergne; T. Lecroq & C. Dubessy. miRabel: a web tool for an effective prediction of microRNA targets and their related biological pathways. 4ème journée de l'IRIB, Rouen, France, 2015. aff.
BibTeX: @inproceedings{irib2015b, author = {A. Quillet and C. Saad and G. Ferry and Y. Anouar and N. Vergne and T. Lecroq and C. Dubessy}, title = {{miRabel}: a web tool for an effective prediction of {microRNA} targets and their related biological pathways}, booktitle = {4ème journée de l'IRIB}, address = {Rouen, France}, year = {2015}, note = {aff} }
007 AFF A. Quillet; C. Saad; G. Ferry; Y. Anouar; N. Vergne; T. Lecroq & C. Dubessy. miRabel: a web tool for an effective prediction of microRNA targets and their related biological pathways. JOBIM, Clermont-Ferrand, France, 2015. aff.
BibTeX: @inproceedings{jobim2015b, author = {A. Quillet and C. Saad and G. Ferry and Y. Anouar and N. Vergne and T. Lecroq and C. Dubessy}, title = {{miRabel}: a web tool for an effective prediction of {microRNA} targets and their related biological pathways}, booktitle = {JOBIM}, address = {Clermont-Ferrand, France}, year = {2015}, note = {aff} }
007 AFF A. Quillet; M.-C. Tellier; D. Cartier; C. Bérard; N. Vergne; M. Courel; L. Yon; P. Caron; A. Tabarin; Y. Anouar & C. Dubessy. MicroRNAs as putative molecular regulators of secretion in pheochromocytoma. 4ème journée de l'IRIB, Rouen, France, 2015. aff.
BibTeX: @inproceedings{irib2015c, author = {A. Quillet and M.-C. Tellier and D. Cartier and C. Bérard and N. Vergne and M. Courel and L. Yon and P. Caron and A. Tabarin and Y. Anouar and C. Dubessy}, title = {{MicroRNAs} as putative molecular regulators of secretion in pheochromocytoma}, booktitle = {4ème journée de l'IRIB}, address = {Rouen, France}, year = {2015}, note = {aff} }
007 AFF Schuers, M. Interroger Medline en français : c'est possible !. CMGF Paris, 2015. Accepté.
BibTeX: @inproceedings{Schuers2015, author = {Schuers, M}, title = {Interroger Medline en français : c'est possible !}, booktitle = {CMGF Paris}, year = {2015}, note = {Accepté} }
007 AFF Schuers, M; Griffon, N; Kerdelhué, G; Grosjean, J & Darmoni, SJ. Évaluation de l'association entre langue et qualité des requêtes pour la recherche bibliographique: essai randomisé. 4ème journée de l'IRIB, Rouen, France, 2015.
BibTeX: @inproceedings{Schuers2015b, author = {Schuers, M and Griffon, N and Kerdelhué, G and Grosjean, J and Darmoni, SJ}, title = {Évaluation de l'association entre langue et qualité des requêtes pour la recherche bibliographique: essai randomisé}, booktitle = {4ème journée de l'IRIB}, address = {Rouen, France}, year = {2015} }
007 AFF Tvardik, N; Bouvry, C; Kergoulay, I; Darmoni, SJ & Metzger, M. The terminology needs for evaluation of care pathways. WHO - family of international classifications network annual meeting 2015, October, 2015.
Abstract: Electronic medical records (EHR) are a very important source of information for secondary use as epidemiological analysis and health services evaluation. The normalisation of the medical terms extracted from medical documents is an essential step of the preprocessing. Its quality partly depends on the medical terminologies available in the corresponding language. The objective of this presentation is to highlight the terminology needs for optimizing the data analysis of medical documents in the context of care pathway evaluation.
BibTeX: @inproceedings{Tvardik2015, author = {Tvardik, N and Bouvry, C and Kergoulay, I and Darmoni, SJ and Metzger, M}, title = {The terminology needs for evaluation of care pathways}, booktitle = {WHO - family of international classifications network annual meeting 2015}, month = {October}, year = {2015} }
007 AFF P.-J. Viailly; Sylvain Mareschal; Philippe Bertrand; Sydney Dubois; Elodie Bohers; Catherine Maingonnat; Hélène Dauchel; Thierry Lecroq; Herve Tilly & Fabrice Jardin . GenerateReports: an Ion Torrent plugin summarizing a whole NGS experiment for clinical interpretation . ECCB, Dublin, Ireland, 2015. aff.
BibTeX: @inproceedings{eccb2015, author = {P.-J. Viailly and Sylvain Mareschal and Philippe Bertrand and Sydney Dubois and Elodie Bohers and Catherine Maingonnat and Hélène Dauchel and Thierry Lecroq and Herve Tilly and Fabrice Jardin }, title = {GenerateReports: an Ion Torrent plugin summarizing a whole NGS experiment for clinical interpretation }, booktitle = {ECCB}, address = {Dublin, Ireland}, year = {2015}, note = {aff} }
007 AFF P.-J. Viailly; Sylvain Mareschal; Philippe Bertrand; Sydney Dubois; Elodie Bohers; Catherine Maingonnat; Hélène Dauchel; Thierry Lecroq; Herve Tilly & Fabrice Jardin . GenerateReports: an Ion Torrent plugin summarizing a whole NGS experiment for clinical interpretation . 4ème journée de l'IRIB, Rouen, France, 2015. aff.
BibTeX: @inproceedings{irib2015a, author = {P.-J. Viailly and Sylvain Mareschal and Philippe Bertrand and Sydney Dubois and Elodie Bohers and Catherine Maingonnat and Hélène Dauchel and Thierry Lecroq and Herve Tilly and Fabrice Jardin }, title = {GenerateReports: an Ion Torrent plugin summarizing a whole NGS experiment for clinical interpretation }, booktitle = {4ème journée de l'IRIB}, address = {Rouen, France}, year = {2015}, note = {aff} }
007 AFF P.-J. Viailly; Sylvain Mareschal; Philippe Bertrand; Sydney Dubois; Elodie Bohers; Catherine Maingonnat; Hélène Dauchel; Thierry Lecroq; Herve Tilly & Fabrice Jardin . GenerateReports: an Ion Torrent plugin summarizing a whole NGS experiment for clinical interpretation . JOBIM, Clermont-Ferrand, France, 2015. aff.
BibTeX: @inproceedings{jobim2015a, author = {P.-J. Viailly and Sylvain Mareschal and Philippe Bertrand and Sydney Dubois and Elodie Bohers and Catherine Maingonnat and Hélène Dauchel and Thierry Lecroq and Herve Tilly and Fabrice Jardin }, title = {GenerateReports: an Ion Torrent plugin summarizing a whole NGS experiment for clinical interpretation }, booktitle = {JOBIM}, address = {Clermont-Ferrand, France}, year = {2015}, note = {aff} }
007 AFF Watbled, Ludivine; Beuscart-Zephir, Marie-Catherine; Guerlinger, Sandra; Douze, Laura; Lepage, Eric; Darmoni, Stéfan J. & Marcilly, Romaric. Work System Characteristics Impacting the Performance and Quality of the Discharge Letter Process.. Stud Health Technol Inform , Volume 218, Pages 145-150, 2015. PREPS EVAL-SI.
Abstract: Studies on the impact of a Health Information Technology seldom consider socio-technical characteristics of the work system in which the technology is implemented. Yet those dimensions may act as hidden variables that could explain the inconsistency of impact studies' results in terms of performance, quality and satisfaction. This paper reports on the identification of those variables in the discharge letter (DL) process. Human Factors experts performed an analysis of the work system of the DL process in 17 medical units. The DL process is composed of three sub-processes running with work system differing according to the distribution of tasks, the technology implemented and the work organization. Hidden variables identified are: verification by the physician, technology's integration, number of editing cycles, physicians' preferences etc. Those variables can be collected automatically or by questionnaire. Statistical analyses will have to be performed to know which variable explain impact indicators.
BibTeX: @article{Watbled2015, author = {Watbled, Ludivine and Beuscart-Zephir, Marie-Catherine and Guerlinger, Sandra and Douze, Laura and Lepage, Eric and Darmoni, Stéfan J. and Marcilly, Romaric}, title = {Work System Characteristics Impacting the Performance and Quality of the Discharge Letter Process.}, journal = {Stud Health Technol Inform}, year = {2015}, volume = {218}, pages = {145--150}, note = {PREPS EVAL-SI} }
008 OS Maxime Crochemore & Thierry Lecroq. String Matching. Encyclopedia of Algorithms, Springer, 2015.
BibTeX: @incollection{DBLP:reference/algo/CrochemoreL15b, author = {Maxime Crochemore and Thierry Lecroq}, title = {String Matching}, booktitle = {Encyclopedia of Algorithms}, publisher = {Springer}, year = {2015} }
010 AP Gabriele Fici; Tomasz Kociumaka; Thierry Lecroq; Arnaud Lefebvre & Élise Prieur-Gaston. Fast Computation of Abelian Runs. CoRR , Volume abs/1506.08518, 2015. ap.
BibTeX: @article{DBLP:journals/corr/FiciKLLP15, author = {Gabriele Fici and Tomasz Kociumaka and Thierry Lecroq and Arnaud Lefebvre and {\'{E}}lise Prieur{-}Gaston}, title = {Fast Computation of Abelian Runs}, journal = {CoRR}, year = {2015}, volume = {abs/1506.08518}, note = {ap} }
010 AP Gabriele Fici; Alessio Langiu; Thierry Lecroq; Arnaud Lefebvre; Filippo Mignosi & Élise Prieur-Gaston. Abelian Powers and Repetitions in Sturmian Words. CoRR , Volume abs/1506.02797, 2015. ap.
BibTeX: @article{DBLP:journals/corr/FiciLLLMP15, author = {Gabriele Fici and Alessio Langiu and Thierry Lecroq and Arnaud Lefebvre and Filippo Mignosi and {\'{E}}lise Prieur{-}Gaston}, title = {Abelian Powers and Repetitions in Sturmian Words}, journal = {CoRR}, year = {2015}, volume = {abs/1506.02797}, note = {ap} }
010 AP Gabriele Fici; Thierry Lecroq; Arnaud Lefebvre & Élise Prieur-Gaston. Online Computation of Abelian Runs. CoRR , Volume abs/1501.01429, 2015. ap.
BibTeX: @article{DBLP:journals/corr/FiciLLP15, author = {Gabriele Fici and Thierry Lecroq and Arnaud Lefebvre and {\'{E}}lise Prieur{-}Gaston}, title = {Online Computation of Abelian Runs}, journal = {CoRR}, year = {2015}, volume = {abs/1501.01429}, note = {ap} }
Charlet, J. & Darmoni, S. J.. Knowledge Representation and Management. From Ontology to Annotation. Findings from the Yearbook 2015 Section on Knowledge Representation and Management.. Yearb Med Inform , Aug, Volume 10, Number 1, Pages 134-136, 2015.
Abstract: To summarize the best papers in the field of Knowledge Representation and Management (KRM).A comprehensive review of medical informatics literature was performed to select some of the most interesting papers of KRM published in 2014.Four articles were selected, two focused on annotation and information retrieval using an ontology. The two others focused mainly on ontologies, one dealing with the usage of a temporal ontology in order to analyze the content of narrative document, one describing a methodology for building multilingual ontologies.Semantic models began to show their efficiency, coupled with annotation tools.
BibTeX: @article{Charlet2015, author = {Charlet, J. and Darmoni, S. J.}, title = {Knowledge Representation and Management. From Ontology to Annotation. Findings from the Yearbook 2015 Section on Knowledge Representation and Management.}, month = {Aug}, journal = {Yearb Med Inform}, year = {2015}, volume = {10}, number = {1}, pages = {134--136}, url = {http://dx.doi.org/10.15265/IY-2015-038}, doi = {10.15265/IY-2015-038} }
2014 001 ACL-int Barton, C; Iliopoulos, C S; Lee, I; Mouchard, L; Park, K & Pissis, S.P.. Extending alignments with $k$-mismatches and $-gaps. Theoretical Computer Science , Volume 525, Pages 80-88, 2014.
Abstract: Recently, the problem of extending an alignment with k-mismatches and a single gap for pairwise sequence alignment was introduced (Flouri et al., 2011). The authors considered the problem of extending an alignment under the Hamming distance model by also allowing the insertion of a single gap; and presented a Î˜ ( m Î² ) -time algorithm to solve it, where m is the length of the shortest sequence to be extended, and Î² is the maximum allowed length of the single gap. Very recently, it was shown (Flouri et al., 2012) that this problem is strongly and directly motivated by the next-generation re-sequencing application: aligning tens of millions of short DNA sequences against a reference genome. In this article, we consider an extension of this problem: extending an alignment with k-mismatches and two gaps; and present a Î˜ ( m Î² ) -time algorithm to solve it. This extension is proved to be fundamental in the next-generation re-sequencing application (Alachiotis et al., 2012). In addition, we present a generalisation of our solution to solve the problem of extending an alignment with k-mismatches and â„“-gaps in time Î˜ ( m Î² â„“ ) . The presented solutions work provided that all gaps in the alignment must occur in one of the two sequences.
BibTeX: @article{Barton, author = {Barton, C and Iliopoulos, C S and Lee, I and Mouchard, L and Park, K and Pissis, S.P.}, title = {Extending alignments with $k$-mismatches and $\ell$-gaps}, journal = {Theoretical Computer Science}, year = {2014}, volume = {525}, pages = {80--88}, url = {http://www.sciencedirect.com/science/article/pii/S0304397513004660}, doi = {10.1016/j.tcs.2013.06.012} }
001 ACL-int Bouhamed, H; Masmoudi, A; Lecroq, T & Rebai, A. A new approach for bayesian classifier learning structure via k2 algorithm. Neurocomputing , 2014. Accepted.
BibTeX: @article{Bouhamed2013, author = {Bouhamed, H and Masmoudi, A and Lecroq, T and Rebai, A}, title = {A new approach for bayesian classifier learning structure via k2 algorithm}, journal = {Neurocomputing}, year = {2014}, note = {Accepted} }
001 ACL-int H. Bouhamed; A. Masmoudi; T. Lecroq & A. Rebai. Reducing the structure space of Bayesian classifiers using some general algorithms. Journal of Mathematical Modelling and Algorithms in Operations Research , 2014. Accepted.
BibTeX: @article{Bouhamed2014b, author = {H. Bouhamed and A. Masmoudi and T. Lecroq and A. Rebai}, title = {Reducing the structure space of Bayesian classifiers using some general algorithms}, journal = {Journal of Mathematical Modelling and Algorithms in Operations Research}, year = {2014}, note = {Accepted} }
001 ACL-int Duval, J. -P.; Lecroq, T. & Lefebvre, A.. Linear computation of unbordered conjugate on unordered alphabet. Theoretical Computer Science , February, Volume 522, Pages 77-84, 2014.
Abstract: We present an algorithm that, given a word w of length n on an unordered alphabet, computes one of its unbordered conjugates. If such a conjugate does not exist, the algorithm computes one of its conjugates that is a power of an unbordered word. The time complexity of the algorithm is O ( n ) : the number of comparisons between letters of w is bounded by 4n.
BibTeX: @article{Duval2014, author = {Duval, J. -P. and Lecroq, T. and Lefebvre, A.}, title = {Linear computation of unbordered conjugate on unordered alphabet}, month = {February}, journal = {Theoretical Computer Science}, year = {2014}, volume = {522}, pages = {77--84}, url = {http://www.sciencedirect.com/science/article/pii/S0304397513009109}, doi = {10.1016/j.tcs.2013.12.008} }
001 ACL-int Fici, Gabriele; Lecroq, Thierry; Lefebvre, Arnaud & Prieur-Gaston, Ã‰lise. Algorithms for computing Abelian periods of words. Discrete Applied Mathematics , January, Volume 163, Part 3, Pages 287-297, 2014.
Abstract: Constantinescu and Ilie [S. Constantinescu, L. Ilie. Fine and Wilfâ€™s theorem for abelian periods, Bulletin of the European Association for Theoretical Computer Science 89 (2006) 167â€“170] introduced the notion of an Abelian period of a word. A word of length n over an alphabet of size Ïƒ can have Î˜ ( n 2 ) distinct Abelian periods. The Brute-Force algorithm computes all the Abelian periods of a word in time O ( n 2 Ã— Ïƒ ) using O ( n Ã— Ïƒ ) space. We present an offline algorithm based on a select function having the same worst-case theoretical complexity as the Brute-Force one, but outperforming it in practice. We then present online algorithms that also enable us to compute all the Abelian periods of all the prefixes of w .
BibTeX: @article{Fici2014, author = {Fici, Gabriele and Lecroq, Thierry and Lefebvre, Arnaud and Prieur-Gaston, Ã‰lise}, title = {Algorithms for computing Abelian periods of words}, month = {January}, journal = {Discrete Applied Mathematics}, year = {2014}, volume = {163, Part 3}, pages = {287--297}, url = {http://www.sciencedirect.com/science/article/pii/S0166218X13003624}, doi = {10.1016/j.dam.2013.08.021} }
001 ACL-int Griffon, N.; Charlet, J. & Darmoni, S. J.. Managing free text for secondary use of health data.. Yearb Med Inform , Volume 9, Number 1, Pages 167-169, 2014.
Abstract: To summarize the best papers in the field of Knowledge Representation and Management (KRM).A comprehensive review of medical informatics literature was performed to select some of the most interesting papers of KRM and natural language processing (NLP) published in 2013.Four articles were selected, one focuses on Electronic Health Record (EHR) interoperability for clinical pathway personalization based on structured data. The other three focus on NLP (corpus creation, de-identification, and co-reference resolution) and highlight the increase in NLP tools performances.NLP tools are close to being seriously concurrent to humans in some annotation tasks. Their use could increase drastically the amount of data usable for meaningful use of EHR.
BibTeX: @article{Griffon2014c, author = {Griffon, N. and Charlet, J. and Darmoni, S. J.}, title = {Managing free text for secondary use of health data.}, journal = {Yearb Med Inform}, year = {2014}, volume = {9}, number = {1}, pages = {167--169}, url = {http://dx.doi.org/10.15265/IY-2014-0037}, doi = {10.15265/IY-2014-0037} }
001 ACL-int Griffon, N; Kerdelhué, G; Hamek, S; Hassler, S; Boog, C; Lamy, JB; Duclos, C; Venot, A & Darmoni, SJ. Design and usability study of an iconic user interface to ease information retrieval of medical guidelines. Journal of the American Medical Informatics Association , March, Volume 21, Number e2, Pages e270-277, 2014.
Abstract: BACKGROUND AND OBJECTIVE: Doc'CISMeF (DC) is a semantic search engine used to find resources in CISMeF-BP, a quality controlled health gateway, which gathers guidelines available on the internet in French. Visualization of Concepts in Medicine (VCM) is an iconic language that may ease information retrieval tasks. This study aimed to describe the creation and evaluation of an interface integrating VCM in DC in order to make this search engine much easier to use. METHODS: Focus groups were organized to suggest ways to enhance information retrieval tasks using VCM in DC. A VCM interface was created and improved using the ergonomic evaluation approach. 20 physicians were recruited to compare the VCM interface with the non-VCM one. Each evaluator answered two different clinical scenarios in each interface. The ability and time taken to select a relevant resource were recorded and compared. A usability analysis was performed using the System Usability Scale (SUS). RESULTS: The VCM interface contains a filter based on icons, and icons describing each resource according to focus group recommendations. Some ergonomic issues were resolved before evaluation. Use of VCM significantly increased the success of information retrieval tasks (OR=11; 95% CI 1.4 to 507). Nonetheless, it took significantly more time to find a relevant resource with VCM interface (101 vs 65 s; p=0.02). SUS revealed 'good' usability with an average score of 74/100. CONCLUSIONS: VCM was successfully implemented in DC as an option. It increased the success rate of information retrieval tasks, despite requiring slightly more time, and was well accepted by end-users.
BibTeX: @article{Griffon2014a, author = {Griffon, N and Kerdelhué, G and Hamek, S and Hassler, S and Boog, C and Lamy, JB and Duclos, C and Venot, A and Darmoni, SJ}, title = {Design and usability study of an iconic user interface to ease information retrieval of medical guidelines}, month = {March}, journal = {Journal of the American Medical Informatics Association}, year = {2014}, volume = {21}, number = {e2}, pages = {e270-277}, doi = {10.1136/amiajnl-2012-001548} }
001 ACL-int Griffon, N; Kerdelhué, G; Soualmia, LF; Merabti, T; Grosjean, J; Lamy, JB; Venot, A; Duclos, C & Darmoni, SJ. Evaluating alignment quality between iconic language and reference terminologies using similarity metrics. BMC Medical Informatics and Decision Making , Volume 14, Pages 17, 2014.
BibTeX: @article{Griffon2014, author = {Griffon, N and Kerdelhué, G and Soualmia, LF and Merabti, T and Grosjean, J and Lamy, JB and Venot, A and Duclos, C and Darmoni, SJ}, title = {Evaluating alignment quality between iconic language and reference terminologies using similarity metrics}, journal = {BMC Medical Informatics and Decision Making}, year = {2014}, volume = {14}, pages = {17}, doi = {10.1186/1472-6947-14-17} }
001 ACL-int Griffon, N; Schuers, M; Soualmia, LF; Grosjean, J; Kerdelhué, G; Kergoulay, I; Dahamna, B & Darmoni, SJ. A Search Engine to Access PubMed Monolingual Subsets: Proof of Concept - Evaluation in French. J Med Internet Res , December, Volume 16, Number 12, Pages e271, 2014.
BibTeX: @article{Griffon2014d, author = {Griffon, N and Schuers, M and Soualmia, LF and Grosjean, J and Kerdelhué, G and Kergoulay, I and Dahamna, B and Darmoni, SJ}, title = {A Search Engine to Access PubMed Monolingual Subsets: Proof of Concept - Evaluation in French}, month = {December}, journal = {J Med Internet Res}, year = {2014}, volume = {16}, number = {12}, pages = {e271}, doi = {doi:10.2196/jmir.3836} }
001 ACL-int Haddoud, M & Abdeddaïm, S. Accurate keyphrase extraction by discriminating overlapping phrases. Journal of Information Science , Volume 40, Number 4, Pages 488-500, 2014.
BibTeX: @article{Haddoud2014, author = {Haddoud, M and Abdeddaïm, S}, title = {Accurate keyphrase extraction by discriminating overlapping phrases}, journal = {Journal of Information Science}, year = {2014}, volume = {40}, number = {4}, pages = {488-500} }
001 ACL-int Lamy, J. -B; Séroussi, B.; Griffon, N.; Kerdelhué, G.; Jaulent, M. -C & Bouaud, J.. Toward a Formalization of the Process to Select IMIA Yearbook Best Papers. Methods of Information in Medicine , 2014.
BibTeX: @article{Lamy2014a, author = {Lamy, J. -B and Séroussi, B. and Griffon, N. and Kerdelhué, G. and Jaulent, M. -C and Bouaud, J.}, title = {Toward a Formalization of the Process to Select {IMIA} Yearbook Best Papers}, journal = {Methods of Information in Medicine}, year = {2014}, url = {http://www.schattauer.de/en/magazine/subject-areas/journals-a-z/methods/contents/preprint-online/november-14-2014/issue/special/manuscript/23692/show.html}, doi = {10.3414/ME14-01-0031} }
001 ACL-int Lecroq, T. & Soualmia, L. F.. Managing Large-Scale Genomic Datasets and Translation into Clinical Practice:. IMIA Yearbook, Volume 9, Number 1, Pages 212-214, 2014.
BibTeX: @inproceedings{Lecroq2014, author = {Lecroq, T. and Soualmia, L. F.}, title = {Managing Large-Scale Genomic Datasets and Translation into Clinical Practice:}, booktitle = {IMIA Yearbook}, year = {2014}, volume = {9}, number = {1}, pages = {212--214}, url = {http://www.schattauer.de/index.php?id=1214&doi=10.15265/IY-2014-0039}, doi = {10.15265/IY-2014-0039} }
001 ACL-int S. Mareschal; S. Dubois; T. Lecroq & F. Jardin. Rgb: a scriptable genome browser for R. Bioinformatics , Volume 30, Number 15, Pages 2204-2205, 2014.
BibTeX: @article{Mareschal2014, author = {S. Mareschal and S. Dubois and T. Lecroq and F. Jardin}, title = {Rgb: a scriptable genome browser for {R}}, journal = {Bioinformatics}, year = {2014}, volume = {30}, number = {15}, pages = {2204-2205} }
001 ACL-int Marie, I.; Gehanno, J-F.; Bubenheim, M.; Duval-Modeste, A-B.; Joly, P.; Dominique, S.; Bravard, P.; Noël, D.; Cailleux, A-F.; Weber, J.; Lagoutte, P.; Benichou, J. & Levesque, H.. Prospective study to evaluate the association between systemic sclerosis and occupational exposure and review of the literature.. Autoimmun Rev , Feb, Volume 13, Number 2, Pages 151-156, 2014.
Abstract: Systemic sclerosis (SSc) has complex pathogenesis and likely multifactorial causes. Environmental exposures have been suggested to play a role in SSc pathogenesis, including occupational exposure to pollutants and chemicals as well as use of drugs leading to modulation of immune response. Thus, this case-control study aimed to assess: the relationship between SSc and occupational exposure; and the risk of SSc related to occupational exposure in male and female patients.From 2005 to 2008, 100 patients with a definite diagnosis of SSc were included in the study; 3 age, gender, and smoking habits matched controls were selected for each patient. A committee of experts evaluated blindly occupational exposure to crystalline silica, white spirit, organic solvents, ketones, welding fumes, epoxy resins, and pesticides; an occupational exposure score was calculated for all subjects. Our findings were compared with previous data in the literature.Increased ORs for SSc were found for: crystalline silica (p<0.0001), white spirit (p<0.0001), aromatic solvents (p=0.0002), chlorinated solvents (p=0.014), trichlorethylene (p=0.044), ketones (p=0.002) and welding fumes (p=0.021). Elevated risk associated with high final cumulative score in SSc was observed for: crystalline silica, white spirit, chlorinated solvents, trichlorethylene, aromatic solvents, any type of solvents, ketones and welding fumes. A marked association between SSc and occupational exposure was further found for: 1) crystalline silica, chlorinated solvents, trichloroethylene, white spirit, ketones and welding fumes in male patients; and 2) white spirit, aromatic solvents, any type of solvent and ketones in female patients. Finally, we did not find an association between SSc and: 1) the use of drugs that have been speculated to play a role in SSc onset (anorexigens, pentazocine, bromocriptine, l-tryptophan); 2) implants - that are prosthesis, silicone implants, and contact lenses; and 3) dyeing hair. In the literature, SSc has been associated with occupational exposure to silica and solvents, while the association between SSc and specific organic solvents and welding fumes has been anecdotally reported.The following occupational factors have an impact in the development of SSc: crystalline silica, white spirit, aromatic solvents, chlorinated solvents, trichlorethylene, ketones and welding fumes. The risk of SSc appears to be markedly associated with high cumulative exposure. Finally, the association between SSc and occupational exposure may be variable according to gender.
BibTeX: @article{Marie2014, author = {Marie, I. and Gehanno, J-F. and Bubenheim, M. and Duval-Modeste, A-B. and Joly, P. and Dominique, S. and Bravard, P. and Noël, D. and Cailleux, A-F. and Weber, J. and Lagoutte, P. and Benichou, J. and Levesque, H.}, title = {Prospective study to evaluate the association between systemic sclerosis and occupational exposure and review of the literature.}, month = {Feb}, journal = {Autoimmun Rev}, year = {2014}, volume = {13}, number = {2}, pages = {151--156}, url = {http://dx.doi.org/10.1016/j.autrev.2013.10.002}, doi = {10.1016/j.autrev.2013.10.002} }
001 ACL-int Stevenn Volant; Caroline Bérard; Marie-Laure Martin-Magniette & Stéphane Robin. Hidden Markov Models with mixtures as emission distributions. Statistics and Computing , Volume 24, Number 4, Pages 493-504, 2014.
BibTeX: @article{Volant2014, author = {Stevenn Volant and Caroline B{\'e}rard and Marie-Laure Martin-Magniette and St{\'e}phane Robin}, title = {Hidden Markov Models with mixtures as emission distributions}, journal = {Statistics and Computing}, year = {2014}, volume = {24}, number = {4}, pages = {493-504}, url = {http://arxiv.org/abs/1206.5102}, doi = {10.1007/s11222-013-9383-7} }
001 ACL-int Ferhat Ziram; Dominique Cellier & Francois Charlot. Statistical Analysis of the number of self-overlapping leftmost repeats in an homogeneous stationnary Markov chain on finite states. Communications in Statistics – Theory and Methods , 2014. Accepted.
BibTeX: @article{Ziram2014, author = {Ferhat Ziram and Dominique Cellier and Fran\c cois Charlot}, title = {Statistical Analysis of the number of self-overlapping leftmost repeats in an homogeneous stationnary Markov chain on finite states}, journal = {Communications in Statistics – Theory and Methods}, year = {2014}, note = {Accepted} }
002 ACL-nat Avillach, P.; Kerdelhué, G.; Devos, P.; Maisonneuve, H. & Darmoni, S. J.. Limiter une requête Medline/PubMed aux articles publiés dans les revues les plus citées de chaque discipline. Revue d'Épidémiologie et de Santé Publique , Volume 62, Number 6, Pages 361-365, 2014.
Abstract: RésuméObjectif Medline/PubMed est la base documentaire la plus utilisée dans le domaine de la santé. L’objectif de ce travail était de proposer une nouvelle méthode générique pour limiter une requête quelconque effectuée en utilisant PubMed en utilisant le facteur d’impact « relatif », en se limitant aux catégories A et B du score SIGAPS, c’est-à-dire, aux « meilleurs articles » au sens du facteur d’impact. Matériel et méthodes Nous avons utilisé le corpus complet de PubMed comme référence, puis dix pathologies fréquentes en termes d’indexation dans PubMed, et les citations de quatre prix Nobel. Le facteur d’impact relatif (FIR) est calculé par discipline médicale défini dans le Journal Citation Reports. Les deux requêtes incluant les journaux de catégorie A (ou A ou B) ont pu être ajoutées à une requête quelconque de PubMed, ce qui était un élément central en termes de faisabilité. Résultats Le filtre par la catégorie A de SIGAPS est plus large que celui des Core Clinical Journals (CCJ) en sélectionnant 15,6 % du corpus de PubMed versus 8,6 % pour le CCJ. Le temps de réponse sur l’ensemble du corpus de PubMed est inférieur à deux secondes. Dans cinq pathologies sur dix, le filtre FIR est plus efficace que le filtre CCJ. Pour les quatre prix Nobel, le filtre FIR est beaucoup plus efficace que le filtre FIR. Conclusion L’étude de faisabilité d’utiliser le facteur d’impact relatif comme filtre d’une requête quelconque de Medline/PubMed est positive. AbstractBackground Medline/PubMed is the most frequently used medical bibliographic research database. The aim of this study was to propose a new generic method to limit any Medline/PubMed query based on the relative impact factor and the A & B categories of the SIGAPS score. Material and methods The entire PubMed corpus was used for the feasibility study, then ten frequent diseases in terms of PubMed indexing and the citations of four Nobel prize winners. The relative impact factor (RIF) was calculated by medical specialty defined in Journal Citation Reports. The two queries, which included all the journals in category A (or A OR B), were added to any Medline/PubMed query as a central point of the feasibility study. Results Limitation using the SIGAPS category A was larger than the when using the Core Clinical Journals (CCJ): 15.65% of PubMed corpus vs 8.64% for CCJ. The response time of this limit applied to the entire PubMed corpus was less than two seconds. For five diseases out of ten, limiting the citations with the RIF was more effective than with the CCJ. For the four Nobel prize winners, limiting the citations with the RIF was more effective than the CCJ. Conclusion The feasibility study to apply a new filter based on the relative impact factor on any Medline/PubMed query was positive.
BibTeX: @article{Avillach2014, author = {Avillach, P. and Kerdelhué, G. and Devos, P. and Maisonneuve, H. and Darmoni, S. J.}, title = {Limiter une requête Medline/{PubMed} aux articles publiés dans les revues les plus citées de chaque discipline}, journal = {Revue d'Épidémiologie et de Santé Publique}, year = {2014}, volume = {62}, number = {6}, pages = {361-365}, url = {http://www.sciencedirect.com/science/article/pii/S0398762014007081}, doi = {10.1016/j.respe.2014.09.008} }
002 ACL-nat Chebil, W; Soualmia, LF; Omri, M & Darmoni, SJ. Extraction possibiliste de concepts MeSH à partir de documents biomédicaux. Revue d’Intelligence Artificielle , Volume 28, Number 6, Pages 729-752, 2014.
Abstract: Nous proposons dans cet article une nouvelle approche d’indexation de documents biomédicaux basée sur les réseaux possibilistes permettant de les apparier partiellement aux termes du thésaurus MeSH (Medical Subject Headings). La principale contribution de notre approche est le traitement de l’imprécision et de l’incertitude liée à la tâche d’indexation à travers l’utilisation de la théorie des possibilités. En effet, nous proposons d’améliorer l’estimation de la pertinence d’un document étant donné un concept en utilisant deux mesures : la possibilité et la nécessité. La possibilité estime le degré de rejet d’un document non pertinent étant donné un concept. La nécessité de la pertinence d’un document évalue dans quelle mesure un document est pertinent pour le concept. De plus, notre approche permet de réduire les limites de l’appariement partiel qui génère de l’information inutile, bien que ce type d’appariement permette de trouver dans le document d’autres variantes du vocabulaire contrôlé. Pour ce faire, nous proposons de filtrer l’index en utilisant les connaissances fournies par l’UMLS (Unified Medical Langage System). Filtrer l’index permet de ne garder que les concepts pertinents parmi ceux ayant un sous-ensemble de leurs mots dans le document. Les expérimentations réalisées sur les deux corpus OSHUMED et CISMeF ont montré des résultats encourageants.
BibTeX: @article{Chebil2014a, author = {Chebil, W and Soualmia, LF and Omri, M and Darmoni, SJ}, title = {Extraction possibiliste de concepts MeSH à partir de documents biomédicaux}, journal = {Revue d’Intelligence Artificielle}, year = {2014}, volume = {28}, number = {6}, pages = {729-752}, url = {http://ria.revuesonline.com/article.jsp?articleId=20003}, doi = {10.3166/ria.28.729-752} }
002 ACL-nat Darmoni, Stefan; Griffon, Nicolas & Massari, Philippe. Les systèmes d'aide à la décision médicale. Annales des Mines - Réalités industrielles , November, Volume 2014, Number 4, Pages 47-50, 2014.
BibTeX: @article{Darmoni2014, author = {Darmoni, Stefan and Griffon, Nicolas and Massari, Philippe}, title = {Les systèmes d'aide à la décision médicale}, month = {November}, journal = {Annales des Mines - Réalités industrielles}, year = {2014}, volume = {2014}, number = {4}, pages = {47--50}, url = {http://www.cairn.info/article.php?ID_ARTICLE=RINDU_144_0047}, doi = {10.3917/rindu.144.0047} }
004 ACTI Ben Nsira, N.; Lecroq, T. & Elloumi, M.. On-line string matching in highly similar DNA sequences. Proceedings of the 2nd International Conference on Algorithms for Big Data (ICABD 2014), Palermo, Italy, CEUR Workshop Proceedings, Volume 1146, CEUR-WS.org, 2014.
BibTeX: @inproceedings{bennsira2014, author = {Ben Nsira, N. and Lecroq, T. and Elloumi, M.}, title = {On-line string matching in highly similar {DNA} sequences}, booktitle = {Proceedings of the 2nd International Conference on Algorithms for Big Data (ICABD 2014)}, address = {Palermo, Italy}, publisher = {CEUR-WS.org}, year = {2014}, series = {CEUR Workshop Proceedings}, volume = {1146} }
004 ACTI Cabot, C; Grosjean, J; Lelong, R; Lefebvre, A; Lecroq, T; Soualmia, LF & Darmoni, SJ. Omic Data Modelling for Information Retrieval. Proceedings of the 2nd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO, 2014.
BibTeX: @inproceedings{Cabot2014, author = {Cabot, C and Grosjean, J and Lelong, R and Lefebvre, A and Lecroq, T and Soualmia, LF and Darmoni, SJ}, title = {Omic Data Modelling for Information Retrieval}, booktitle = {Proceedings of the 2nd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO}, year = {2014}, url = {http://iwbbio.ugr.es/2014/papers/IWBBIO_2014_paper_50.pdf} }
004 ACTI B. Cazaux; T. Lecroq & E. Rivals. From Indexing Data Structures to de Bruijn Graphs. Proceedings of the 25th Annual Symposium on Combinatorial Pattern Matching (CPM), Moscow, Russia, Lecture Notes in Computer Science, Volume 8486, Pages 89-99, Springer, 2014.
BibTeX: @inproceedings{Cazaux2014, author = {B. Cazaux and T. Lecroq and E. Rivals}, title = {From Indexing Data Structures to de Bruijn Graphs}, booktitle = {Proceedings of the 25th Annual Symposium on Combinatorial Pattern Matching (CPM)}, address = {Moscow, Russia}, publisher = {Springer}, year = {2014}, series = {Lecture Notes in Computer Science}, volume = {8486}, pages = {89-99} }
004 ACTI Chniti, Amina; Traore, Lamine; Hussain, Sajjad; Griffon, Nicolas; Darmoni, Stefan; Charlet, Jean; Sadou, Eric; Ouagne, David; Lepage, Eric & Daniel, Christel. A Semantic Interoperability Framework for Facilitating Cross-Hospital Exchanges.. Stud Health Technol Inform , Volume 205, Pages 1255, 2014.
BibTeX: @inproceedings{Chniti2014a, author = {Chniti, Amina and Traore, Lamine and Hussain, Sajjad and Griffon, Nicolas and Darmoni, Stefan and Charlet, Jean and Sadou, Eric and Ouagne, David and Lepage, Eric and Daniel, Christel}, title = {A Semantic Interoperability Framework for Facilitating Cross-Hospital Exchanges.}, journal = {Stud Health Technol Inform}, year = {2014}, volume = {205}, pages = {1255} }
004 ACTI D'hondt, E et Grau, B et Darmoni, S et Névéol, A et Schuers, M et Zweigenbaum, P. LIMSI @ 2014 Clinical Decision Support Track. TREC Working Notes, 2014.
BibTeX: @inproceedings{Dhondt2014, author = {D'hondt, E et Grau, B et Darmoni, S et Névéol, A et Schuers, M et Zweigenbaum, P}, title = {LIMSI @ 2014 Clinical Decision Support Track}, booktitle = {TREC Working Notes}, year = {2014}, url = {https://perso.limsi.fr/neveol/DhondtTREC2014WorkingNotes.pdf} }
004 ACTI Gicquel, Q; Kergoulay, I; Gerbier-Colomban, S; Chariout, S; Bittar, A; Segond, F; Darmoni, SJ & Metzger, MH. Annotation methods to develop and evaluate an expert system based on natural language processing in electronic medical records. MIE, 2014. Accepted.
BibTeX: @inproceedings{Gicquel2014, author = {Gicquel, Q and Kergoulay, I and Gerbier-Colomban, S and Chariout, S and Bittar, A and Segond, F and Darmoni, SJ and Metzger, MH}, title = {Annotation methods to develop and evaluate an expert system based on natural language processing in electronic medical records}, booktitle = {MIE}, year = {2014}, note = {Accepted} }
004 ACTI Griffon, N; Merabti, T; Cormont, S; Tariel-Laurent, S; Massari, P; Lepage, E; Chniti, A; Daniel, C & Darmoni, SJ. Preservation of Information in Terminology Transcoding. Stud Health Technol Inform MIE, Volume 205, Pages 156-160, 2014. Accepted.
BibTeX: @inproceedings{Griffon2014b, author = {Griffon, N and Merabti, T and Cormont, S and Tariel-Laurent, S and Massari, P and Lepage, E and Chniti, A and Daniel, C and Darmoni, SJ}, title = {Preservation of Information in Terminology Transcoding}, booktitle = {Stud Health Technol Inform MIE}, year = {2014}, volume = {205}, pages = {156-160}, note = {Accepted}, doi = {10.3233/978-1-61499-432-9-156} }
004 ACTI Grosjean, J; Soualmia, LF; Bouarech, K; Jonquet, C & Darmoni, SJ. Comparing BioPortal and HeTOP: towards a unique biomedical ontology portal ?. IWBBIO 2014, 2014.
BibTeX: @inproceedings{Grosjean2014, author = {Grosjean, J and Soualmia, LF and Bouarech, K and Jonquet, C and Darmoni, SJ}, title = {Comparing BioPortal and HeTOP: towards a unique biomedical ontology portal ?}, booktitle = {IWBBIO 2014}, year = {2014}, url = {http://iwbbio.ugr.es/2014/papers/IWBBIO_2014_paper_27.pdf} }
004 ACTI Grosjean, Julien; Soualmia, Lina F.; Bouarech, Khedidja; Jonquet, Clément & Darmoni, Stéfan J.. An Approach to Compare Bio-Ontologies Portals.. Stud Health Technol Inform , Volume 205, Pages 1008-1012, 2014.
Abstract: Background: main biomedical information retrieval systems are based on controlled vocabularies and most specifically on terminologies or ontologies (T/O). These classification structures allow indexing, coding, annotating different kind of documents. Many T/O have been created for different purposes and it became a problem for finding specific concepts in the multitude of existing nomenclatures. The NCBO (National Center for Biomedical Ontologies) BioPortal and the CISMeF (Catalogue et Index des Sites Médicaux de langue Française) HeTOP projects have been developed to tackle this issue. Objective: the present work consists in comparing both portals. Methods: we hereby are proposing a set of criteria to compare bio-ontologies portals in terms of goals, features, technologies and usability. Results: BioPortal and HeTOP have been compared based on the given criteria. While both portals are designed to store and make T/O available to the community and are sharing many basic features, they differ on several points mainly because of their basic purposes. Conclusion: thanks to the comparison criteria, we can assume that a merge between BioPortal and HeTOP is possible in terms of functionalities. The main difficulties will be about merging the data repositories and applying different policies on T/O content.
BibTeX: @inproceedings{Grosjean2014a, author = {Grosjean, Julien and Soualmia, Lina F. and Bouarech, Khedidja and Jonquet, Clément and Darmoni, Stéfan J.}, title = {An Approach to Compare Bio-Ontologies Portals.}, journal = {Stud Health Technol Inform}, year = {2014}, volume = {205}, pages = {1008--1012} }
004 ACTI Merabti, A; Soualmia, LF. & Darmoni, SJ. Detecting Noun Phrases in Biomedical Terminologies: The First Step in Managing the Evolution of Knowledge. Health Information Science, January, Lecture Notes in Computer Science, Number 8423, Pages 109-120, Springer International Publishing, 2014.
Abstract: In order to identify variations between two or several versions of Clinical Practice Guidelines, we propose a method based on the detection of noun phrases. Currently, we are developing a comparison approach to extract similar and different elements between medical documents in French in order to identify any significant changes such as new medical terms or concepts, new treatments etc. In this paper, we describe a basic initial step for this comparison approach i.e. detecting noun phrases. This step is based on patterns constructed from six main medical terminologies used in document indexing. The patterns are constructed by using a Tree Tagger. To avoid a great number of generated patterns, the most relevant ones are selected that are able identify more than 80% of the six terminologies used in this study. These steps allowed us to obtain a manageable list of 262 patterns which have been evaluated. Using this list of patterns, 708 maximal noun phrases were found, with, 364 correct phrases which represent a 51.41% precision. However by detecting these phrases manually, 602 maximal noun phrases were found which represent a 60.47% recall and therefore a 55.57% F-measure. We attempted to improve these results by increasing the number of patterns from 262 to 493. A total of 729 maximal noun phrases were obtained, with 365 which were correct, and corresponded to a 50.07% precision, 60.63% recall and 54.85% F-measure.
BibTeX: @incollection{Merabti2014, author = {Merabti, A and Soualmia, LF. and Darmoni, SJ}, title = {Detecting Noun Phrases in Biomedical Terminologies: The First Step in Managing the Evolution of Knowledge}, booktitle = {Health Information Science}, month = {January}, publisher = {Springer International Publishing}, year = {2014}, series = {Lecture Notes in Computer Science}, number = {8423}, pages = {109--120}, doi = {10.1007/978-3-319-06269-3_12} }
004 ACTI Merabti, A; Soualmia, LF & Darmoni, SJ. Using Biomedical Terminologies to extract Noun Phrases for managing knowledge evolution. Proceedings of the 2nd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO, 2014. Accepted.
BibTeX: @inproceedings{Merabti2014a, author = {Merabti, A and Soualmia, LF and Darmoni, SJ}, title = {Using Biomedical Terminologies to extract Noun Phrases for managing knowledge evolution}, booktitle = {Proceedings of the 2nd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO}, year = {2014}, note = {Accepted} }
004 ACTI Névéol, A; Grosjean, J; Darmoni, SJ & Zweigenbaum, P. Language Resources for French in the Biomedical Domain. Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14), Reykjavik, Iceland, may, European Language Resources Association (ELRA), 2014.
BibTeX: @inproceedings{NEVEOL14.604, author = {Névéol, A and Grosjean, J and Darmoni, SJ and Zweigenbaum, P}, title = {Language Resources for French in the Biomedical Domain}, booktitle = {Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14)}, address = {Reykjavik, Iceland}, month = {may}, publisher = {European Language Resources Association (ELRA)}, year = {2014}, url = {http://www.lrec-conf.org/proceedings/lrec2014/pdf/604_Paper.pdf} }
005 ACTN Chniti, A; Griffon, N; Traore, L; Hussain, S & Daniel, C. Terminologies et référentiels d’interopérabilité sémantique en Santé. JFIM, 2014.
BibTeX: @inproceedings{Chniti2014, author = {Chniti, A and Griffon, N and Traore, L and Hussain, S and Daniel, C}, title = {Terminologies et référentiels d’interopérabilité sémantique en Santé}, booktitle = {JFIM}, year = {2014}, url = {http://ceur-ws.org/Vol-1379/paper-05.pdf} }
005 ACTN Joulakian, M; Griffon, N; Schuers, M; Lepage, E; Savoye-Collet, C; Skalli, S; Massari, P & Darmoni, SJ. Indicateurs en biologie et en imagerie au sein des systèmes d’information de santé. JFIM, 2014.
BibTeX: @inproceedings{Joulakian2014, author = {Joulakian, M and Griffon, N and Schuers, M and Lepage, E and Savoye-Collet, C and Skalli, S and Massari, P and Darmoni, SJ}, title = {Indicateurs en biologie et en imagerie au sein des systèmes d’information de santé}, booktitle = {JFIM}, year = {2014} }
005 ACTN Lamy, JB; Soualmia, LF; Venot, A & Duc. Validation de la sémantique d'un langage iconique médical à l'aide d'une ontologie : méthodes et applications. Actes des 25° journées francophones d'Ingénierie des Connaissances, IC'14, Clermont-Ferrand, France, May, Pages 51-62, 2014.
BibTeX: @inproceedings{Lamy2014, author = {Lamy, JB and Soualmia, LF and Venot, A and Duc}, title = {Validation de la sémantique d'un langage iconique médical à l'aide d'une ontologie : méthodes et applications}, booktitle = {Actes des 25° journées francophones d'Ingénierie des Connaissances, IC'14}, address = {Clermont-Ferrand, France}, month = {May}, year = {2014}, pages = {51-62}, url = {https://hal.archives-ouvertes.fr/hal-01004802/document} }
005 ACTN Lelong, R; Merabti, T; Grosjean, J; Joulakian, M; Griffon, N; Dahamna, B; Cuggia, M; Pereira, S; Grabar, N; Thiessard, F; Massari, P & Darmoni, SJ. Moteur de recherche sémantique au sein du dossier du patient informatisé : langage de requêtes spécifique. JFIM, 2014.
BibTeX: @inproceedings{Lelong2014, author = {Lelong, R and Merabti, T and Grosjean, J and Joulakian, M and Griffon, N and Dahamna, B and Cuggia, M and Pereira, S and Grabar, N and Thiessard, F and Massari, P and Darmoni, SJ}, title = {Moteur de recherche sémantique au sein du dossier du patient informatisé : langage de requêtes spécifique}, booktitle = {JFIM}, year = {2014} }
005 ACTN Metzger, M; Giquel, Q; Rabarijaona, D; Segond, F; Bittar, A; Dini, L; Soualmia, LF & Darmoni, SJ. Usage secondaire du dossier médical informatisé à des fins épidémiologiques et d’évaluation de la qualité des soins : le projet SYNODOS. JFIM, 2014.
BibTeX: @inproceedings{Metzger2014, author = {Metzger, M and Giquel, Q and Rabarijaona, D and Segond, F and Bittar, A and Dini, L and Soualmia, LF and Darmoni, SJ}, title = {Usage secondaire du dossier médical informatisé à des fins épidémiologiques et d’évaluation de la qualité des soins : le projet SYNODOS}, booktitle = {JFIM}, year = {2014} }
005 ACTN Segond, F; Ponomareva, A; Rabarijaona, D; Bittar, A; Kergourlay, I; Darmoni, SJ; Gicquel, Q & Metzher, MH. Bien représenter pour mieux raisonner : deux approches pour le dossier patient. Atelier IC et Santé, Clermont Ferrand, Mai, 2014. Accepté.
Abstract: Le Dossier Patient Informatisé (DPI) constitue une source d’information pour des applications aussi variées que la recherche médicale, l’aide à la décision, la médecine factuelle ou la surveillance épidémiologique. Les publications utilisant l’analyse textuelle pour traiter du dossier patient sont en progression constante. Bien que donnant de très bons résultats, une telle approche fait apparaitre un certain nombre de défis, tels que la nécessité d’intégrer connaissances linguistiques et connaissances métier. Se basant sur une expérience précédente, cet article montre comment lier l’analyse linguistique, la représentation des connaissances, les ontologies médicales et le raisonnement afin de fournir un système générique permettant d’extraire, de structurer et d’exploiter l’information provenant des DPIs.
BibTeX: @inproceedings{Segond2014, author = {Segond, F and Ponomareva, A and Rabarijaona, D and Bittar, A and Kergourlay, I and Darmoni, SJ and Gicquel, Q and Metzher, MH}, title = {Bien représenter pour mieux raisonner : deux approches pour le dossier patient}, booktitle = {Atelier IC et Santé}, address = {Clermont Ferrand}, month = {Mai}, year = {2014}, note = {Accepté} }
007 AFF C. Cabot; J. Grosjean; R. Lelong; A. Lefebvre; T. Lecroq; L. F. Soualmia & S. J. Darmoni. Integrating omic and clinical data in electronic health records for visualisation and retrieval. 3ème Journée Scientifique de l'IRIB, Caugé, France, 2014.
BibTeX: @inproceedings{cabot2014b, author = {C. Cabot and J. Grosjean and R. Lelong and A. Lefebvre and T. Lecroq and L. F. Soualmia and S. J. Darmoni}, title = {Integrating omic and clinical data in electronic health records for visualisation and retrieval}, booktitle = {3ème Journ\'ee Scientifique de l'IRIB}, address = {Caug\'e, France}, year = {2014} }
007 AFF Chloé Cabot; Mélissa Mary; Chadi Saad; Alexandre Renaux; Alexis Bertrand; Amandine Velt; Arnaud Lefebvre; Caroline Bérard; Nicolas Vergne & Hélène Dauchel. GC- VC/DGE: a user-friendly web application for Going over Concordance across results from NGS bioinformatics analytic pipelines. ECCB 2014, Strasbourg, France, 2014.
BibTeX: @inproceedings{Cabot2014a, author = {Chloé Cabot and Mélissa Mary and Chadi Saad and Alexandre Renaux and Alexis Bertrand and Amandine Velt and Arnaud Lefebvre and Caroline Bérard and Nicolas Vergne and Hélène Dauchel}, title = {GC- VC/DGE: a user-friendly web application for Going over Concordance across results from NGS bioinformatics analytic pipelines}, booktitle = {ECCB 2014}, address = {Strasbourg, France}, year = {2014} }
007 AFF Chloé Cabot; Mélissa Mary; Chadi Saad; Alexandre Renaux; Alexis Bertrand; Amandine Velt; Arnaud Lefebvre; Caroline Bérard; Nicolas Vergne & Hélène Dauchel. GC- VC/DGE: a user-friendly web application for Going over Concordance across results from NGS bioinformatics analytic pipelines. 3ème Journée Scientifique de l'IRIB, Caugé, France, 2014.
BibTeX: @inproceedings{Cabot2014b, author = {Chloé Cabot and Mélissa Mary and Chadi Saad and Alexandre Renaux and Alexis Bertrand and Amandine Velt and Arnaud Lefebvre and Caroline Bérard and Nicolas Vergne and Hélène Dauchel}, title = {GC- VC/DGE: a user-friendly web application for Going over Concordance across results from NGS bioinformatics analytic pipelines}, booktitle = {3ème Journ\'ee Scientifique de l'IRIB}, address = {Caug\'e, France}, year = {2014} }
007 AFF Kerdelhué, G; Grosjean, J & Darmoni, SJ. A PubMed third party for French Language (and possibly others). 14th EAHIL Conference, 2014.
BibTeX: @inproceedings{Kerdelhue2014, author = {Kerdelhué, G and Grosjean, J and Darmoni, SJ}, title = {A PubMed third party for French Language (and possibly others)}, booktitle = {14th EAHIL Conference}, year = {2014} }
007 AFF Arnaud Lefebvre; Alexandra Martins; Karim Labrèche; Vivien Deshaies; Alan Lahure; Pascaline Gaildrat & Hélène Dauchel. HExoSplice: a new software based on overlapping hexamer scores for prediction and stratification of exonic variants altering splicing regulation of human genes. ECCB 2014, Strasbourg, France, 2014.
BibTeX: @inproceedings{Lefebvre2014, author = {Arnaud Lefebvre and Alexandra Martins and Karim Labrèche and Vivien Deshaies and Alan Lahure and Pascaline Gaildrat and Hélène Dauchel}, title = {HExoSplice: a new software based on overlapping hexamer scores for prediction and stratification of exonic variants altering splicing regulation of human genes}, booktitle = {ECCB 2014}, address = {Strasbourg, France}, year = {2014} }
007 AFF Arnaud Lefebvre; Alexandra Martins; Karim Labrèche; Vivien Deshaies; Alan Lahure; Pascaline Gaildrat; Hélène Dauchel; C. Cabot; J. Grosjean; R. Lelong; A. Lefebvre; T. Lecroq; L. F. Soualmia & S. J. Darmoni. HExoSplice: a bioinformatics software based on overlapping hexamer scores for prediction and stratification of exonic variants altering splicing regulation of human genes. 3ème Journée Scientifique de l'IRIB, Caugé, France, 2014.
BibTeX: @inproceedings{Lefebvre2014b, author = {Arnaud Lefebvre and Alexandra Martins and Karim Labrèche and Vivien Deshaies and Alan Lahure and Pascaline Gaildrat and Hélène Dauchel and C. Cabot and J. Grosjean and R. Lelong and A. Lefebvre and T. Lecroq and L. F. Soualmia and S. J. Darmoni}, title = {HExoSplice: a bioinformatics software based on overlapping hexamer scores for prediction and stratification of exonic variants altering splicing regulation of human genes}, booktitle = {3ème Journ\'ee Scientifique de l'IRIB}, address = {Caug\'e, France}, year = {2014} }
007 AFF Mary, M; Gansel, X & Soualmia, LF. LOINC & SNOMED-CT: usability and challenges to code identification tests and results for automated in vitro diagnostics systems.. 13th European Conference on Computational Biology, Strasbourg, France, September, 2014.
BibTeX: @inproceedings{Mary2014, author = {Mary, M and Gansel, X and Soualmia, LF}, title = {LOINC \& SNOMED-CT: usability and challenges to code identification tests and results for automated in vitro diagnostics systems.}, booktitle = {13th European Conference on Computational Biology}, address = {Strasbourg, France}, month = {September}, year = {2014} }
007 AFF Névéol, A; Déleger, L; Burgun, A; D'hondt, E; Griffon, N; Grouin, C; Hamon, T; Lavergne, T; Ligozat, AL; Pham, AD; rabary, C; Tannier, X; Tapi-Nzal, MD & Zweigenbaum, P. CABeRneT: Compréhension Automatique de Textes Biomédicaux pour la Recherche Translationnelle. forum Digiteo STIC du Campus, Décembre, 2014.
BibTeX: @inproceedings{Neveol2014, author = {Névéol, A and Déleger, L and Burgun, A and D'hondt, E and Griffon, N and Grouin, C and Hamon, T and Lavergne, T and Ligozat, AL and Pham, AD and rabary, C and Tannier, X and Tapi-Nzal, MD and Zweigenbaum, P}, title = {CABeRneT: Compréhension Automatique de Textes Biomédicaux pour la Recherche Translationnelle}, booktitle = {forum Digiteo STIC du Campus}, month = {Décembre}, year = {2014} }
007 AFF Pierre-Julien Viaillly; Arnaud Lefebvre & Hélène Dauchel. FunEVA: a user-friendly web application for Functional Effect Variation Analysis of human coding variations and their prioritization. ECCB 2014, Strasbourg, France, 2014.
BibTeX: @inproceedings{Viailly2014, author = {Pierre-Julien Viaillly and Arnaud Lefebvre and Hélène Dauchel}, title = {FunEVA: a user-friendly web application for Functional Effect Variation Analysis of human coding variations and their prioritization}, booktitle = {ECCB 2014}, address = {Strasbourg, France}, year = {2014} }
007 AFF Pierre-Julien Viaillly; Arnaud Lefebvre & Hélène Dauchel. FunEVA: a user-friendly web application for Functional Effect Variation Analysis of human coding variations and their prioritization. 3ème Journée Scientifique de l'IRIB, Caugé, France, 2014.
BibTeX: @inproceedings{Viailly2014b, author = {Pierre-Julien Viaillly and Arnaud Lefebvre and Hélène Dauchel}, title = {FunEVA: a user-friendly web application for Functional Effect Variation Analysis of human coding variations and their prioritization}, booktitle = {3ème Journ\'ee Scientifique de l'IRIB}, address = {Caug\'e, France}, year = {2014} }
008 OS Crochemore, M & Lecroq, T. Pattern matching and text data compression algorithms. Computing Handbook, Boca Raton, FL, Volume 1, Pages 15:1-15:57, Chapman & Hall/CRC Press, 2014. to appear.
BibTeX: @incollection{CrL2014, author = {Crochemore, M and Lecroq, T}, title = {Pattern matching and text data compression algorithms}, booktitle = {Computing Handbook}, address = {Boca Raton, FL}, publisher = {Chapman \& Hall/CRC Press}, year = {2014}, volume = {1}, pages = {15:1--15:57}, edition = {3rd}, note = {to appear} }
008 OS Duclos, C.; Burgun, A.; Lamy, J. B.; Landais, P.; Rodrigues, J. M.; Soualmia, L. & Zweigenbaum, P.. Medical Vocabulary, Terminological Resources and Information Coding in the Health Domain. Medical Informatics, e-Health, January, Health Informatics, Pages 11-41, Springer Paris, 2014.
Abstract: This chapter explains why it is hard to use medical language in computer applications and why the computer must adopt the human interpretation of medical words to avoid misunderstandings linked to ambiguity, homonymy and synonymy. Terminological resources are specific representations of medical language for dedicated use in particular health domains. We describe here the components of terminology (terms, concepts, relationships between concepts, definitions, constraints). The various artefacts of terminological resources (e.g. thesaurus, classification, nomenclature) are defined. We also provide examples of the dedicated use of terminological resources, such as disease coding, the indexing of biomedical publications, reasoning in decision support systems and data entry into electronic medical records. ICD 10, SNOMED CT, and MeSH are among the terminologies used in the examples. Alignment methods are described, making it possible to identify equivalent terms in different terminologies and to bridge different domains in health. We also present plans for multi-terminological servers, such as the UMLS (Unified Medical Language Systems), which provide a key vocabulary linking heterogeneous health terminologies in different languages.
BibTeX: @incollection{Duclos2014, author = {Duclos, C. and Burgun, A. and Lamy, J. B. and Landais, P. and Rodrigues, J. M. and Soualmia, L. and Zweigenbaum, P.}, title = {Medical Vocabulary, Terminological Resources and Information Coding in the Health Domain}, booktitle = {Medical Informatics, e-Health}, month = {January}, publisher = {Springer Paris}, year = {2014}, series = {Health Informatics}, pages = {11--41}, url = {http://link.springer.com/chapter/10.1007/978-2-8178-0478-1_2}, doi = {10.1007/978-2-8178-0478-1_2} }
008 OS Venot, A.; Charlet, J.; Darmoni, S.; Duclos, C.; Dufour, J. C. & Soualmia, L.. Management and Dissemination of Health Knowledge. Medical Informatics, e-Health, January, Health Informatics, Pages 43-64, Springer Paris, 2014.
Abstract: This chapter describes the various types of document available via the Internet for the dissemination of health knowledge. It describes the process for the publication of scientific articles reporting the results of research. The concepts of journal impact factor, citation base and h-index are explained. The Cochrane collaboration for literature reviews and meta-analysis is described. The goals of national and international clinical guidelines are explained and examples are provided of websites providing access to such guidelines. The various types of training materials available from e-learning platforms for medical students are described. This chapter also takes into account drug monographs, which are particularly useful for prescription and disease knowledge bases. Examples of resources useful to members of the public are also provided and we describe the methods for accessing health knowledge, including details of the resource indexing process and the MeSH thesaurus frequently used for indexing. The quality of health information on the Internet is also considered and the principal quality criteria are listed. The HON foundation and certification are described.
BibTeX: @incollection{Venot2014, author = {Venot, A. and Charlet, J. and Darmoni, S. and Duclos, C. and Dufour, J. C. and Soualmia, L.}, title = {Management and Dissemination of Health Knowledge}, booktitle = {Medical Informatics, e-Health}, month = {January}, publisher = {Springer Paris}, year = {2014}, series = {Health Informatics}, pages = {43--64}, url = {http://link.springer.com/chapter/10.1007/978-2-8178-0478-1_3}, doi = {10.1007/978-2-8178-0478-1_3} }
009 DO Lecroq, T. Preface of the special issue for LSD/LAW 2012. Journal of Discrete Algorithms , Volume 24, Pages 1, 2014.
BibTeX: @article{Lec2014, author = {Lecroq, T}, title = {Preface of the special issue for {LSD/LAW} 2012}, journal = {Journal of Discrete Algorithms}, year = {2014}, volume = {24}, pages = {1} }
010 AP Névéol, A et Darmoni, SJ et Zweigenbaum, P. Les ressources pour le traitement automatique de la langue biomédicale en français: appel à la communauté. Newsletter de l'Association Française d'Informatique Médicale , 2014.
BibTeX: @article{Neveol2014a, author = {Névéol, A et Darmoni, SJ et Zweigenbaum, P}, title = {Les ressources pour le traitement automatique de la langue biomédicale en français: appel à la communauté}, journal = {Newsletter de l'Association Française d'Informatique Médicale}, year = {2014}, url = {http://france-aim.org/aim/sites/default/files/News4_0.pdf} }
2013 001 ACL-int Barton, Carl; Giraud, Mathieu; Iliopoulos, Costas S.; Lecroq, Thierry; Mouchard, Laurent & Pissis, Solon P.. Querying highly similar sequences.. International Journal of Computational Biology and Drug Design , Volume 6, Number 1-2, Pages 119-130, 2013.
BibTeX: @article{Barton2013, author = {Barton, Carl and Giraud, Mathieu and Iliopoulos, Costas S. and Lecroq, Thierry and Mouchard, Laurent and Pissis, Solon P.}, title = {Querying highly similar sequences.}, journal = {International Journal of Computational Biology and Drug Design}, year = {2013}, volume = {6}, number = {1-2}, pages = {119--130}, doi = {10.1504/IJCBDD.2013.052206} }
001 ACL-int Braeckman, Lutgart; De Clercq, Bart; Janssens, Heidi; Gehanno, Jean-François; Bulat, Petar; Pauncu, Elena-Ana; Smits, Paul; van Dijk, Frank; Vanderlinde, Ruben & Valcke, Martin. Development and evaluation of a new occupational medicine teaching module to advance self-efficacy and knowledge among medical students.. J Occup Environ Med , Nov, Volume 55, Number 11, Pages 1276-1280, 2013.
Abstract: Self-efficacy is defined as a person's beliefs in his or her abilities to successfully complete a task, and has been shown to influence student motivation and academic achievement. The purpose of this study was to evaluate the impact of a new European teaching module in occupational medicine on undergraduate students' self-efficacy and knowledge in the subject matter.Pre-, in-between, and posttraining tests were used to assess self-efficacy and knowledge building of 261 third-year medical students on occupational health issues. Determinants of self-efficacy and knowledge were also identified. Repeated measurement data were analyzed with multilevel statistical procedures.The level of self-efficacy and knowledge in occupational medicine increased after the training. Students who frequently attended the lectures scored significantly higher than sporadic attendees. There was no relation between the level of self-efficacy and the final knowledge score.Teaching with the new occupational medicine module was effective. Lecture attendance is an important determinant of self-efficacy and performance. Self-efficacy was not associated with knowledge score. Encouraging classroom participation may enhance student achievement.
BibTeX: @article{Braeckman2013, author = {Braeckman, Lutgart and {De Clercq}, Bart and Janssens, Heidi and Gehanno, Jean-François and Bulat, Petar and Pauncu, Elena-Ana and Smits, Paul and {van Dijk}, Frank and Vanderlinde, Ruben and Valcke, Martin}, title = {Development and evaluation of a new occupational medicine teaching module to advance self-efficacy and knowledge among medical students.}, month = {Nov}, journal = {J Occup Environ Med}, year = {2013}, volume = {55}, number = {11}, pages = {1276--1280}, url = {http://dx.doi.org/10.1097/JOM.0b013e3182a50016}, doi = {10.1097/JOM.0b013e3182a50016} }
001 ACL-int Bérard, Caroline; Seifert, Michael; Mary-Huard, Tristan & Martin-Magniette, Marie-Laure. MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates.. BMC Bioinformatics , Sep, Volume 14, Number 1, Pages 271, 2013.
Abstract: Chromatin immunoprecipitation coupled with hybridization to a tiling array (ChIP-chip) is a cost-effective and routinely used method to identify protein-DNA interactions or chromatin/histone mod-ifications. The robust identification of ChIP-enriched regions is frequently complicated by noisymeasurements. This identification can be improved by accounting for dependencies between adja-cent probes on chromosomes and by modeling of biological replicates.MultiChIPmixHMM is a user-friendly R package to analyse ChIP-chip data modeling spatial depen-dencies between directly adjacent probes on a chromosome and enabling a simultaneous analysis ofreplicates. It is based on a linear regression mixture model, designed to perform a joint modeling ofimmunoprecipitated and input measurements.We show the utility of MultiChIPmixHMM by analyzing histone modifications of Arabidopsisthaliana. MultiChIPmixHMM is implemented in R and including functions in C, freely availablefrom the CRAN web site: http://cran.r-project.org.
BibTeX: @article{Berard2013, author = {Bérard, Caroline and Seifert, Michael and Mary-Huard, Tristan and Martin-Magniette, Marie-Laure}, title = {MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates.}, month = {Sep}, journal = {BMC Bioinformatics}, year = {2013}, volume = {14}, number = {1}, pages = {271}, url = {http://dx.doi.org/10.1186/1471-2105-14-271}, doi = {10.1186/1471-2105-14-271} }
001 ACL-int El-Falah, Tarek; Lecroq, Thierry & Elloumi, Mourad. Extraction of Infrequent Simple Motifs from a Finite Set of Sequences using a Lattice Structure. Recent Patents on DNA & Gene Sequences , July, Volume 7, Number 2, Pages 123-127, 2013.
BibTeX: @article{El-Falah2013, author = {El-Falah, Tarek and Lecroq, Thierry and Elloumi, Mourad}, title = {Extraction of Infrequent Simple Motifs from a Finite Set of Sequences using a Lattice Structure}, month = {July}, journal = {Recent Patents on {DNA} \& Gene Sequences}, year = {2013}, volume = {7}, number = {2}, pages = {123--127}, url = {http://www.eurekaselect.com/113670/article}, doi = {10.2174/1872215611307020006} }
001 ACL-int Faro, S & Lecroq, T. The Exact Online String Matching Problem: a Review of the Most Recent Results. ACM Computing Surveys , Volume 45, Number 2, Pages 13:1-13:42, 2013.
BibTeX: @article{Faro2013, author = {Faro, S and Lecroq, T}, title = {The Exact Online String Matching Problem: a Review of the Most Recent Results}, journal = {ACM Computing Surveys}, year = {2013}, volume = {45}, number = {2}, pages = {13:1-13:42}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/acmsurv2013.pdf}, doi = {10.1145/2431211.2431212} }
001 ACL-int Gehanno, JF; Rollin, L & Darmoni, SJ. Is the coverage of google scholar enough to be used alone for systematic reviews. BMC Medical Informatics and Decision Making , January, Volume 13, Number 1, Pages 7, 2013.
Abstract: In searches for clinical trials and systematic reviews, it is said that Google Scholar (GS) should never be used in isolation, but in addition to PubMed, Cochrane, and other trusted sources of information. We therefore performed a study to assess the coverage of GS specifically for the studies included in systematic reviews and evaluate if GS was sensitive enough to be used alone for systematic reviews.
BibTeX: @article{Gehanno2013, author = {Gehanno, JF and Rollin, L and Darmoni, SJ}, title = {Is the coverage of google scholar enough to be used alone for systematic reviews}, month = {January}, journal = {{BMC} Medical Informatics and Decision Making}, year = {2013}, volume = {13}, number = {1}, pages = {7}, url = {http://www.biomedcentral.com/1472-6947/13/7/abstract}, doi = {10.1186/1472-6947-13-7} }
001 ACL-int Gehanno, J. F.; Bulat, P.; Martinez-Jarreta, B.; Pauncu, E. A.; Popescu, F.; Smits, P B A.; van Dijk, F J H. & Braeckman, L.. Undergraduate teaching of occupational medicine in European schools of medicine.. Int Arch Occup Environ Health , Apr, 2013.
Abstract: PURPOSE: General practitioners play or should play a role in occupational medicine (OM), either in diagnosing occupational diseases or in counseling on return to work. Nevertheless, their training has been reported to be insufficient in most single country studies. AIMS: The objectives of this study were to analyze the content and extent of undergraduate teaching of OM in European medical schools. METHODS: An e-mail questionnaire survey of the teaching of OM to undergraduates was undertaken from December 2010 to April 2011 in all medical schools and medical faculties listed in 27 European countries (n = 305). RESULTS: Among the 305 universities identified, 135 answered to the questionnaire, giving a response rate of 44 The mean number of hours given to formal instruction in occupational medicine to medical undergraduates was 25.5 h. Nevertheless, this number of hours varied widely between countries, but also within countries. Overall, 27 % of medical schools gave their students 10 h of teaching or less, 52 % 20 h or less and 69 % 30 h or less. Whereas occupational diseases and principles of prevention were covered in most schools, disability and return to work were very poorly represented among the topics that were taught to students. CONCLUSION: Dedicated undergraduate teaching on occupational health or OM in European medical schools is present in most medical schools, usually at a low level, but is very variable between and within countries. Medical schools across Europe are very unequal to provide qualifying doctors education on the topics they will frequently come across in their working lives.
BibTeX: @article{Gehanno2013a, author = {Gehanno, J. F. and Bulat, P. and Martinez-Jarreta, B. and Pauncu, E. A. and Popescu, F. and Smits, P B A. and {van Dijk}, F J H. and Braeckman, L.}, title = {Undergraduate teaching of occupational medicine in European schools of medicine.}, month = {Apr}, journal = {Int Arch Occup Environ Health}, year = {2013}, url = {http://dx.doi.org/10.1007/s00420-013-0878-5}, doi = {10.1007/s00420-013-0878-5} }
001 ACL-int Gerbier-Colomban, Solweig; Gicquel, Quentin; Millet, Anne-Laure; Riou, Christophe; Grando, Jacqueline; Darmoni, Stefan; Potinet-Pagliaroli, Véronique & Metzger, Marie-Hélène. Evaluation of syndromic algorithms for detecting patients with potentially transmissible infectious diseases based on computerised emergency-department data.. BMC Med Inform Decis Mak , Volume 13, Pages 101, 2013.
Abstract: The objective of this study was to ascertain the performance of syndromic algorithms for the early detection of patients in healthcare facilities who have potentially transmissible infectious diseases, using computerised emergency department (ED) data.A retrospective cohort in an 810-bed University of Lyon hospital in France was analysed. Adults who were admitted to the ED and hospitalised between June 1, 2007, and March 31, 2010 were included (N=10895). Different algorithms were built to detect patients with infectious respiratory, cutaneous or gastrointestinal syndromes. The performance parameters of these algorithms were assessed with regard to the capacity of our infection-control team to investigate the detected cases.For respiratory syndromes, the sensitivity of the detection algorithms was 82.70 and the specificity was 82.37 For cutaneous syndromes, the sensitivity of the detection algorithms was 78.08 and the specificity was 95.93 For gastrointestinal syndromes, the sensitivity of the detection algorithms was 79.41 and the specificity was 81.97This assessment permitted us to detect patients with potentially transmissible infectious diseases, while striking a reasonable balance between true positives and false positives, for both respiratory and cutaneous syndromes. The algorithms for gastrointestinal syndromes were not specific enough for routine use, because they generated a large number of false positives relative to the number of infected patients. Detection of patients with potentially transmissible infectious diseases will enable us to take precautions to prevent transmission as soon as these patients come in contact with healthcare facilities.
BibTeX: @article{Gerbier-Colomban2013, author = {Gerbier-Colomban, Solweig and Gicquel, Quentin and Millet, Anne-Laure and Riou, Christophe and Grando, Jacqueline and Darmoni, Stefan and Potinet-Pagliaroli, Véronique and Metzger, Marie-Hélène}, title = {Evaluation of syndromic algorithms for detecting patients with potentially transmissible infectious diseases based on computerised emergency-department data.}, journal = {BMC Med Inform Decis Mak}, year = {2013}, volume = {13}, pages = {101}, url = {http://dx.doi.org/10.1186/1472-6947-13-101}, doi = {10.1186/1472-6947-13-101} }
001 ACL-int Golbreich, C; Grosjean, J & Darmoni, SJ. The Foundational Model of Anatomy in OWL 2 and its use.. Artif Intell Med , Feb, Volume 57, Number 2, Pages 119-132, 2013.
Abstract: OBJECTIVE: The objective is to represent the Foundational Model of Anatomy (FMA) in the OWL 2 Web Ontology Language (informally OWL 2), and to use it in a European cross-lingual portal of health terminologies for indexing and searching Web resources. Formalizing the FMA in OWL 2 is essential for semantic interoperability, to improve its design, and to ensure its reliability and correctness, which is particularly important for medical applications. METHOD AND MATERIAL: The native FMA was implemented in frames and stored in a MySQL database backend. The main strength of the method is to leverage OWL 2 expressiveness and to rely on the naming conventions of the FMA, to make explicit some implicit semantics, while improving its ontological model and fixing some errors. Doing so, the semantics (meaning) of the formal definitions and axioms are anatomically correct. A flexible tool enables the generation of a new version in OWL 2 at each Protégé FMA update. While it creates by default a 'standard' version of the FMA in OWL 2 (FMA-OWL), many options allow for producing other variants customized to users' applications. Once formalized in OWL 2, it was possible to use an inference engine to check the ontology and detect inconsistencies. Next, the FMA-OWL was used to derive a lightweight FMA terminology for a European cross-lingual portal of terminologies/ontologies for indexing and searching resources. The transformation is mainly based on a reification process. RESULT: Complete representations of the entire FMA in OWL 1 or OWL 2 are now available. The formalization tool is flexible and easy to use, making it possible to obtain an OWL 2 version for all existing public FMA. A number of errors were detected in the native FMA and several patterns of recurrent errors were identified in the original FMA. This shows how the underlying OWL 2 ontology is essential to ensure that the lightweight derived terminology is reliable. The FMA OWL 2 ontology has been applied to derive an anatomy terminology that is used in a European cross-lingual portal of health terminologies. This portal is daily used by librarians to index Web health resources. In August 2011, 6481 out of 81,450 health resources of CISMeF catalog (http://www.chu-rouen.fr/cismef/ - accessed 29.08.12) (7.96 were indexed with at least one FMA entity. CONCLUSION: The FMA is a central terminology used to index and search Web resources. To the best of our knowledge, neither a complete representation of the entire FMA in OWL 2, nor an anatomy terminology available in a cross-lingual portal, has been developed to date. The method designed to represent the FMA ontology in OWL 2 presented in this article is general and may be extended to other ontologies. Using a formal ontology for quality assurance and deriving a lightweight terminology for biomedical applications is a general and promising strategy.
BibTeX: @article{Golbreich2012, author = {Golbreich, C and Grosjean, J and Darmoni, SJ}, title = {The Foundational Model of Anatomy in OWL 2 and its use.}, month = {Feb}, journal = {Artif Intell Med}, year = {2013}, volume = {57}, number = {2}, pages = {119-132}, url = {http://dx.doi.org/10.1016/j.artmed.2012.11.002}, doi = {10.1016/j.artmed.2012.11.002} }
001 ACL-int Griffon, N.; Charlet, J.; Darmoni, Sj; , Section Editors for the I. M. I. A Yearbook 2013, Section on Knowledge Representation & Management. Knowledge representation and management: towards an integration of a semantic web in daily health practice.. Yearb Med Inform , Volume 8, Number 1, Pages 155-158, 2013.
Abstract: To summarize the best papers in the field of Knowledge Representation and Management (KRM).A synopsis of the four selected articles for the IMIA Yearbook 2013 KRM section is provided, as well as highlights of current KRM trends, in particular, of the semantic web in daily health practice. The manual selection was performed in three stages: first a set of 3,106 articles, then a second set of 86 articles followed by a third set of 15 articles, and finally the last set of four chosen articles.Among the four selected articles (see Table 1), one focuses on knowledge engineering to prevent adverse drug events; the objective of the second is to propose mappings between clinical archetypes and SNOMED CT in the context of clinical practice; the third presents an ontology to create a question-answering system; the fourth describes a biomonitoring network based on semantic web technologies.These four articles clearly indicate that the health semantic web has become a part of daily practice of health professionals since 2012. In the review of the second set of 86 articles, the same topics included in the previous IMIA yearbook remain active research fields: Knowledge extraction, automatic indexing, information retrieval, natural language processing, management of health terminologies and ontologies.
BibTeX: @article{Griffon2013, author = {Griffon, N. and Charlet, J. and Darmoni, Sj and , Section Editors for the I. M. I. A Yearbook 2013, Section on Knowledge Representation and Management}, title = {Knowledge representation and management: towards an integration of a semantic web in daily health practice.}, journal = {Yearb Med Inform}, year = {2013}, volume = {8}, number = {1}, pages = {155--158} }
001 ACL-int Lamy, Jean-Baptiste; Soualmia, Lina F.; Kerdelhué, Gaëtan; Venot, Alain & Duclos, Catherine. Validating the semantics of a medical iconic language using ontological reasoning.. J Biomed Inform , Sep, 2013.
Abstract: To help clinicians read medical texts such as clinical practice guidelines or drug monographs, we proposed an iconic language called VCM. This language can use icons to represent the main medical concepts, including diseases, symptoms, treatments and follow-up procedures, by combining various pictograms, shapes and colors. However, the semantics of this language have not been formalized, and users may create inconsistent icons, e.g. by combining the "tumor" shape and the "sleeping" pictograms into a "tumor of sleeping" icon.This work aims to represent the VCM language using DLs and OWL for evaluating its semantics by reasoners, and in particular for determining inconsistent icons. We designed an ontology for formalized the semantics of VCM icons using the Protégé editor and scripts for translating the VCM lexicon in OWL. We evaluated the ability of the ontology to determine icon consistency for a set of 100 random icons. The evaluation showed good results for determining icon consistency, with a high sensitivity. The ontology may also be useful for the design of mapping between VCM and other medical terminologies, for generating textual labels for icons, and for developing user interfaces for creating VCM icons.
BibTeX: @article{Lamy2012, author = {Lamy, Jean-Baptiste and Soualmia, Lina F. and Kerdelhué, Gaëtan and Venot, Alain and Duclos, Catherine}, title = {Validating the semantics of a medical iconic language using ontological reasoning.}, month = {Sep}, journal = {J Biomed Inform}, year = {2013}, url = {http://dx.doi.org/10.1016/j.jbi.2012.08.006}, doi = {10.1016/j.jbi.2012.08.006} }
001 ACL-int Lecroq, T.; Soualmia, L. F.; , Section Editors for the I. M. I. A Yearbook Section on Bioinformatics & Translational Informatics. From genome sequencing to bedside. Findings from the section on bioinformatics and translational informatics.. Yearb Med Inform , Volume 8, Number 1, Pages 175-177, 2013.
Abstract: To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and evidence-based medicine.We provide a synopsis of the articles selected for the IMIA Yearbook 2013, from which we attempt to derive a synthetic overview of current and future activities in the field. Three steps of selection were performed by querying PubMed and Web of Science. A first set of 5,549 articles was refined into a second set of 1,272 articles from which 15 articles were retained for peer-review.The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding the Human Genome and Medicine. Exploiting genomic data depends on having the appropriate reference annotation available. In the first article, the goal of the GENCODE Consortium is to produce and publish The GENCODE human reference gene set. As a result it is composed by merged manual and automatic annotations, which are frequently updated from public experimental databases. The quality of genome sequencing is platform-dependant. In the second article, a generic database independent from the sequencing technologies, Huvariome, can help to identify errors and inconsistencies in sequencing. To understand complex diseases of patients it will be of great importance to detect rare gene variants. This is the aim of the third study. Finally, in the last article, the plasma's DNA of healthy individual and patients suffering from cancer is compared.The current research activities attest to the continuous convergence of Bioinformatics and Medical Informatics for clinical practice. For instance, a direct use of high throughput sequencing technologies for patients could aid the diagnosis of complex diseases (such as cancer) without invasive surgery (such as biopsy) but only with blood analysis. However, ongoing genomic tests will generate massive amounts of data and will imply new trends in the near future: "Big Data" and smart health management.
BibTeX: @article{Lecroq2013, author = {Lecroq, T. and Soualmia, L. F. and , Section Editors for the I. M. I. A Yearbook Section on Bioinformatics and Translational Informatics}, title = {From genome sequencing to bedside. Findings from the section on bioinformatics and translational informatics.}, journal = {Yearb Med Inform}, year = {2013}, volume = {8}, number = {1}, pages = {175--177} }
001 ACL-int Rollin, L.; Ladner, J.; Gislard, A.; Monfrin, F.; Larchevesque, J-Y.; Deslandes, P. & Gehanno, J-F.. Hazard information needs and information seeking in French workers.. Occup Med (Lond) , Oct, Volume 63, Number 7, Pages 473-478, 2013.
Abstract: Data about perceived needs of workers for information on occupational hazards or diseases (OHDs) are scarce and the behaviour of workers seeking information on these matters is not well known.To describe workers' needs and behaviour in seeking information about OHDs.All workers attending for consultation at an occupational health service in Upper Normandy within 1 week were invited to fill in an anonymous questionnaire.Of the 2640 workers responding 58% declared a need for information about OHD, but only 37% actually sought that information. Whereas 82% of workers mentioned the internet and their general physician (GP) as sources of information on OHD, only 43% mentioned their occupational physician (OP). Furthermore, information received from OPs was not considered more reliable than that from GPs.Workers report a need for information about OHDs. Although most of them trust information given by OPs, they do not use OPs to obtain OHD information, but instead use less reliable sources such as the internet or their GPs.
BibTeX: @article{Rollin2013, author = {Rollin, L. and Ladner, J. and Gislard, A. and Monfrin, F. and Larchevesque, J-Y. and Deslandes, P. and Gehanno, J-F.}, title = {Hazard information needs and information seeking in French workers.}, month = {Oct}, journal = {Occup Med (Lond)}, year = {2013}, volume = {63}, number = {7}, pages = {473--478}, url = {http://dx.doi.org/10.1093/occmed/kqt091}, doi = {10.1093/occmed/kqt091} }
001 ACL-int Saussereau, Elodie; Lacroix, Christian; Guerbet, Michel; Cellier, Dominique; Spiroux, Joël & Goullé, Jean-Pierre. Determination of Levels of Current Drugs in Hospital and Urban Wastewater. Bulletin of Environmental Contamination and Toxicology , Pages 1-6, Springer US, 2013.
BibTeX: @article{Saussereau2013, author = {Saussereau, Elodie and Lacroix, Christian and Guerbet, Michel and Cellier, Dominique and Spiroux, Joël and Goullé, Jean-Pierre}, title = {Determination of Levels of Current Drugs in Hospital and Urban Wastewater}, journal = {Bulletin of Environmental Contamination and Toxicology}, publisher = {Springer US}, year = {2013}, pages = {1-6}, url = {http://dx.doi.org/10.1007/s00128-013-1030-7}, doi = {10.1007/s00128-013-1030-7} }
001 ACL-int Soualmia, LF; Sakji, S; Letord, C; Rollin, L; Massari, P & Darmoni, SJ. Improving information retrieval with multiple health terminologies in a quality-controlled gateway. BMC Health Information Science and Systems , Pages 1-8, 2013.
BibTeX: @article{Soualmia2013, author = {Soualmia, LF and Sakji, S and Letord, C and Rollin, L and Massari, P and Darmoni, SJ}, title = {Improving information retrieval with multiple health terminologies in a quality-controlled gateway}, journal = {BMC Health Information Science and Systems}, year = {2013}, pages = {1-8}, url = {http://www.hissjournal.com/content/1/1/8}, doi = {10.1186/2047-2501-1-8} }
001 ACL-int Yepes, AJJ; Prieur-Gaston, E & Névéol, A. Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text. BMC Bioinformatics , Volume 14, Number 1, Pages 146, 2013.
Abstract: BACKGROUND: Most of the institutional and research information in the biomedical domain is available in the form of English text. Even in countries where English is an official language, such as the United States, language can be a barrier for accessing biomedical information for non-native speakers. Recent progress in machine translation suggests that this technique could help make English texts accessible to speakers of other languages. However, the lack of adequate specialized corpora needed to train statistical models currently limits the quality of automatic translations in the biomedical domain. RESULTS: We show how a large-sized parallel corpus can automatically be obtained for the biomedical domain, using the MEDLINE database. The corpus generated in this work comprises article titles obtained from MEDLINE and abstract text automatically retrieved from journal websites, which substantially extends the corpora used in previous work. After assessing the quality of the corpus for two language pairs (English/French and English/Spanish) we use the Moses package to train a statistical machine translation model that outperforms previous models for automatic translation of biomedical text. CONCLUSIONS: We have built translation data sets in the biomedical domain that can easily be extended to other languages available in MEDLINE. These sets can successfully be applied to train statistical machine translation models. While further progress should be made by incorporating out-of-domain corpora and domain-specific lexicons, we believe that this work improves the automatic translation of biomedical texts.
BibTeX: @article{Yepes2013, author = {Yepes, AJJ and Prieur-Gaston, E and Névéol, A}, title = {Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text}, journal = {BMC Bioinformatics}, year = {2013}, volume = {14}, number = {1}, pages = {146}, url = {http://www.biomedcentral.com/1471-2105/14/146/abstract}, doi = {10.1186/1471-2105-14-146} }
003 INV Mouchard, L. Toward Efficient Compression of NGS Data. Theo Murphy International Scientific Meeting Storage and indexing of massive data", Royal Society, Chicheley, UK, February, 2013.
BibTeX: @inproceedings{Mouchard2013, author = {Mouchard, L}, title = {Toward Efficient Compression of NGS Data}, booktitle = {Theo Murphy International Scientific Meeting \Storage and indexing of massive data", Royal Society}, address = {Chicheley, UK}, month = {February}, year = {2013} }
004 ACTI Chebil, W; Soualmia, LF & Darmoni, SJ. BioDI: A new approach to improve Biomedical Documents Indexing. Proceedings of the 24th International Conference on Database and Expert Systems Applications, DEXA, August, Lecture Notes in Computer Science, Pages 78-87, Springer, 2013.
Abstract: The partial match between biomedical documents and controlled vocabularies allows to find in the documents more terms variants than those existing in the dictionaries. However, it generates irrelevant information. We propose a new approach for indexing biomedical documents with the Medical Subject Headings (MeSH) thesaurus that aims to overcome the limitation of the partial match. In fact, our indexing approach proposes to restrict the stemming process in the step of pretreatment. The step of the descriptors extraction is based essentially on the vector space model and combines semantic and statistic methods to compute a score to estimate the relevance of a descriptor given a document. The knowledge provided by the Unified Medical Language System (UMLS) is used then for filtering. The filtering method aims to keep only relevant descriptors. The experiments of our approach that have been carried out on the OHSUMED collection, showed very encouraging results.
BibTeX: @inproceedings{Chebil2013, author = {Chebil, W and Soualmia, LF and Darmoni, SJ}, title = {BioDI: A new approach to improve Biomedical Documents Indexing}, booktitle = {Proceedings of the 24th International Conference on Database and Expert Systems Applications, DEXA}, month = {August}, publisher = {Springer}, year = {2013}, series = {Lecture Notes in Computer Science}, pages = {78-87}, doi = {10.1007/978-3-642-40285-2_9} }
004 ACTI Chebil, W; Soualmia, LF & Darmoni, SJ. BNDI:A Bayesian Network for biomedial Documents Indexing with MeSH thesaurus. Proceedings of the International Conference on Reasoning and Optimization in Information Systems (ROIS), Hammam- Sousse, Tunisia, September, Pages 134-139, 2013.
BibTeX: @inproceedings{Chebil2013a, author = {Chebil, W and Soualmia, LF and Darmoni, SJ}, title = {BNDI:A Bayesian Network for biomedial Documents Indexing with MeSH thesaurus}, booktitle = {Proceedings of the International Conference on Reasoning and Optimization in Information Systems (ROIS)}, address = {Hammam- Sousse, Tunisia}, month = {September}, year = {2013}, pages = {134-139} }
004 ACTI Dupuch, M; Segond, F; Bittar, A; Dini, L; Soualmia, LF; Darmoni, SJ; Gicquel, Q & Metzger, MH. Separate the grain from the chaff: make the best use of language and knowledge technologies to model textual medical data extracted from electronic health records. Proceedings of the LTC'13 6th Language & Technology Conference: Human Language Technologies as a Challenge for Computer Science and Linguistics, Poznań, Poland, December, 2013.
BibTeX: @inproceedings{Dupuch2013, author = {Dupuch, M and Segond, F and Bittar, A and Dini, L and Soualmia, LF and Darmoni, SJ and Gicquel, Q and Metzger, MH}, title = {Separate the grain from the chaff: make the best use of language and knowledge technologies to model textual medical data extracted from electronic health records}, booktitle = {Proceedings of the LTC'13 6th Language \& Technology Conference: Human Language Technologies as a Challenge for Computer Science and Linguistics}, address = {Poznań, Poland}, month = {December}, year = {2013} }
004 ACTI Fici, Gabriele; Langiu, Alessio; Lecroq, Thierry; Lefebvre, Arnaud; Mignosi, Filippo & Prieur-Gaston, Ã‰lise. Abelian Repetitions in Sturmian Words. Developments in Language Theory, January, Lecture Notes in Computer Science, Number 7907, Pages 227-238, Springer Berlin Heidelberg, 2013.
Abstract: We investigate abelian repetitions in Sturmian words. We exploit a bijection between factors of Sturmian words and subintervals of the unitary segment that allows us to study the periods of abelian repetitions by using classical results of elementary Number Theory. If k m denotes the maximal exponent of an abelian repetition of period m, we prove that limsup km/mâ‰¥5âˆškm/mtextbackslashge textbackslashsqrt5 for any Sturmian word, and the equality holds for the Fibonacci infinite word. We further prove that the longest prefix of the Fibonacci infinite word that is an abelian repetition of period F j , j textgreater 1, has length F j ( F j + 1 + F j âˆ’ 1 + 1) âˆ’ 2 if j is even or F j ( F j + 1 + F j âˆ’ 1 ) âˆ’ 2 if j is odd. This allows us to give an exact formula for the smallest abelian periods of the Fibonacci finite words. More precisely, we prove that for j â‰¥ 3, the Fibonacci word f j has abelian period equal to F n , where n=âŒŠj/2âŒ‹n = textbackslashlfloorj/2textbackslashrfloor if j=0,1,2mod4j = 0, 1, 2textbackslashmod4 , or n=1+âŒŠj/2âŒ‹n = 1 + textbackslashlfloorj/2textbackslashrfloor if j=3mod4 j = 3textbackslashmod4 .
BibTeX: @incollection{Fici2013a, author = {Fici, Gabriele and Langiu, Alessio and Lecroq, Thierry and Lefebvre, Arnaud and Mignosi, Filippo and Prieur-Gaston, Ã‰lise}, title = {Abelian Repetitions in Sturmian Words}, booktitle = {Developments in Language Theory}, month = {January}, publisher = {Springer Berlin Heidelberg}, year = {2013}, series = {Lecture Notes in Computer Science}, number = {7907}, pages = {227--238}, url = {http://link.springer.com/chapter/10.1007/978-3-642-38771-5_21} }
004 ACTI Merabti, A; Soualmia, LF & Darmoni, SJ. Aligning bio-terminologies and bio-ontologies lexicons : a preliminary study. Proceedings of the 10th International Conference on Terminology and Artificial Intelligence, October, 2013.
BibTeX: @inproceedings{Merabti2013b, author = {Merabti, A and Soualmia, LF and Darmoni, SJ}, title = {Aligning bio-terminologies and bio-ontologies lexicons : a preliminary study}, booktitle = {Proceedings of the 10th International Conference on Terminology and Artificial Intelligence}, month = {October}, year = {2013} }
004 ACTI Merabti, T; Soualmia, LF.; Grosjean, J; Letord, C & Darmoni, SJ. Assisting the Translation of SNOMED CT into French.. Stud Health Technol Inform MEDINFO 2013 - Proceedings of the 14th World Congress on Medical Informatics, Volume 192, Pages 47-51, 2013.
Abstract: The objective of this study is to evaluate to approaches assisting the translation of SNOMED CT into French. Two types of approaches were combined: a concept-based one, which relies on conceptual information of the UMLS Metathesaurus and a lexical-based one, which relieson NLP techniques. In addition to the French terminologies (whether included in UMLS or not). Using the concept-based approach, a set of 156,157 (39.4 SNOMED CT terms were translated to at least one French term from UMLS. Expanded to the French terms from UMLS terminologies translated by CISMeF, 2,548 (+0.7 additional SNOMED CT terms were translated to at least one French term. Using the lexical-based approach, a set of 145,737 (36.8 SNOMED CT terms were translated to at least one French term from HeTOP. The qualitative evaluation showed that 44% of the translations were rated as "relevant". Overall, the two approaches have provided the translation of 168,750 (42.6 SNOMED CT terms into French using different bilingual terminological sources included in UMLS or in HeTOP.
BibTeX: @inproceedings{Merabti2013a, author = {Merabti, T and Soualmia, LF. and Grosjean, J and Letord, C and Darmoni, SJ}, title = {Assisting the Translation of SNOMED CT into French.}, booktitle = {MEDINFO 2013 - Proceedings of the 14th World Congress on Medical Informatics}, journal = {Stud Health Technol Inform}, year = {2013}, volume = {192}, pages = {47--51} }
004 ACTI Joong Chae Na; Heejin Park; Maxime Crochemore; Jan Holub; Costas S. Iliopoulos; Laurent Mouchard & Kunsoo Park. Suffix Tree of an Alignment: An Efficient Index for Similar Data. Proceedings of the 24th International Workshop on Combinatorial Algorithms (IWOCA 2013), Rouen, France, 2013.
BibTeX: @inproceedings{Na2013a, author = {Joong Chae Na and Heejin Park and Maxime Crochemore and Jan Holub and Costas S. Iliopoulos and Laurent Mouchard and Kunsoo Park}, title = {Suffix Tree of an Alignment: An Efficient Index for Similar Data}, booktitle = {Proceedings of the 24th International Workshop on Combinatorial Algorithms (IWOCA 2013)}, address = {Rouen, France}, year = {2013} }
004 ACTI Joong Chae Na; Heejin Park; Sunho Lee; Minsung Hong; Thierry Lecroq; Laurent Mouchard & Kunsoo Park. Suffix Array of Alignment: A Practical Index for Similar Data. Proceedings of the 20th Symposium on String Processing and Information Retrieval, Jerusalem, Israel, jan, Number 8214, Pages 243-254, Springer International Publishing, 2013.
Abstract: The suffix tree of alignment is an index data structure for similar strings. Given an alignment of similar strings, it stores all suffixes of the alignment, called alignment-suffixes. An alignment-suffix represents one suffix of a string or suffixes of multiple strings starting at the same position in the alignment. The suffix tree of alignment makes good use of similarity in strings theoretically. However, suffix trees are not widely used in biological applications because of their huge space requirements, and instead suffix arrays are used in practice. In this paper we propose a space-economical version of the suffix tree of alignment, named the suffix array of alignment (SAA). Given an alignment Ï of similar strings, the SAA for Ï is a lexicographically sorted list of all the alignment-suffixes of Ï. The SAA supports pattern search as efficiently as the generalized suffix array. Our experiments show that our index uses only 14% of the space used by the generalized suffix array to index 11 human genome sequences. The space efficiency of our index increases as the number of the genome sequences increases. We also present an efficient algorithm for constructing the SAA.
BibTeX: @inproceedings{Na2013b, author = {Joong Chae Na and Heejin Park and Sunho Lee and Minsung Hong and Thierry Lecroq and Laurent Mouchard and Kunsoo Park}, title = {Suffix Array of Alignment: A Practical Index for Similar Data}, booktitle = {Proceedings of the 20th Symposium on String Processing and Information Retrieval}, address = {Jerusalem, Israel}, month = {jan}, publisher = {Springer International Publishing}, year = {2013}, number = {8214}, pages = {243--254}, doi = {10.1007/978-3-319-02432-5_27} }
005 ACTN Darmoni, SJ; Soualmia, LF; Griffon, N; Grosjean, J; Kerdelhué, G; Kergoulay, I; Thirion, B & Dahamna, B. MLPubMed : une base de données bibliographique multi-lingue. Colloque RITS, 2013.
BibTeX: @inproceedings{Darmoni2013, author = {Darmoni, SJ and Soualmia, LF and Griffon, N and Grosjean, J and Kerdelhué, G and Kergoulay, I and Thirion, B and Dahamna, B}, title = {MLPubMed : une base de données bibliographique multi-lingue}, booktitle = {Colloque RITS}, year = {2013} }
005 ACTN Darmoni, SJ; Soualmia, LF; Griffon, N; Kerdelhué, G; Kergourlay, I; Thirion, B & Dahamna, B. MLPubMed : une base de données bibliographique multi-lingue. Pré-symposium French Special Interest Group of the International Medical Informatics Association, FR SIG IMIA, August, 2013. In press.
BibTeX: @inproceedings{Darmoni2013a, author = {Darmoni, SJ and Soualmia, LF and Griffon, N and Kerdelhué, G and Kergourlay, I and Thirion, B and Dahamna, B}, title = {MLPubMed : une base de données bibliographique multi-lingue}, booktitle = {Pré-symposium French Special Interest Group of the International Medical Informatics Association, FR SIG IMIA}, month = {August}, year = {2013}, note = {In press} }
006 COM Fici, G.; Langiu, A.; Lecroq, T.; Lefebvre, A.; Mignosi, F. & Prieur-Gaston, É.. Sturmian Words and Abelian Repetitions. , 2013. Montpellier, {F}rance.
BibTeX: @misc{seqbio2013a, author = {{F}ici, {G}. and Langiu, A. and {L}ecroq, {T}. and {L}efebvre, {A}. and Mignosi, F. and {P}rieur-{G}aston, {\'E}.}, title = {Sturmian Words and Abelian Repetitions}, year = {2013}, note = {Montpellier, {F}rance} }
006 COM Giquel, Q; Dini, L; Kergourlay, I; Arnod-Prin, P; Chariout, S; Bittar, A; Soualmia, LF; Guedez, P; Segond, F; Ruhlman, M; Darmoni, SJ & Metzger, M. SYstème de Normalisation et d'Organisation de Données médicales textuelles pour l'Observation en Santé (SYNODOS). Pré-symposium French Special Interest Group of the International Medical Informatics Association, FR SIG IMIA, August, 2013.
BibTeX: @inproceedings{Giquel2013, author = {Giquel, Q and Dini, L and Kergourlay, I and Arnod-Prin, P and Chariout, S and Bittar, A and Soualmia, LF and Guedez, P and Segond, F and Ruhlman, M and Darmoni, SJ and Metzger, M}, title = {SYstème de Normalisation et d'Organisation de Données médicales textuelles pour l'Observation en Santé (SYNODOS)}, booktitle = {Pré-symposium French Special Interest Group of the International Medical Informatics Association, FR SIG IMIA}, month = {August}, year = {2013} }
006 COM Na, J.-C..; Park, H.; Lee, S.; Hong, M. Lecroq, T.; Mouchard, L. & Park, K.. Suffix Tree and Suffix Array of an Alignment. , 2013. Montpellier, {F}rance.
BibTeX: @misc{seqbio2013b, author = {{N}a, {J.-C.}. and Park, H. and Lee, S. and Hong, M. {L}ecroq, {T}. and {M}ouchard, {L}. and {P}ark, {K}.}, title = {Suffix Tree and Suffix Array of an Alignment}, year = {2013}, note = {Montpellier, {F}rance} }
006 COM Névéol, A; Grouin, C; and Darmoni, SJ & Zweigenbaum, P. Dé-identification d’un corpus clinique pour le traitement automatique du français. Pré-symposium French Special Interest Group of the International Medical Informatics Association, FR SIG IMIA, August, 2013.
BibTeX: @inproceedings{Neveol2013, author = {Névéol, A and Grouin, C and and Darmoni, SJ and Zweigenbaum, P}, title = {Dé-identification d’un corpus clinique pour le traitement automatique du français}, booktitle = {Pré-symposium French Special Interest Group of the International Medical Informatics Association, FR SIG IMIA}, month = {August}, year = {2013} }
007 AFF Darmoni, SJ.; Soualmia, LF; Griffon, N; Grosjean, J; Kerdelhué, G; Kergourlay, I & Dahamna, B. Multi-lingual Search Engine to Access PubMed Monolingual Subsets: A Feasibility Study.. Stud Health Technol Inform MEDINFO 2013 - Proceedings of the 14th World Congress on Medical Informatics, Volume 192, Pages 966, 2013.
Abstract: PubMed contains many articles in languages other than English but it is difficult to find them using the English version of the Medical Subject Headings (MeSH) Thesaurus. The aim of this work is to propose a tool allowing access to a PubMed subset in one language, and to evaluate its performance. Translations of MeSH were enriched and gathered in the information system. PubMed subsets in main European languages were also added in our database, using a dedicated parser. The CISMeF generic semantic search engine was evaluated on the response time for simple queries. MeSH descriptors are currently available in 11 languages in the information system. All the 654,000 PubMed citations in French were integrated into CISMeF database. None of the response times exceed the threshold defined for usability (2 seconds). It is now possible to freely access biomedical literature in French using a tool in French; health professionals and lay people with a low English language may find it useful. It will be expended to several European languages: German, Spanish, Norwegian and Portuguese.
BibTeX: @inproceedings{Darmoni2013b, author = {Darmoni, SJ. and Soualmia, LF and Griffon, N and Grosjean, J and Kerdelhué, G and Kergourlay, I and Dahamna, B}, title = {Multi-lingual Search Engine to Access PubMed Monolingual Subsets: A Feasibility Study.}, booktitle = {MEDINFO 2013 - Proceedings of the 14th World Congress on Medical Informatics}, journal = {Stud Health Technol Inform}, year = {2013}, volume = {192}, pages = {966} }
007 AFF Grosjean, J; Merabti, T; Soualmia, LF; Letord, C; Charlet, J; Robinson, P & Darmoni, SJ. Integrating the Human Phenotype Ontology into HeTOP Terminology-Ontology Server.. Stud Health Technol Inform MEDINFO 2013 - Proceedings of the 14th World Congress on Medical Informatics, Volume 192, Pages 961, 2013.
Abstract: The Human Phenotype Ontology (HPO) is a controlled vocabulary which provides phenotype data related to genes or diseases. The Health Terminology/Ontology Portal (HeTOP) is a tool dedicated to both human beings and computers to access and browse biomedical terminologies or ontologies (T/O). The objective of this work was to integrate the HPO into HeTOP in order to enhance both works. This integration is a success and allows users to search and browse the HPO with a dedicated interface. Furthermore, the HPO has been enhanced with the addition of content such as new synonyms, translations, mappings. Integrating T/O such as the HPO into HeTOP is a benefit to vocabularies because it allows enrichment of them and it is also a benefit for HeTOP which provides a better service to both humans and machines.
BibTeX: @inproceedings{Grosjean2013, author = {Grosjean, J and Merabti, T and Soualmia, LF and Letord, C and Charlet, J and Robinson, P and Darmoni, SJ}, title = {Integrating the Human Phenotype Ontology into HeTOP Terminology-Ontology Server.}, booktitle = {MEDINFO 2013 - Proceedings of the 14th World Congress on Medical Informatics}, journal = {Stud Health Technol Inform}, year = {2013}, volume = {192}, pages = {961} }
007 AFF Kiefer-Meyer, MC; Ovide, C; Tair, W; Bérard, C; Vergne, N; Lecroq, T; Lerouge, P; Tournier, I; Dauchel, H & Bardor, M. Towards a better understanding of Phaeodactylum tricornutum's morphogenesis. 1st Plant Genomics Congress, London, UK, 2013.
BibTeX: @inproceedings{Kiefer-Meyer2013, author = {Kiefer-Meyer, MC and Ovide, C and Tair, W and Bérard, C and Vergne, N and Lecroq, T and Lerouge, P and Tournier, I and Dauchel, H and Bardor, M}, title = {Towards a better understanding of Phaeodactylum tricornutum's morphogenesis}, booktitle = {1st Plant Genomics Congress}, address = {London, UK}, year = {2013} }
007 AFF Merabti, A; Soualmia, LF & Darmoni, SJ. Mise en correspondance de terminologies et ontologies biomédicales pour un accès facilité aux connaissances. 13e Conférence Francophone sur l'Extraction et la Gestion des Connaissances (EGC'13), 2013. Accepté.
BibTeX: @inproceedings{Merabti2013, author = {Merabti, A and Soualmia, LF and Darmoni, SJ}, title = {Mise en correspondance de terminologies et ontologies biomédicales pour un accès facilité aux connaissances}, booktitle = {13e Conférence Francophone sur l'Extraction et la Gestion des Connaissances (EGC'13)}, year = {2013}, note = {Accepté} }
007 AFF Soualmia, Lina F.; Letord, Catherine; Merabti, Tayeb; Griffon, Nicolas; Manel, Jacques & Darmoni, Stéfan J.. Translating MeSH Concepts.. Stud Health Technol Inform MEDINFO 2013 - Proceedings of the 14th World Congress on Medical Informatics, Volume 192, Pages 1007, 2013.
Abstract: The concept-oriented structure of the MeSH® thesaurus is not yet in common use. Nevertheless, it has been shown that a concept-based querying of PubMed may be of interest. To take full advantage of the concept-oriented structure of MeSH in the information retrieval tool associated with the CISMeF catalogue, it was necessary to translate such concepts into French.
BibTeX: @inproceedings{Soualmia2013a, author = {Soualmia, Lina F. and Letord, Catherine and Merabti, Tayeb and Griffon, Nicolas and Manel, Jacques and Darmoni, Stéfan J.}, title = {Translating MeSH Concepts.}, booktitle = {MEDINFO 2013 - Proceedings of the 14th World Congress on Medical Informatics}, journal = {Stud Health Technol Inform}, year = {2013}, volume = {192}, pages = {1007} }
009 DO Combinatorial Algorithms: 24th International Workshop, IWOCA 2013, Rouen, France, July 10-12, 2013, Revised Selected Papers. , Lecture Notes in Computer Science, Number 8288, Springer-Verlag, 2013.
BibTeX: @book{Lecroq2013a,, title = {Combinatorial Algorithms: 24th International Workshop, IWOCA 2013, Rouen, France, July 10-12, 2013, Revised Selected Papers}, publisher = {Springer-Verlag}, year = {2013}, series = {Lecture Notes in Computer Science}, number = {8288} }
010 AP Joong Chae Na; Heejin Park; Maxime Crochemore; Jan Holub; Costas S. Iliopoulos; Laurent Mouchard & Kunsoo Park. Suffix Tree of Alignment: An Efficient Index for Similar Data. CoRR , Volume abs/1305.1744, 2013.
BibTeX: @article{Na2013, author = {Joong Chae Na and Heejin Park and Maxime Crochemore and Jan Holub and Costas S. Iliopoulos and Laurent Mouchard and Kunsoo Park}, title = {Suffix Tree of Alignment: An Efficient Index for Similar Data}, journal = {CoRR}, year = {2013}, volume = {abs/1305.1744} }
011 TH H. Bouhamed. L'apprentissage automatique : de la sélection de variables à l'apprentissage de structure d'un classifieur bayésien. School: University of Rouen, France and University of Sfax, Tunisia, 2013.
BibTeX: @phdthesis{bouhamed2013, author = {H. Bouhamed}, title = {L'apprentissage automatique : de la sélection de variables à l'apprentissage de structure d'un classifieur bayésien}, school = {University of Rouen, France and University of Sfax, Tunisia}, year = {2013} }
011 TH N. Griffon. Modélisation, création et évaluation de flux de terminologies et de terminologies d'interface : application à la production d'examens complémentaires de biologie et d'imagerie médicale. School: University of Rouen, France, 2013.
BibTeX: @phdthesis{griffon2013, author = {N. Griffon}, title = {Modélisation, création et évaluation de flux de terminologies et de terminologies d'interface : application à la production d'examens complémentaires de biologie et d'imagerie médicale}, school = {University of Rouen, France}, year = {2013} }
2012 001 ACL-int Bouhamed, H; Lecroq, T & Rebai, A. New Filter method for categorical variables' selection. International Journal of Computer Science Issues , Volume 9, Number 3 (2), Pages 10-19, 2012.
BibTeX: @article{Bouhamed2012b, author = {Bouhamed, H and Lecroq, T and Rebai, A}, title = {New Filter method for categorical variables' selection}, journal = {International Journal of Computer Science Issues}, year = {2012}, volume = {9}, number = {3 (2)}, pages = {10-19}, url = {http://www.ijcsi.org/papers/IJCSI-9-3-2-10-19.pdf} }
001 ACL-int Coutant, S; Cabot, C; Lefebvre, A; Léonard, M; Prieur-Gaston, E; Campion, D; Lecroq, T & Dauchel, H. EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics. BMC Bioinformatics , Volume 13, Number Suppl 14, Pages S9, 2012.
BibTeX: @article{Coutant2012a, author = {Coutant, S and Cabot, C and Lefebvre, A and Léonard, M and Prieur-Gaston, E and Campion, D and Lecroq, T and Dauchel, H}, title = {EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics}, journal = {BMC Bioinformatics}, year = {2012}, volume = {13}, number = {Suppl 14}, pages = {S9}, url = {http://www.biomedcentral.com/1471-2105/13/S14/S9}, doi = {10.1186/1471-2105-13-S14-S9} }
001 ACL-int Darmoni, SJ; Soualmia, LF; Letord, C; Griffon, N; Jaulent, MC; Thirion, B & Névéol, A. Improving information retrieval using MeSH Concepts: a test case on rare and chronic diseases. J Med Libr Assoc , Volume 100, Number 3, Pages 176-83, 2012.
BibTeX: @article{Darmoni2012a, author = {Darmoni, SJ and Soualmia, LF and Letord, C and Griffon, N and Jaulent, MC and Thirion, B and Névéol, A}, title = {Improving information retrieval using MeSH Concepts: a test case on rare and chronic diseases}, journal = {J Med Libr Assoc}, year = {2012}, volume = {100}, number = {3}, pages = {176-83}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411256/pdf/mlab-100-03-176.pdf}, doi = {10.3163/1536-5050.100.3.007} }
001 ACL-int Gehanno, JF; Rollin, L; Ladner, J & Darmoni, SJ. How is Occupational Medicine represented in the major journals in general medicine?. Occupational and Environmental Medicine , June, Volume 69, Number 8, Pages 603-5, 2012.
BibTeX: @article{Gehanno2012, author = {Gehanno, JF and Rollin, L and Ladner, J and Darmoni, SJ}, title = {How is Occupational Medicine represented in the major journals in general medicine?}, month = {June}, journal = {Occupational and Environmental Medicine}, year = {2012}, volume = {69}, number = {8}, pages = {603-5}, doi = {10.1136/oemed-2011-100044} }
001 ACL-int Gehanno, Jean-François & Rollin, Laetitia. Influenza vaccination coverage among health professionals before and after the A(H1N1) influenza pandemic in France. Infection control and hospital epidemiology: the official journal of the Society of Hospital Epidemiologists of America , July, Volume 33, Number 7, Pages 757-758, 2012. {PMID:} 22669240.
BibTeX: @article{Gehanno2012a, author = {Gehanno, Jean-François and Rollin, Laetitia}, title = {Influenza vaccination coverage among health professionals before and after the {A(H1N1)} influenza pandemic in France}, month = {July}, journal = {Infection control and hospital epidemiology: the official journal of the Society of Hospital Epidemiologists of America}, year = {2012}, volume = {33}, number = {7}, pages = {757--758}, note = {{PMID:} 22669240}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22669240}, doi = {10.1086/666338} }
001 ACL-int Goullé, Jean-Pierre; Saussereau, Elodie; Mahieu, Loïc; Cellier, Dominique; Spiroux, Joël & Guerbet, Michel. Importance of anthropogenic metals in hospital and urban wastewater: its significance for the environment.. Bull Environ Contam Toxicol , Dec, Volume 89, Number 6, Pages 1220-1224, 2012.
Abstract: Thirty-four metals were analyzed by ICP-MS. Among these elements, anthropogenic silver, gadolinium and platinum, were representative markers of medical activities in hospital and urban wastewater. On working days, median hospital wastewater concentrations for anthropogenic silver, gadolinium, and platinum were approximately three, 13 and 27 times higher respectively than the Municipal wastewater. A drastic reduction of their emission was observed during non-working days (minus 94 % for gadolinium and 87 % for platinum). A large percentage of these metals are not trapped in the Treatment Plant, i.e. 88 % for gadolinium and 69 % for platinum. More than 4 kg and 350 g for gadolinium and platinum are respectively discharged per year in the River Seine. Therefore, it is imperative to eliminate these elements in the Plant.
BibTeX: @article{Goulle2012, author = {Goullé, Jean-Pierre and Saussereau, Elodie and Mahieu, Loïc and Cellier, Dominique and Spiroux, Joël and Guerbet, Michel}, title = {Importance of anthropogenic metals in hospital and urban wastewater: its significance for the environment.}, month = {Dec}, journal = {Bull Environ Contam Toxicol}, year = {2012}, volume = {89}, number = {6}, pages = {1220--1224}, url = {http://dx.doi.org/10.1007/s00128-012-0829-y}, doi = {10.1007/s00128-012-0829-y} }
001 ACL-int Griffon, N; Chebil, W; Rollin, L; Kerdelhue, G; Thirion, B; Gehanno, JF & Darmoni, SJ. Performance evaluation of Unified Medical Language System®'s synonyms expansion to query PubMed. BMC Medical Informatics and Decision Making , Feb, Volume 12, Number 1, Pages 12, 2012.
Abstract: BACKGROUND: PubMed is the main access to medical literature on the Internet. In order to enhance the performance of its information retrieval tools, primarily non-indexed citations, the authors propose a method: expanding users' queries using Unified Medical Language System's (UMLS) synonyms i.e. all the terms gathered under one unique Concept Unique Identifier. METHODS: This method was evaluated using queries constructed to emphasize the differences between this new method and the current PubMed automatic term mapping. Four experts assessed citation relevance. RESULTS: Using UMLS, we were able to retrieve new citations in 45.5% of queries, which implies a small increase in recall. The new strategy led to a heterogeneous 23.7% mean increase in non-indexed citation retrieved. Of these, 82% have been published less than 4 months earlier. The overall mean precision was 48.4% but differed according to the evaluators, ranging from 36.7% to 88.1% (Inter rater agreement was poor: kappa = 0.34). CONCLUSIONS: This study highlights the need for specific search tools for each type of user and use-cases. The proposed strategy may be useful to retrieve recent scientific advancement.
BibTeX: @article{Griffon2012, author = {Griffon, N and Chebil, W and Rollin, L and Kerdelhue, G and Thirion, B and Gehanno, JF and Darmoni, SJ}, title = {Performance evaluation of Unified Medical Language System®'s synonyms expansion to query PubMed}, month = {Feb}, journal = {BMC Medical Informatics and Decision Making}, year = {2012}, volume = {12}, number = {1}, pages = {12}, doi = {10.1186/1472-6947-12-12} }
001 ACL-int Jung, M; Hoerbst, A; Hackl, W O; Kirrane, F; Borbolla, D; Jaspers, M W M; Oertle, M; Koutkias, V; Ferret, L; Massari, P; Lawton, K; Riedmann, D; Darmoni, S; Maglaveras, N; Lovis, C & Ammenwerth, E. Attitude of Physicians Towards Automatic Alerting in Computerized Physician Order Entry Systems. A Comparative International Survey. Methods of information in medicine , November, Volume 52, Number 1, 2012.
Abstract: Objectives: To analyze the attitude of physicians towards alertin g in CPOE systems in different hospitals in different countries, addressing various organizational and technical settings and the view of physicians not currently using a CPOE.Methods: A cross-sectional quantitative and qualitative questionnaire survey. We invited 2,600 physicians in eleven hospitals from nine countries to participate. Eight of the hospitals had different CPOE systems in use, and three of the participating hospitals were not using a CPOE system.Results: 1,018 physicians participated. The general attitude of the physicians towards CPOE alerting is positive and is found to be mostly independent of the country, the specific organizational settings in the hospitals and their personal experience with CPOE systems. Both quantitative and qualitative results show that the majority of the physicians, both CPOE-users and non-users, appreciate the benefits of alerting in CPOE systems on medication safety. However, alerting should be better adapted to the clinical context and make use of more sophisticated ways to present alert information. The vast majority of physicians agree that additional information regarding interactions is useful on demand. Around half of the respondents see possible alert overload as a major problem; in this regard, physicians in hospitals with sophisticated alerting strategies show partly better attitude scores.Conclusions: Our results indicate that the way alerting information is presented to the physicians may play a role in their general attitude towards alerting, and that hospitals with a sophisticated alerting strategy with less interruptive alerts tend towards more positive attitudes. This aspect needs to be further investigated in future studies.
BibTeX: @article{jung_attitude_2012, author = {Jung, M and Hoerbst, A and Hackl, W O and Kirrane, F and Borbolla, D and Jaspers, M W M and Oertle, M and Koutkias, V and Ferret, L and Massari, P and Lawton, K and Riedmann, D and Darmoni, S and Maglaveras, N and Lovis, C and Ammenwerth, E}, title = {Attitude of Physicians Towards Automatic Alerting in Computerized Physician Order Entry Systems. A Comparative International Survey}, month = {November}, journal = {Methods of information in medicine}, year = {2012}, volume = {52}, number = {1}, doi = {10.3414/ME12-02-0007} }
001 ACL-int Lecroq, T; Pauchet, A; Chanoni, E & Ayala Solano, G. Pattern discovery in annotated dialogues using dynamic programming. International Journal of Intelligent Information and Database Systems , October, Volume 6, Number 6, Pages 603-618, 2012.
BibTeX: @article{Lecroq2012, author = {Lecroq, T and Pauchet, A and Chanoni, E and Ayala Solano, G}, title = {Pattern discovery in annotated dialogues using dynamic programming}, month = {October}, journal = {International Journal of Intelligent Information and Database Systems}, year = {2012}, volume = {6}, number = {6}, pages = {603-618}, doi = {10.1504/IJIIDS.2012.050097} }
001 ACL-int Léonard, M.; Mouchard, L. & Salson, M.. On the number of elements to reorder when updating a suffix array. Journal of Discrete Algorithms , Volume 11, Pages 87-99, 2012.
Abstract: textlessptextgreatertextlessbr/textgreaterRecently new algorithms appeared for updating the Burrows-Wheeler Transform or the suffix array, when the text they index is modified. These algorithms proceed by reordering entries and the number of such reordered entries may be as high as the length of the text. However, in practice, these algorithms are faster for updating the Burrows-Wheeler Transform or the suffix array than the fastest reconstruction algorithms.textlessbr/textgreaterIn this article we focus on the number of elements to be reordered for real-life texts. We show that this number is related to LCP values and that, on average, Lave entries are reordered, where Lave denotes the average LCP value, defined as the average length of the longest common prefix between two consecutive sorted suffixes. Since we know little about the LCP distribution for real-life texts, we conduct experiments on a corpus that consists of DNA sequences and natural language texts. The results show that apart from texts containing large repetitions, the average LCP value is close to the one expected on a random text.textless/ptextgreater
BibTeX: @article{Leonard2012, author = {Léonard, M. and Mouchard, L. and Salson, M.}, title = {On the number of elements to reorder when updating a suffix array}, journal = {Journal of Discrete Algorithms}, year = {2012}, volume = {11}, pages = {87-99}, url = {http://www.sciencedirect.com/science/article/pii/S1570866711000037}, doi = {10.1016/j.jda.2011.01.002} }
001 ACL-int Rollin, L. & Gehanno, J.-F.. Research on return to work in European Union countries. Occupational Medicine , January, Volume 62, Number 3, Pages 210-5, 2012.
Abstract: Background Research on return to work (RTW) is increasing. It is important to benefit from studies originating from different countries since certain factors influencing the RTW process are specific to each country.Aims To compare RTW research in Europe with the USA and to describe research on RTW in Europe.Methods Medline was scanned with specific search strings to identify studies concerning RTW in Europe, in the USA and in the rest of the world. Characteristics of the European studies were analyzed with two specific tools for bibliometrics research.Results Four thousand five hundred and twenty-five studies were identified (1100, 1005 and 2420 coming from Europe, the USA and the rest of the world, respectively). The European countries producing the greatest number of research papers standardized for population of that country were Sweden, the Netherlands, Finland and Denmark. Sweden was 5.7 times more prolific than the USA. Specialties covered by the European publications included occupational medicine (the subject of 66% of the articles), neurology (36, environment and public health (32, physical medicine and rehabilitation (26 and rheumatology (24.Conclusions There is a worldwide trend upwards in the number of publications on RTW. Europe recently overtook the USA in the number of publications per head of population, although there were large differences in publication rates among the European countries. The publications of European researchers on RTW are spread over a wide variety of journals, making access to this research difficult.
BibTeX: @article{Rollin2012, author = {Rollin, L. and Gehanno, {J.-F.}}, title = {Research on return to work in European Union countries}, month = {January}, journal = {Occupational Medicine}, year = {2012}, volume = {62}, number = {3}, pages = {210-5}, url = {http://occmed.oxfordjournals.org/content/early/2012/01/12/occmed.kqr207.abstract}, doi = {10.1093/occmed/kqr207} }
001 ACL-int Soualmia, LF; Prieur-Gaston, E; Moalla, Z; Lecroq, T & Darmoni, SJ. Matching health information seekers' queries to medical terms.. BMC Bioinformatics , Volume 13, Number Suppl 14, Pages S11, 2012.
BibTeX: @article{Soualmia2012, author = {Soualmia, LF and Prieur-Gaston, E and Moalla, Z and Lecroq, T and Darmoni, SJ}, title = {Matching health information seekers' queries to medical terms.}, journal = {BMC Bioinformatics}, year = {2012}, volume = {13}, number = {Suppl 14}, pages = {S11}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439674/}, doi = {10.1186/1471-2105-13-S14-S11} }
002 ACL-nat Chebil, W; Soualmia, LF; Dahamna, B & Darmoni, SJ. Indexation automatique de documents en santé : évaluation et analyse de sources d'erreurs. IRBM, Ingénierie et Recherche Biomédicale / IRBM BioMedical Engineering and Research , Volume 33, Number 5-6, Pages 316-329, 2012.
BibTeX: @article{Chebil2012, author = {Chebil, W and Soualmia, LF and Dahamna, B and Darmoni, SJ}, title = {Indexation automatique de documents en santé : évaluation et analyse de sources d'erreurs}, journal = {IRBM, Ingénierie et Recherche Biomédicale / IRBM BioMedical Engineering and Research}, year = {2012}, volume = {33}, number = {5-6}, pages = {316-329}, doi = {10.1016/j.irbm.2012.10.002} }
002 ACL-nat Griffon, N et Devos, P et Gehanno, JF et Darmoni, SJ. Existe-t-il une corrélation entre le score SIGAPS et les publications en français ?. La Presse Médicale , 2012.
BibTeX: @article{Griffon2012a, author = {Griffon, N et Devos, P et Gehanno, JF et Darmoni, SJ}, title = {Existe-t-il une corrélation entre le score SIGAPS et les publications en français ?}, journal = {La Presse Médicale}, year = {2012}, doi = {10.1016/j.lpm.2012.03.015} }
002 ACL-nat Lamy, J.-B.; Beuscart-Zéphir, M.-C.; Boog, C.; Darmoni, S.; Favre, M.; Guigue, L.; Hamek, S.; Hassler, S.; Kerdelhué, G.; Leroy, N.; Mitouard, T.; Pereira, S.; Simon, C.; Venot, A. & Duclos, C.. Langage iconique et interfaces interactives en médecine : application aux dossiers patients, guides de bonnes pratiques et moteurs de recherche médicaux. IRBM , April, Volume 33, Number 2, Pages 129-136, 2012.
Abstract: Face au patient, le médecin n'a que très peu de temps disponible pour consulter les informations médicales présentes dans le dossier patient, les guides de bonnes pratiques ou les moteurs de recherche médicaux. Une solution à ce problème consiste à proposer des outils graphiques visuels permettant au médecin d'accéder très rapidement à l'information, comme le langage iconique Visualisation des connaissances médicales (VCM) que nous avons proposé, il y a quelques années, pour représenter à l'aide d'icônes les principaux concepts médicaux : maladies, risques, antécédents, traitements, examens... afin de faciliter la lecture des monographies des médicaments. L'objectif du travail actuel est d'étendre le langage VCM et de proposer de nouvelles applications afin de résoudre les problèmes d'accès à l'information rencontrés par les médecins. Pour cela, nous avons d'abord analysé les difficultés que les médecins généralistes et hospitaliers rencontre dans cette tà¢che, puis nous en avons déduits les applications possibles et les complémentations nécessaires à apporter à VCM. Nous avons ensuite réalisé des prototypes de ces applications, qui sont en cours d'évaluation.
BibTeX: @article{Lamy, author = {Lamy, {J.-B.} and {Beuscart-Zéphir}, {M.-C.} and Boog, C. and Darmoni, S. and Favre, M. and Guigue, L. and Hamek, S. and Hassler, S. and Kerdelhué, G. and Leroy, N. and Mitouard, T. and Pereira, S. and Simon, C. and Venot, A. and Duclos, C.}, title = {Langage iconique et interfaces interactives en médecine : application aux dossiers patients, guides de bonnes pratiques et moteurs de recherche médicaux}, month = {April}, journal = {{IRBM}}, year = {2012}, volume = {33}, number = {2}, pages = {129-136}, url = {http://www.sciencedirect.com/science/article/pii/S1959031812000176}, doi = {10.1016/j.irbm.2012.01.016} }
002 ACL-nat Proux, D.; Hagège, C.; Gicquel, Q.; Kergourlay, I.; Pereira, S.; Rondeau, G.; Darmoni, S.; Segond, F. & Metzger, M.-H.. ALADIN : développement d'un outil sémantique d'analyse des documents textuels médicaux pour la détection d'infections associées aux soins. IRBM , April, Volume 33, Number 2, Pages 137-142, 2012.
Abstract: Cet article résume le travail de mise au point d'un outil d'analyse du contenu textuel de dossiers hospitaliers afin d'y détecter des indices permettant de suspecter des cas d'infections associées aux soins. Des mécanismes de traitement de l'anonymat, de la terminologie, des entités nommées, de la temporalité ont été mis au point, ainsi qu'une caractérisation opérationnelle des scénarios à risques. Les résultats obtenus et les suites envisagées sont décrits dans cet article.
BibTeX: @article{Proux, author = {Proux, D. and Hagège, C. and Gicquel, Q. and Kergourlay, I. and Pereira, S. and Rondeau, G. and Darmoni, S. and Segond, F. and Metzger, {M.-H.}}, title = {{ALADIN} : développement d'un outil sémantique d'analyse des documents textuels médicaux pour la détection d'infections associées aux soins}, month = {April}, journal = {{IRBM}}, year = {2012}, volume = {33}, number = {2}, pages = {137-142}, url = {http://www.sciencedirect.com/science/article/pii/S195903181200019X}, doi = {10.1016/j.irbm.2012.01.018} }
003 INV Gehanno, J.-F.. Information sur les dangers et les risques. 32eme congres National de Médecine et Santé au Travail, Clermont-Ferrand, June, 2012.
BibTeX: @inproceedings{Gehanno2012b, author = {Gehanno, J.-F.}, title = {Information sur les dangers et les risques}, booktitle = {32eme congres National de Médecine et Santé au Travail}, address = {Clermont-Ferrand}, month = {June}, year = {2012} }
003 INV Gehanno, J.-F.. Grossesse et travail. Salon de Gynécologie Obstétrique Pratique, Paris, March, 2012.
BibTeX: @inproceedings{Gehanno2012c, author = {Gehanno, J.-F.}, title = {Grossesse et travail}, booktitle = {Salon de Gynécologie Obstétrique Pratique}, address = {Paris}, month = {March}, year = {2012} }
004 ACTI Bouhamed, H; Masmoudi, A; Lecroq, T & Rebai, A. A new approach for Bayesian classifier learning structure via K2 Algorithm. Proceedings of the 8th International Conference on Intelligent Computing (ICIC2012), Huangshan, China, July, Communications in Computer and Information Science, Number 304, Pages 387-393, Springer-Verlag, 2012.
BibTeX: @inproceedings{Bouhamed2012a, author = {Bouhamed, H and Masmoudi, A and Lecroq, T and Rebai, A}, title = {A new approach for Bayesian classifier learning structure via K2 Algorithm}, booktitle = {Proceedings of the 8th International Conference on Intelligent Computing (ICIC2012)}, address = {Huangshan, China}, month = {July}, publisher = {Springer-Verlag}, year = {2012}, series = {Communications in Computer and Information Science}, number = {304}, pages = {387--393}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/icic2012.pdf}, doi = {10.1007/978-3-642-31837-5_56} }
004 ACTI Bouhamed, H; Masmoudi, A; Rebai, A & Lecroq, T. A New learning structure heuristic of Bayesian networks from data. International Conference on Machine Learning and Data Mining (MLDM), Berlin, Germany, lncs, Number 7376, Pages 183-197, Springer-Verlag, 2012.
BibTeX: @inproceedings{Bouhamed2012, author = {Bouhamed, H and Masmoudi, A and Rebai, A and Lecroq, T}, title = {A New learning structure heuristic of Bayesian networks from data}, booktitle = {International Conference on Machine Learning and Data Mining (MLDM)}, address = {Berlin, Germany}, publisher = {Springer-Verlag}, year = {2012}, series = {lncs}, number = {7376}, pages = {183--197}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/mldm2012.pdf}, doi = {10.1007/978-3-642-31537-4_15} }
004 ACTI Braeckman, L; Valcke, M; van Dik, F; Gehanno, JF; Pauncu, EA; Popescu, F; Hanna, M & Bulat, P. EMUTOM : A European Module on Undergraduate Teaching in Occupational Medicine. 30th International Congress on Occupational Health, March, Icoh, 2012.
BibTeX: @inproceedings{Braeckman2012, author = {Braeckman, L and Valcke, M and van Dik, F and Gehanno, JF and Pauncu, EA and Popescu, F and Hanna, M and Bulat, P}, title = {{EMUTOM} : A European Module on Undergraduate Teaching in Occupational Medicine}, booktitle = {30th International Congress on Occupational Health}, month = {March}, publisher = {Icoh}, year = {2012}, url = {http://icoh.confex.com/icoh/2012/webprogram/Paper8046.html} }
004 ACTI Darmoni, SJ; Grosjean, J; Merabti, T; Griffon, N; Dahamna, B & Dutoit, D. Combining WordNet and Crosslingual multi-terminology health portal to access health information. 6th International Global Wordnet Conference (GWC2012), Matsue, Japan, January, Pages 94-99, 2012.
BibTeX: @inproceedings{Darmoni2012, author = {Darmoni, SJ and Grosjean, J and Merabti, T and Griffon, N and Dahamna, B and Dutoit, D}, title = {Combining WordNet and Crosslingual multi-terminology health portal to access health information}, booktitle = {6th International Global Wordnet Conference (GWC2012)}, address = {Matsue, Japan}, month = {January}, year = {2012}, pages = {94-99}, url = {http://lang.cs.tut.ac.jp/gwc2012/index.html} }
004 ACTI J.-P. Duval; T. Lecroq & A. Lefebvre. Linear Computation of Unbordered Conjugate. Mons Days of Theoretical Computer Science (JM 2012), Louvain, Belgium, 2012.
BibTeX: @inproceedings{Duval2012, author = {J.-P. Duval and T. Lecroq and A. Lefebvre}, title = {Linear Computation of Unbordered Conjugate}, booktitle = {Mons Days of Theoretical Computer Science (JM 2012)}, address = {Louvain, Belgium}, year = {2012}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/jm2012.pdf} }
004 ACTI Faro, S & Lecroq, T. A Multiple Sliding Windows Approach to Speed Up String Matching Algorithms. 11th International Symposium on Experimental Algorithms (SEA 2012), Bordeaux, France, lncs, Number 7276, Pages 172-183, Springer-Verlag, 2012.
BibTeX: @inproceedings{Faro2012, author = {Faro, S and Lecroq, T}, title = {A Multiple Sliding Windows Approach to Speed Up String Matching Algorithms}, booktitle = {11th International Symposium on Experimental Algorithms (SEA 2012)}, address = {Bordeaux, France}, publisher = {Springer-Verlag}, year = {2012}, series = {lncs}, number = {7276}, pages = {172--183}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/sea2012.pdf}, doi = {10.1007/978-3-642-30850-5_16} }
004 ACTI Faro, S & Lecroq, T. A Fast Suffix Automata Based Algorithm for Exact Online String Matching. 17th International Conference on Implementation and Application of Automata (CIAA), Porto, Portugal, Lecture Notes in Computer Science, Volume 7381, Pages 149-158, 2012.
BibTeX: @inproceedings{Faro2012a, author = {Faro, S and Lecroq, T}, title = {A Fast Suffix Automata Based Algorithm for Exact Online String Matching}, booktitle = {17th International Conference on Implementation and Application of Automata (CIAA)}, address = {Porto, Portugal}, year = {2012}, series = {Lecture Notes in Computer Science}, volume = {7381}, pages = {149-158}, doi = {10.1007/978-3-642-31606-7_13} }
004 ACTI Faro, S & Lecroq, T. Fast Searching in Biological Sequences Using Multiple Hash Functions. IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012), Larnaca, Cyprus, 2012.
BibTeX: @inproceedings{Faro2012b, author = {Faro, S and Lecroq, T}, title = {Fast Searching in Biological Sequences Using Multiple Hash Functions}, booktitle = {IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012)}, address = {Larnaca, Cyprus}, year = {2012} }
004 ACTI G. Fici; T. Lecroq; A. Lefebvre; É. Prieur-Gaston & W. F. Smyth. Quasi-Linear Time Computation of the Smallest Abelian Period of a Word. Prague Stringology Conference 2012 (PSC 2012), Prague, Tcheque Republic, 2012.
BibTeX: @inproceedings{Fici2012a, author = {G. Fici and T. Lecroq and A. Lefebvre and \'E. Prieur-Gaston and W. F. Smyth}, title = {Quasi-Linear Time Computation of the Smallest Abelian Period of a Word}, booktitle = {Prague Stringology Conference 2012 (PSC 2012)}, address = {Prague, Tcheque Republic}, year = {2012} }
004 ACTI Griffon, N & Darmoni, SJ. A cross lingual semantic search engine dedicated to medical teaching resources. MEI - Medical Education Informatics, Thessaloniki, Greece, April, 2012.
Abstract: Background: The Catalogue of French-speaking health resources available on the Internet (French acronym: CISMeF) is a portal that gathers French medical Web resources (n 90,000). Doc'UMVF is a semantic search engine that allows searching in this database but filtering only medical teaching materials (n=9,697). Currently, Doc'UMVF is based on multi-terminology indexing, consequently, it works with the French (n 500,000) and English terms (n 1,000,000) of the 32 terminologies included in information system (IS). Using terminologies translated in other language than only French and English would allow cross lingual indexing and information retrieval of teaching material. Objective: To make Doc'UMVF working in several languages. Method: Some terminologies integrated in CISMeF IS have been translated in numerous languages (e.g. International classification of disease, tenth revision, is available in 11 languages, Medical Subject Heading in 16 languages, etc). An enhanced version of the IS was necessary to manage multiple translations and Doc'UMVF has to be adapted to this new IS. Results: HeTOP is a portal that allows cross lingual access to multiple terminologies. A semantic search engine based on such tool could be useful in at least two use-cases. First, for resources that exist in numerous languages, like European Medical Agency (EMA) resources, there is only need for one indexing in one language to allow their retrieval in many European languages. Second, this provides a language independent tool: any teacher, whatever his speaking language was, may index his own teaching material in his own language and any student, whatever his speaking language was, may find it. Conclusions: Doc'UMVF will soon work in the new IS. Nevertheless, its natural language processing tools work only in French, therefore its use should be reserved to advanced user (those who know terminologies). There is not too much development to achieve an operational language independent search engine dedicated to teaching material.
BibTeX: @inproceedings{Griffon2012d, author = {Griffon, N and Darmoni, SJ}, title = {A cross lingual semantic search engine dedicated to medical teaching resources}, booktitle = {MEI - Medical Education Informatics}, address = {Thessaloniki, Greece}, month = {April}, year = {2012}, url = {http://www.mei2012.org/content/cross-lingual-semantic-search-engine-dedicated-medical-teaching-resources} }
004 ACTI Griffon, N; Savoye-Collet, C; Massari, P; Daniel, C & Darmoni, SJ. An interface terminology for medical imaging ordering purposes. AMIA Annual Symposium proceedings, Chicago, November, Pages 1237-1243, 2012.
BibTeX: @inproceedings{Griffon2012b, author = {Griffon, N and Savoye-Collet, C and Massari, P and Daniel, C and Darmoni, SJ}, title = {An interface terminology for medical imaging ordering purposes}, booktitle = {AMIA Annual Symposium proceedings}, address = {Chicago}, month = {November}, year = {2012}, pages = {1237--1243}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540496/} }
004 ACTI Grosjean, J; Merabti, T; Griffon, N; Dahamna, B & Darmoni, SJ. Teaching medicine with a terminology/ontology portal. Stud Health Technol Inform MIE, Pisa, Italy, August, Volume 180, Pages 949-53, 2012.
Abstract: 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 (URL: http://hetop.eu/) and provides free access to ICD10 and FMA in ten languages. Conclusion: HeTOP is a rich tool, useful for a wide range of applications and users, especially in education and resource indexing but also in information retrieval or performing audits in terminology management.
BibTeX: @inproceedings{Grosjean2012a, author = {Grosjean, J and Merabti, T and Griffon, N and Dahamna, B and Darmoni, SJ}, title = {Teaching medicine with a terminology/ontology portal}, booktitle = {MIE}, address = {Pisa, Italy}, month = {August}, journal = {Stud Health Technol Inform}, year = {2012}, volume = {180}, pages = {949-53}, doi = {10.3233/978-1-61499-101-4-949} }
004 ACTI Pottier, C; Hannequin, D; Coutant, S; Rovelet-Lecrux, A; Wallon, D; Rousseau, S; Legallic, C; Paquet, C; Bombois, S; Pariente, J; Thomas-Anterion, C; Michon, A; Croisile, B; Etcharry-Bouyx, F; Berr, C; Dartigues, J; Amouyel, P; Dauchel, H; Boutoleau-Bretonnière, C; Thauvin, C; Frebourg, T; Lambert, J & Campion, D. High frequency of potentially pathogenic SORL1 mutations in autosomal dominant early-onset Alzheimer disease. European Human Genetics Conference, Nürnberg, Germany, Volume 17, Number 9, Pages 875-9, 2012.
BibTeX: @inproceedings{Pottier2012a, author = {Pottier, C and Hannequin, D and Coutant, S and Rovelet-Lecrux, A and Wallon, D and Rousseau, S and Legallic, C and Paquet, C and Bombois, S and Pariente, J and Thomas-Anterion, C and Michon, A and Croisile, B and Etcharry-Bouyx, F and Berr, C and Dartigues, J and Amouyel, P and Dauchel, H and Boutoleau-Bretonnière, C and Thauvin, C and Frebourg, T and Lambert, J and Campion, D}, title = {High frequency of potentially pathogenic SORL1 mutations in autosomal dominant early-onset Alzheimer disease}, booktitle = {European Human Genetics Conference}, address = {Nürnberg, Germany}, year = {2012}, volume = {17}, number = {9}, pages = {875-9}, doi = {10.1038/mp.2012.15} }
004 ACTI Thiessard, F; Mougin, F; Diallo, G; Jouhet, V; Cossin, S; Garcelon, N; Campillo, B; Jouini, W; Grosjean, J; Massari, P; Griffon, N; Dupuch, M; Tayalati, F; Dugas, E; Balvet, A; Grabar, N; Pereira, S; Frandji, B; Darmoni, SJ & Cuggia, M. RAVEL: Retrieval And Visualization in ELectronic health records.. Stud Health Technol Inform Quality of Life through Quality of Information - Proceedings of MIE2012, Volume 180, Pages 194-198, 2012.
Abstract: Because of the ever-increasing amount of information in patients' EHRs, healthcare professionals may face difficulties for making diagnoses and/or therapeutic decisions. Moreover, patients may misunderstand their health status. These medical practitioners need effective tools to locate in real time relevant elements within the patients' EHR and visualize them according to synthetic and intuitive presentation models. The RAVEL project aims at achieving this goal by performing a high profile industrial research and development program on the EHR considering the following areas: (i) semantic indexing, (ii) information retrieval, and (iii) data visualization. The RAVEL project is expected to implement a generic, loosely coupled to data sources prototype so that it can be transposed into different university hospitals information systems.
BibTeX: @inproceedings{Thiessard2012, author = {Thiessard, F and Mougin, F and Diallo, G and Jouhet, V and Cossin, S and Garcelon, N and Campillo, B and Jouini, W and Grosjean, J and Massari, P and Griffon, N and Dupuch, M and Tayalati, F and Dugas, E and Balvet, A and Grabar, N and Pereira, S and Frandji, B and Darmoni, SJ and Cuggia, M}, title = {RAVEL: Retrieval And Visualization in ELectronic health records.}, booktitle = {Quality of Life through Quality of Information - Proceedings of MIE2012}, journal = {Stud Health Technol Inform}, year = {2012}, volume = {180}, pages = {194--198}, doi = {10.3233/978-1-61499-101-4-194} }
005 ACTN Bouhaddou, O; Darmoni, SJ & Thonnet, M. Expérience avec le réseau national d'échange d'information médicale aux USA.. Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM)., Tunis, Septembre, Informatique et Santé, Pages 287-296, Springer, 2012.
BibTeX: @inproceedings{Bouhaddou2011, author = {Bouhaddou, O and Darmoni, SJ and Thonnet, M}, title = {Expérience avec le réseau national d'échange d'information médicale aux USA.}, booktitle = {Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM).}, address = {Tunis}, month = {Septembre}, publisher = {Springer}, year = {2012}, series = {Informatique et Santé}, pages = {287-296}, url = {http://www.springerlink.com/content/r6318566m2w01705/}, doi = {10.1007/978-2-8178-0285-5_25} }
005 ACTN Dirieh Dibad, AD; Soualmia, LF; Merabti, T; Grosjean, J; Sakji, S; Massari, P & Darmoni, SJ. Un modèle de données adapté à la recherche d'information dans le dossier patient informatisé : étude, conception et évaluation.. Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM)., Tunis, Septembre, Informatique et Santé, Pages 251-262, Springer, 2012.
BibTeX: @inproceedings{Dirieh2011, author = {Dirieh Dibad, AD and Soualmia, LF and Merabti, T and Grosjean, J and Sakji, S and Massari, P and Darmoni, SJ}, title = {Un modèle de données adapté à la recherche d'information dans le dossier patient informatisé : étude, conception et évaluation.}, booktitle = {Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM).}, address = {Tunis}, month = {Septembre}, publisher = {Springer}, year = {2012}, series = {Informatique et Santé}, pages = {251-262}, url = {http://www.springerlink.com/content/rx6402278w6m7863/}, doi = {10.1007/978-2-8178-0285-5_22} }
005 ACTN Griffon, N; Massari, P; Joubert, M; Staccini, P & Darmoni, SJ. Pertinence médicale des cooccurrences diagnostic-acte dans les résumés standardisés de sortie. PCSI (Patient Classification Systems International), Avignon, France, October, 2012.
BibTeX: @inproceedings{Griffon2012c, author = {Griffon, N and Massari, P and Joubert, M and Staccini, P and Darmoni, SJ}, title = {Pertinence médicale des cooccurrences diagnostic-acte dans les résumés standardisés de sortie}, booktitle = {PCSI (Patient Classification Systems International)}, address = {Avignon, France}, month = {October}, year = {2012} }
005 ACTN Joubert, M; Vandenbussche, PY; Dahamna, B; Abdoune, H; Merabti, T; Pereira, S; Boyer, C; Staccini, P; Forget, JF; Delahousse, J; Darmoni, SJ & Fieschi, M. InterSTIS : interopérabilité sémantique de terminologies de santé francophones.. Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM)., Tunis, Septembre, Informatique et Santé, Pages 73-83, 2012.
BibTeX: @inproceedings{Joubert2011a, author = {Joubert, M and Vandenbussche, PY and Dahamna, B and Abdoune, H and Merabti, T and Pereira, S and Boyer, C and Staccini, P and Forget, JF and Delahousse, J and Darmoni, SJ and Fieschi, M}, title = {InterSTIS : interopérabilité sémantique de terminologies de santé francophones.}, booktitle = {Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM).}, address = {Tunis}, month = {Septembre}, year = {2012}, series = {Informatique et Santé}, pages = {73-83}, url = {www.springerlink.com/content/r7h673g11160384g/}, doi = {10.1007/978-2-8178-0285-5_7} }
005 ACTN Merabti, T; Soualmia, LF; Grosjean, J; Joubert, M & Darmoni, SJ. Méthodes d'alignement de terminologies médicales et leur intégration dans un portail. IC'2012 : Atelier IC pour l'intéropérabilité sémantique dans les applications en e-Santé, Paris, France, 2012.
BibTeX: @inproceedings{Merabti2012b, author = {Merabti, T and Soualmia, LF and Grosjean, J and Joubert, M and Darmoni, SJ}, title = {Méthodes d'alignement de terminologies médicales et leur intégration dans un portail}, booktitle = {IC'2012 : Atelier IC pour l'intéropérabilité sémantique dans les applications en e-Santé}, address = {Paris, France}, year = {2012}, url = {https://sites.google.com/site/icisante2012/programme} }
005 ACTN Metzger, MH; Gicquel, Q; Kergourlay, I; Cluze, C; Grandbastien, B; Berrouane, Y; Tavolacci, MP; Segond, F; Pereira, S & Darmoni, SJ. Codage standardisé de données médicales textuelles à l'aide d'un serveur multi-terminologique de santé : exemple d'application en épidémiologie hospitalière.. Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM)., Tunis, Septembre, Informatique et Santé, Pages 109-120, 2012.
BibTeX: @inproceedings{Metzger2011, author = {Metzger, MH and Gicquel, Q and Kergourlay, I and Cluze, C and Grandbastien, B and Berrouane, Y and Tavolacci, MP and Segond, F and Pereira, S and Darmoni, SJ}, title = {Codage standardisé de données médicales textuelles à l'aide d'un serveur multi-terminologique de santé : exemple d'application en épidémiologie hospitalière.}, booktitle = {Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM).}, address = {Tunis}, month = {Septembre}, year = {2012}, series = {Informatique et Santé}, pages = {109-120}, doi = {10.1007/978-2-8178-0285-5_10} }
005 ACTN Moalla, Z; Soualmia, LF; Prieur-Gaston, E & Darmoni, SJ. Correction orthographique de requêtes : l'apport des distances de Levenshtein et Stoilos.. Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM)., Tunis, Septembre, Informatique et Santé, Pages 3-12, Springer, 2012.
BibTeX: @inproceedings{Moalla2011, author = {Moalla, Z and Soualmia, LF and Prieur-Gaston, E and Darmoni, SJ}, title = {Correction orthographique de requêtes : l'apport des distances de Levenshtein et Stoilos.}, booktitle = {Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM).}, address = {Tunis}, month = {Septembre}, publisher = {Springer}, year = {2012}, series = {Informatique et Santé}, pages = {3-12}, url = {http://link.springer.com/chapter/10.1007%2F978-2-8178-0285-5_1}, doi = {10.1007/978-2-8178-0285-5_1} }
005 ACTN Pereira, S; Letord, C; Darmoni, SJ & Serrot, E. Extraction des noms de médicaments dans les comptes rendus hospitaliers.. Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM)., Tunis, Septembre, Informatique et Santé, Pages 145-153, Springer, 2012.
BibTeX: @inproceedings{Pereira2011, author = {Pereira, S and Letord, C and Darmoni, SJ and Serrot, E}, title = {Extraction des noms de médicaments dans les comptes rendus hospitaliers.}, booktitle = {Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM).}, address = {Tunis}, month = {Septembre}, publisher = {Springer}, year = {2012}, series = {Informatique et Santé}, pages = {145-153}, doi = {10.1007/978-2-8178-0285-5_13} }
005 ACTN Sakji, S; Elkin, P & Darmoni, SJ. Évaluation de l'indexation des comptes rendus médicaux à l'aide d'un outil états-unien adapté pour le français.. Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM)., Tunis, Septembre, Informatique et Santé, Pages 155-163, Springer, 2012.
BibTeX: @inproceedings{Sakji2011, author = {Sakji, S and Elkin, P and Darmoni, SJ}, title = {Évaluation de l'indexation des comptes rendus médicaux à l'aide d'un outil états-unien adapté pour le français.}, booktitle = {Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM).}, address = {Tunis}, month = {Septembre}, publisher = {Springer}, year = {2012}, series = {Informatique et Santé}, pages = {155-163}, doi = {10.1007/978-2-8178-0285-5_14} }
006 COM Barton, C; Iliopoulos, C; Mouchard, L; Pissis SP; Lecroq, T & Giraud, M. Querying Highly Similar Sequences. International Conference on Intelligent Biology and Medicine (ICIBM 2012), Nashville, TN, USA, 2012.
BibTeX: @inproceedings{Barton2012a, author = {Barton, C and Iliopoulos, C and Mouchard, L and Pissis SP and Lecroq, T and Giraud, M}, title = {Querying Highly Similar Sequences}, booktitle = {International Conference on Intelligent Biology and Medicine (ICIBM 2012)}, address = {Nashville, TN, USA}, year = {2012} }
006 COM Coutant, S. Exome Variations Analyzer. journées du Canceropôle Nord-Ouest, Rouen, France, 2012.
BibTeX: @inproceedings{Coutant2012b, author = {Coutant, S}, title = {Exome Variations Analyzer}, booktitle = {journées du Canceropôle Nord-Ouest}, address = {Rouen, France}, year = {2012} }
006 COM Duval, JP; Lecroq, T & Lefebvre, A. Linear computation of unbordered conjugate. SeqBio12 -Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, Marne-la-Vallée, France, 2012.
BibTeX: @inproceedings{Duval2012a, author = {Duval, JP and Lecroq, T and Lefebvre, A}, title = {Linear computation of unbordered conjugate}, booktitle = {SeqBio12 -Workshop Algorithmique, combinatoire du texte et applications en bio-informatique}, address = {Marne-la-Vallée, France}, year = {2012} }
006 COM Faro, S & Lecroq, T. Three new strategies for exact string matching slides. SeqBio12 -Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, Marne-la-Vallée, France, 2012.
BibTeX: @inproceedings{Faro2012d, author = {Faro, S and Lecroq, T}, title = {Three new strategies for exact string matching slides}, booktitle = {SeqBio12 -Workshop Algorithmique, combinatoire du texte et applications en bio-informatique}, address = {Marne-la-Vallée, France}, year = {2012} }
006 COM Fici, G; Lecroq, T; Lefebvre, A; Prieur-Gaston, E & Smyth, W. F.. Quasi-linear time computation of abelian periods of a word slides. SeqBio12 -Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, Marne-la-Vallée, France, 2012.
BibTeX: @inproceedings{Fici2012c, author = {Fici, G and Lecroq, T and Lefebvre, A and Prieur-Gaston, E and Smyth, W. F.}, title = {Quasi-linear time computation of abelian periods of a word slides}, booktitle = {SeqBio12 -Workshop Algorithmique, combinatoire du texte et applications en bio-informatique}, address = {Marne-la-Vallée, France}, year = {2012} }
006 COM Grosjean, J; Kerdelhué, G; Merabti, T & Darmoni, SJ. The EHTOP: indexing Health resources in a multi-terminology/ontology and cross-lingual world. EAHIL 2012, 2012.
Abstract: The European Health Terminology/ Ontology Portal (EHTOP) is a repository dedicated to European health professionals and students. Currently, it provides access to terminologies and ontologies available in French or in English, but also in German, Italian, Dutch, Spanish, Danish and other 17 languages. EHTOP can be used by humans and by computers via Web services. The main objective of EHTOP is to provide an access to terminologies and ontologies, allowing dynamic browsing and navigation. Methods: To integrate terminologies and ontologies into EHTOP, three steps are necessary: (1) designing a meta-model into which each terminology and ontology can be integrated, (2) developing a process to include terminologies into EHTOP, (3) building and integrating existing and new inter & intra-terminology semantic harmonization into EHTOP. Results: EHTOP is available freely for the ICD-10 and the FMA (URL: http://www.ehtop.eu/). The access to other terminologies/ontologies (MeSH, SNOMED CT, WHO-ATC, ...) is restricted and available only for the scientific community. A total of 32 terminologies are included into EHTOP, with 980,000 concepts, 2,300,000 synonyms, 222,800 definitions and 4,000,000 relations. Since January 2010, the bilingual version of EHTOP is daily used by CISMeF librarians to index health resources in the CISMeF catalogue in a multi-terminology mode. Currently, 600 unique machines are using this bilingual version, whereas 300 users are already registered. Conclusion: EHTOP is a rich tool, useful for a wide range of applications and users for educational purpose, resources indexing, information retrieval or performing audits in terminology management.
BibTeX: @inproceedings{Grosjean2012, author = {Grosjean, J and Kerdelhué, G and Merabti, T and Darmoni, SJ}, title = {The EHTOP: indexing Health resources in a multi-terminology/ontology and cross-lingual world}, booktitle = {EAHIL 2012}, year = {2012} }
007 AFF Coutant, S; Cabot, C; Tair, W; Lefebvre, A; Léonard, M; Prieur-Gaston, E; Campion, D; Lecroq, T & Dauchel, H. EVA: Exome Variation Analyzer, A tool for filtering strategies in medical genomics. 13e édition du colloque JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), 2012. Accepté.
BibTeX: @inproceedings{Coutant2012, author = {Coutant, S and Cabot, C and Tair, W and Lefebvre, A and Léonard, M and Prieur-Gaston, E and Campion, D and Lecroq, T and Dauchel, H}, title = {EVA: Exome Variation Analyzer, A tool for filtering strategies in medical genomics}, booktitle = {13e édition du colloque JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques)}, year = {2012}, note = {Accepté}, url = {http://jobim2012.inria.fr/jobim_actes_2012_online.pdf} }
007 AFF Diallo, G; Grabar, N; Thiessard, F; Garcelon, N; Grosjean, J; Dupuch, M; Pereira, S; Frandji, B; Darmoni, SJ & Cuggia, M. Towards complex queries on data from complex patients. AMIA, Chicago, Illinois, November, 2012.
BibTeX: @inproceedings{Diallo2012, author = {Diallo, G and Grabar, N and Thiessard, F and Garcelon, N and Grosjean, J and Dupuch, M and Pereira, S and Frandji, B and Darmoni, SJ and Cuggia, M}, title = {Towards complex queries on data from complex patients}, booktitle = {AMIA}, address = {Chicago, Illinois}, month = {November}, year = {2012} }
007 AFF Gehanno, JF; Bulat, P; Smits, P; Dijk, E; Pauncu, E; Popescu, F; Jarreta, BM; Hanna, M; Chaudry, A & Braeckman, L. Undergraduate occupational medicine teaching in european schools of medicine. 30th International Congress on Occupational Health, Cancun, Mexico, 2012.
BibTeX: @inproceedings{Gehanno2012e, author = {Gehanno, JF and Bulat, P and Smits, P and Dijk, E and Pauncu, E and Popescu, F and Jarreta, BM and Hanna, M and Chaudry, A and Braeckman, L}, title = {Undergraduate occupational medicine teaching in european schools of medicine}, booktitle = {30th International Congress on Occupational Health}, address = {Cancun, Mexico}, year = {2012} }
007 AFF Grosjean, J; Merabti, T; Griffon, N; Dahamna, B; Soualmia, LF & Darmoni, SJ. Multi-terminology cross-lingual model to create the Health Terminology/Ontology Portal. AMIA, Chicago, 2012.
BibTeX: @inproceedings{Grosjean2012b, author = {Grosjean, J and Merabti, T and Griffon, N and Dahamna, B and Soualmia, LF and Darmoni, SJ}, title = {Multi-terminology cross-lingual model to create the Health Terminology/Ontology Portal}, booktitle = {AMIA}, address = {Chicago}, year = {2012} }
007 AFF Grosjean, J; Soualmia, LF; Merabti, T; Griffon, N; Dahamna, B & Darmoni, SJ. Cross-lingual access to biomedical terminologies and ontologies. SWAT4LS (Semantic Web Applications and Tools for Life Sciences) Workshop, November, 2012. Poster.
BibTeX: @inproceedings{Grosjean2012c, author = {Grosjean, J and Soualmia, LF and Merabti, T and Griffon, N and Dahamna, B and Darmoni, SJ}, title = {Cross-lingual access to biomedical terminologies and ontologies}, booktitle = {SWAT4LS (Semantic Web Applications and Tools for Life Sciences) Workshop}, month = {November}, year = {2012}, note = {Poster}, url = {http://ceur-ws.org/Vol-952/paper_17.pdf} }
007 AFF Merabti, A; Soualmia, LF & Darmoni, SJ. Extracting correspondences between terminologies for an easier access to biomedical information. Nettab2012, Como, Italy, November, Pages 127-129, 2012.
BibTeX: @inproceedings{Merabti2012a, author = {Merabti, A and Soualmia, LF and Darmoni, SJ}, title = {Extracting correspondences between terminologies for an easier access to biomedical information}, booktitle = {Nettab2012}, address = {Como, Italy}, month = {November}, year = {2012}, pages = {127-129}, url = {http://journal.embnet.org/index.php/embnetjournal/article/view/576} }
007 AFF Philipe, N; Salson, M; Lecroq, T; Léonard, M; Commes, T & Rivals, E. Read indexing. EMBnet.journal Bioinformatics in Action COST Action BM1006 Scientific Meeting 2011, Volume 17, Number Supplement B, Pages 45, 2012.
Abstract: The question of read indexing remains broadly unexplored. However, the increase in sequence throughput urges for new algorithmic solutions to query large read collections efficiently. We propose a solution, named Gk arrays, to index large collections of reads, an algorithm to build the structure, and procedures to query it. Once constructed, the index structure is kept in main memory and is repeatedly accessed to answer various types of queries. We compare our data structure to other possible solutions to investigate its scalability and computational efficiency. Gk arrays are implemented in a general purpose library, which may prove useful for assembly purposes, for evaluating the expression level in RNA-seq, and others high throughput sequencing applications.
BibTeX: @inproceedings{Philipe2011, author = {Philipe, N and Salson, M and Lecroq, T and Léonard, M and Commes, T and Rivals, E}, title = {Read indexing}, booktitle = {COST Action BM1006 Scientific Meeting 2011}, journal = {EMBnet.journal Bioinformatics in Action}, year = {2012}, volume = {17}, number = {Supplement B}, pages = {45}, url = {http://journal.embnet.org/index.php/embnetjournal/article/view/289} }
007 AFF Rousselin, A; Legros, A; Baumann, JJ; Sponem, B; Lecroq, T; Dauchel, H; Tournier, I; Coutant, S; Letac, O; Krieger, S; Hardouin, A; Castera, L; Frebourg, T & Vaur, D. Détection des remaniements génomiques par séquençage haut débit dans les cas de prédispositions aux cancers du sein et de l'ovaire. Journées de la Cancéropôle Nord-Ouest, Mai, 2012. Poster.
BibTeX: @inproceedings{Rousselin2012, author = {Rousselin, A and Legros, A and Baumann, JJ and Sponem, B and Lecroq, T and Dauchel, H and Tournier, I and Coutant, S and Letac, O and Krieger, S and Hardouin, A and Castera, L and Frebourg, T and Vaur, D}, title = {Détection des remaniements génomiques par séquençage haut débit dans les cas de prédispositions aux cancers du sein et de l'ovaire}, booktitle = {Journées de la Cancéropôle Nord-Ouest}, month = {Mai}, year = {2012}, note = {Poster} }
007 AFF Smits, P; Braeckman, L; Dijk, E; Gehanno, JF; Pauncu, E; Popescu, F; Hanna, M & Bulat, P. What every doctor should know about work and health : a needs analysis in six european countries. 30th International Congress on Occupational Health, Cancun, Mexico, 2012.
BibTeX: @inproceedings{Smits2012, author = {Smits, P and Braeckman, L and Dijk, E and Gehanno, JF and Pauncu, E and Popescu, F and Hanna, M and Bulat, P}, title = {What every doctor should know about work and health : a needs analysis in six european countries}, booktitle = {30th International Congress on Occupational Health}, address = {Cancun, Mexico}, year = {2012} }
008 OS Duclos, C; Burgun, A; Lamy, JB; Landais, P; Rodrigues, JM; Soualmia, L & Zweigenbaum, P. Le vocabulaire médical, les ressources terminologiques, le codage de l'information en santé in : Informatique Médicale, e-Santé - Fondements et applications. , Springer, 2012.
BibTeX: @inbook{Duclos2013, author = {Duclos, C and Burgun, A and Lamy, JB and Landais, P and Rodrigues, JM and Soualmia, L and Zweigenbaum, P}, title = {Informatique Médicale, e-Santé - Fondements et applications}, publisher = {Springer}, year = {2012}, url = {http://www.springer.com/public+health/book/978-2-8178-0337-1} }
008 OS Merabti, T; Soualmia, LF; Grosjean, J; Joubert, M & Darmoni, SJ. Aligning Biomedical Terminologies in French: Towards Semantic Interoperability in Medical Applications. Medical Informatics, March, Pages 41-68, InTech, 2012.
BibTeX: @incollection{Merabti2012, author = {Merabti, T and Soualmia, {LF} and Grosjean, J and Joubert, M and Darmoni, {SJ}}, title = {Aligning Biomedical Terminologies in French: Towards Semantic Interoperability in Medical Applications}, booktitle = {Medical Informatics}, month = {March}, publisher = {{InTech}}, year = {2012}, pages = {41--68}, url = {http://www.intechopen.com/books/indexing/medical-informatics/methods-to-map-biomedical-terminologies-in-french-contribution-to-semantic-interoperability-between-} }
008 OS Soualmia, LF; Dahamna, B & Darmoni, SJ. Supporting e-Health Information Seekers : from Simple Strategies to Knowledge-based Methods in : eHealth and Remote Monitoring. , Pages 35-62, 2012.
BibTeX: @inbook{Soualmia2012a, author = {Soualmia, LF and Dahamna, B and Darmoni, SJ}, title = {eHealth and Remote Monitoring}, year = {2012}, pages = {35-62}, url = {http://www.intechopen.com/books/ehealth-and-remote-monitoring/supporting-e-health-information-seekers-from-simple-strategies-to-knowledge-based-methods}, doi = {10.5772/50348} }
008 OS Venot, A; Charlet, J; Darmoni, SJ; Duclos, C; Dufour, JC & Soualmia, LF. La gestion et la diffusion des connaissances en santé in : Informatique Médicale, e-Santé - Fondements et applications. , Springer, 2012.
BibTeX: @inbook{Venot2012, author = {Venot, A and Charlet, J and Darmoni, SJ and Duclos, C and Dufour, JC and Soualmia, LF}, title = {Informatique Médicale, e-Santé - Fondements et applications}, publisher = {Springer}, year = {2012}, url = {http://www.springer.com/public+health/book/978-2-8178-0337-1} }
009 DO Mouchard, L & Puglisi, S. Selected papers from the 2011 meeting of LSD/LAW. Journal of Discrete Algorithms , Volume 17, Pages 1-144, 2012.
BibTeX: @article{Mouchard2012, author = {Mouchard, L and Puglisi, S}, title = {Selected papers from the 2011 meeting of LSD/LAW}, journal = {Journal of Discrete Algorithms}, year = {2012}, volume = {17}, pages = {1-144} }
010 AP Faro, S & Lecroq, T. Twenty years of bit-parallelism in string matching. Festschrift for Bov rivoj Melichar, Pages 72-101, 2012.
BibTeX: @inproceedings{Faro2012c, author = {Faro, S and Lecroq, T}, title = {Twenty years of bit-parallelism in string matching}, booktitle = {Festschrift for Bo{\v r}ivoj Melichar}, year = {2012}, pages = {72--101} }
010 AP Fici, G; Langiu, A; Lefebvre, A & Prieur-Gaston, E. Algorithms for computing abelian periods of words. CoRR, abs/1211.5389 , 2012.
BibTeX: @article{Fici2012b, author = {Fici, G and Langiu, A and Lefebvre, A and Prieur-Gaston, E}, title = {Algorithms for computing abelian periods of words}, journal = {CoRR, abs/1211.5389}, year = {2012} }
010 AP Rivals, E; Philippe, N; Salson, M; Léonard, M; Commes, T & Lecroq, T. A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections. ERCIM News , Number 89, Pages 20-21, 2012.
BibTeX: @article{Rivals2012, author = {Rivals, E and Philippe, N and Salson, M and Léonard, M and Commes, T and Lecroq, T}, title = {A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections}, journal = {ERCIM News}, year = {2012}, number = {89}, pages = {20-21}, url = {http://ercim-news.ercim.eu/images/stories/EN89/EN89-web.pdf} }
011 TH Dirieh Dibad, AD. Recherche d'information multi-terminologique - Application au Dossier patient Informatisé. School: University of Rouen, France and University of Djibouti, 2012.
BibTeX: @phdthesis{DiriehDibad2012, author = {Dirieh Dibad, AD}, title = {Recherche d'information multi-terminologique - Application au Dossier patient Informatisé}, school = {University of Rouen, France and University of Djibouti}, year = {2012} }
011 TH Falah, T. E.. Algorithmes de Recherche de Motifs dans un ensemble de Chaînes Codant des Macromolécules Biologiques : cas des motifs simples. School: University Of Rouen, France and university of Tunis El Manar, Tunisie, 2012.
BibTeX: @phdthesis{Falah2012, author = {Falah, T. E.}, title = {Algorithmes de Recherche de Motifs dans un ensemble de Chaînes Codant des Macromolécules Biologiques : cas des motifs simples}, school = {University Of Rouen, France and university of Tunis El Manar, Tunisie}, year = {2012} }
2011 001 ACL-int Gehanno, JF; Ladner, J; Rollin, L; Dahamna, B & Darmoni, SJ. How are the different specialties represented in the major journals in general medicine?. BMC Medical Informatics and Decision Making , Volume 11, Number 1, Pages 3, 2011.
Abstract: BACKGROUND:General practitioners and medical specialists mainly rely on one "general medical" journal to keep their medical knowledge up to date. Nevertheless, it is not known if these journals display the same overview of the medical knowledge in different specialties. The aims of this study were to measure the relative weight of the different specialties in the major journals of general medicine, to evaluate the trends in these weights over a ten-year period and to compare the journals.METHODS:The 14,091 articles published in The Lancet, the NEJM, the JAMA and the BMJ in 1997, 2002 and 2007 were analyzed. The relative weight of the medical specialities was determined by categorization of all the articles, using a categorization algorithm which inferred the medical specialties relevant to each article MEDLINE file from the MeSH terms used by the indexers of the US National Library of Medicine to describe each article.RESULTS:The 14,091 articles included in our study were indexed by 22,155 major MeSH terms, which were categorized into 81 different medical specialties. Cardiology and Neurology were in the first 3 specialties in the 4 journals. Five and 15 specialties were systematically ranked in the first 10 and first 20 in the four journals respectively. Among the first 30 specialties, 23 were common to the four journals. For each speciality, the trends over a 10-year period were different from one journal to another, with no consistency and no obvious explanatory factor.CONCLUSIONS:Overall, the representation of many specialties in the four journals in general and internal medicine included in this study may differ, probably due to different editorial policies. Reading only one of these journals may provide a reliable but only partial overview.
BibTeX: @article{Gehanno2011, author = {Gehanno, JF and Ladner, J and Rollin, L and Dahamna, B and Darmoni, SJ}, title = {How are the different specialties represented in the major journals in general medicine?}, journal = {BMC Medical Informatics and Decision Making}, year = {2011}, volume = {11}, number = {1}, pages = {3}, doi = {10.1186/1472-6947-11-3} }
001 ACL-int Gerbier, Solweig; Yarovaya, Olga; Gicquel, Quentin; Millet, Anne-Laure; Smaldore, Veronique; Pagliaroli, Veronique; Darmoni, Stefan & Metzger, Marie-Helene. Evaluation of natural language processing from emergency department computerized medical records for intra-hospital syndromic surveillance. BMC Medical Informatics and Decision Making , Volume 11, Number 1, Pages 50, 2011.
Abstract: BACKGROUND:The identification of patients who pose an epidemic hazard when they are admitted to a health facility plays a role in preventing the risk of hospital acquired infection. An automated clinical decision support system to detect suspected cases, based on the principle of syndromic surveillance, is being developed at the University of Lyon's Hopital de la Croix-Rousse. This tool will analyse structured data and narrative reports from computerized emergency department (ED) medical records. The first step consists of developing an application (UrgIndex) which automatically extracts and encodes information found in narrative reports. The purpose of the present article is to describe and evaluate this natural language processing system.METHODS:Narrative reports have to be pre-processed before utilizing the French-language medical multi-terminology indexer (ECMT) for standardized encoding. UrgIndex identifies and excludes syntagmas containing a negation and replaces non-standard terms (abbreviations, acronyms, spelling errors...). Then, the phrases are sent to the ECMT through an Internet connection. The indexer's reply, based on Extensible Markup Language, returns codes and literals corresponding to the concepts found in phrases. UrgIndex filters codes corresponding to suspected infections. Recall is defined as the number of relevant processed medical concepts divided by the number of concepts evaluated (coded manually by the medical epidemiologist). Precision is defined as the number of relevant processed concepts divided by the number of concepts proposed by UrgIndex. Recall and precision were assessed for respiratory and cutaneous syndromes.RESULTS:Evaluation of 1,674 processed medical concepts contained in 100 ED medical records (50 for respiratory syndromes and 50 for cutaneous syndromes) showed an overall recall of 85.8% (95% CI: 84.1-87.3). Recall varied from 84.5% for respiratory syndromes to 87.0% for cutaneous syndromes. The most frequent cause of lack of processing was non-recognition of the term by UrgIndex (9.7. Overall precision was 79.1% (95% CI: 77.3-80.8). It varied from 81.4% for respiratory syndromes to 77.0% for cutaneous syndromes.CONCLUSIONS:This study demonstrates the feasibility of and interest in developing an automated method for extracting and encoding medical concepts from ED narrative reports, the first step required for the detection of potentially infectious patients at epidemic risk.
BibTeX: @article{gerbier_evaluation_2011, author = {Gerbier, Solweig and Yarovaya, Olga and Gicquel, Quentin and Millet, {Anne-Laure} and Smaldore, Veronique and Pagliaroli, Veronique and Darmoni, Stefan and Metzger, {Marie-Helene}}, title = {Evaluation of natural language processing from emergency department computerized medical records for intra-hospital syndromic surveillance}, journal = {{BMC} Medical Informatics and Decision Making}, year = {2011}, volume = {11}, number = {1}, pages = {50}, url = {http://www.biomedcentral.com/1472-6947/11/50}, doi = {10.1186/1472-6947-11-50} }
001 ACL-int Lefebvre, F; Merle, V; Savoye, G; Lemée, V; Chapuzet, C; Marini, H; Géhanno, J-F; Chefson-Girault, C; Gueit, I; Freymuth, F; Lerebours, E & Czernichow, P. Nosocomial transmission of measles: do we need extra precautions to avoid it?. The Journal of hospital infection , October, Volume 79, Number 2, Pages 185-187, 2011.
BibTeX: @article{Lefebvre2011, author = {Lefebvre, F and Merle, V and Savoye, G and Lemée, V and Chapuzet, C and Marini, H and Géhanno, J-F and Chefson-Girault, C and Gueit, I and Freymuth, F and Lerebours, E and Czernichow, P}, title = {Nosocomial transmission of measles: do we need extra precautions to avoid it?}, month = {October}, journal = {The Journal of hospital infection}, year = {2011}, volume = {79}, number = {2}, pages = {185--187}, doi = {10.1016/j.jhin.2011.05.025} }
001 ACL-int Merabti, Tayeb; Soualmia, Lina; Grosjean, Julien; Palombi, Olivier; Muller, Jean-Michel & Darmoni, SJ. Translating the Foundational Model of Anatomy into French using knowledge-based and lexical methods. BMC Medical Informatics and Decision Making , Volume 11, Number 1, Pages 65, 2011.
Abstract: BACKGROUND:The Foundational Model of Anatomy (FMA) is the reference ontology regarding human anatomy. FMA vocabulary was integrated into the Health Multi Terminological Portal (HMTP) developed by CISMeF based on the CISMeF Information System which also includes 26 other terminologies and controlled vocabularies, mainly in French. However, FMA is primarily in English. In this context, the translation of FMA English terms into French could also be useful for searching and indexing French anatomy resources. Various studies have investigated automatic methods to assist the translation of medical terminologies or create multilingual medical vocabularies. The goal of this study was to facilitate the translation of FMA vocabulary into French.METHODS:We compare two types of approaches to translate the FMA terms into French. The rst one is UMLS-based on the conceptual information of the UMLS metathesaurus. The second method is lexically-based on several Natural Language Processing (NLP) tools.RESULTS:The UMLS-based approach produced a translation of 3,661 FMA terms into French whereas the lexical approach produced a translation of 3,129 FMA terms into French. A qualitative evaluation was made on 100 FMA terms translated by each method. For the UMLS-based approach, among the 100 translations, 52% were manually rated as "very good" and only 7% translations as "bad". For the lexical approach, among the 100 translations, 47% were rated as "very good" and 20% translations as "bad".CONCLUSIONS:Overall, a low rate of translations were demonstrated by the two methods. The two approaches permitted us to semi-automatically translate 3,776 FMA terms from English into French, this was to added to the existing 10,844 French FMA terms in the HMTP (4,436 FMA French terms and 6,408 FMA terms manually translated).
BibTeX: @article{Merabti2011b, author = {Merabti, Tayeb and Soualmia, Lina and Grosjean, Julien and Palombi, Olivier and Muller, Jean-Michel and Darmoni, SJ}, title = {Translating the Foundational Model of Anatomy into French using knowledge-based and lexical methods}, journal = {BMC Medical Informatics and Decision Making}, year = {2011}, volume = {11}, number = {1}, pages = {65}, url = {http://www.biomedcentral.com/1472-6947/11/65}, doi = {10.1186/1472-6947-11-65} }
001 ACL-int Philippe, Nicolas; Salson, Mikael; Lecroq, Thierry; Leonard, Martine; Commes, Therese & Rivals, Eric. Querying large read collections in main memory: a versatile data structure. BMC Bioinformatics , Volume 12, Number 1, Pages 242, 2011.
Abstract: BACKGROUND:High Throughput Sequencing (HTS) is now heavily exploited for genome (re-)sequencing, metagenomics, epigenomics, and transcriptomics and requires different, but computer intensive bioinformatic analyses. When a reference genome is available, mapping reads on it is the first step of this analysis. Read mapping programs owe their efficiency to the use of involved genome indexing data structures, like the Burrows-Wheeler transform. Recent solutions index both the genome, and the k-mers of the reads using hash-tables to further increase efficiency and accuracy. In various contexts (e.g. assembly or transcriptome analysis), read processing requires to determine the sub-collection of reads that are related to a given sequence, which is done by searching for some k-mers in the reads. Currently, many developments have focused on genome indexing structures for read mapping, but the question of read indexing remains broadly unexplored. However, the increase in sequence throughput urges for new algorithmic solutions to query large read collections efficiently. RESULTS:Here, we present a solution, named Gk arrays, to index large collections of reads, an algorithm to build the structure, and procedures to query it. Once constructed, the index structure is kept in main memory and is repeatedly accessed to answer queries like "given a k-mer, get the reads containing this k-mer (once/at least once)". We compared our structure to other solutions that adapt uncompressed indexing structures designed for long texts and show that it processes queries fast, while requiring much less memory. Our structure can thus handle larger read collections. We provide examples where such queries are adapted to different types of read analysis (SNP detection, assembly, RNA-Seq). CONCLUSIONS:Gk arrays constitute a versatile data structure that enables fast and more accurate read analysis in various contexts. The Gk arrays provide a flexible brick to design innovative programs that mine efficiently genomics, epigenomics, metagenomics, or transcriptomics reads. The Gk arrays library is available under Cecill (GPL compliant) license from http://www.atgc-montpellier.fr/ngs/.
BibTeX: @article{philippe_querying_2011, author = {Philippe, Nicolas and Salson, Mikael and Lecroq, Thierry and Leonard, Martine and Commes, Therese and Rivals, Eric}, title = {Querying large read collections in main memory: a versatile data structure}, journal = {{BMC} Bioinformatics}, year = {2011}, volume = {12}, number = {1}, pages = {242}, url = {http://www.biomedcentral.com/1471-2105/12/242}, doi = {10.1186/1471-2105-12-242} }
001 ACL-int Séralini, Gilles-Eric; Mesnage, Robin; Clair, Emilie; Gress, Steeve; de Vendômois, Joël & Cellier, Dominique. Genetically modified crops safety assessments: present limits and possible improvements. Environmental Sciences Europe , Volume 23, Number 1, Pages 10, 2011.
BibTeX: @article{seralini_genetically_2011, author = {Séralini, {Gilles-Eric} and Mesnage, Robin and Clair, Emilie and Gress, Steeve and de Vendômois, Joël and Cellier, Dominique}, title = {Genetically modified crops safety assessments: present limits and possible improvements}, journal = {Environmental Sciences Europe}, year = {2011}, volume = {23}, number = {1}, pages = {10}, url = {http://www.enveurope.com/content/23/1/10}, doi = {10.1186/2190-4715-23-10} }
002 ACL-nat Joubert, M & le consortium du projet InterSTIS. Interopérabilité sémantique de terminologies de santé francophones. IRBM , Volume 32, Number 2, Pages 80-82, 2011.
Abstract: Contexte La prolifération des documents liés à la santé des individus pose aujourd'hui le problème de leur indexation et de leur recherche dans de vastes bases de données.Objectif Si l'on veut indexer d'autres types de documents que des documents pédagogiques ou de la documentation scientifique, il faut être capable d'indexer des comptes rendus cliniques, des résultats d'examens, des courriers, etc.Matériel et méthode Des terminologies à visées différentes sont alors utilisées : la SNOMED pour le codage d'informations cliniques, la CIM-10 et la CCAM pour le codage épidémiologique et médico-économique, la CISP utilisée par les médecins généralistes, etc. Le but d'InterSTIS était de les unifier et de les rendre interopérables au sein d'un « serveur terminologique multi-sources ». InterSTIS exploite des sources de connaissance de UMLS issues de la National Library of Medicine des États-Unis pour rendre ces terminologies interopérables.Résultat Un serveur terminologique multi-sources opérationnel apte à délivrer des services à des utilisateurs et à des applications. InterSTIS a commencé en janvier 2008 et s'est fini en décembre 2010.
BibTeX: @article{Joubert2011, author = {Joubert, M and le consortium du projet InterSTIS}, title = {Interopérabilité sémantique de terminologies de santé francophones}, journal = {{IRBM}}, year = {2011}, volume = {32}, number = {2}, pages = {80-82}, url = {http://www.sciencedirect.com/science/article/B94S6-5295K6S-6/2/2a900945a16a740449bd22d6bb379b7a}, doi = {10.1016/j.irbm.2011.01.030} }
003 INV Faro, S & Lecroq, T. 2001-2010: ten years of exact string matching algorithms. Proceedings of the Prague Stringology Conference, Prague, Tchèque, République, Pages 1-2, 2011.
BibTeX: @inproceedings{Faro2011, author = {Faro, S and Lecroq, T}, title = {{2001-2010: ten years of exact string matching algorithms}}, booktitle = {{Proceedings of the Prague Stringology Conference}}, address = {Prague, Tch{\`e}que, R{\'e}publique}, year = {2011}, pages = {1-2} }
003 INV Faro, S & Lecroq, T. 2001-2010 : ten years of exact string matching algorithms. SeqBio 2011 : Algorithmique, combinatoire du texte et applications en bio-informatique, Lille, France, 2011.
BibTeX: @inproceedings{Faro2011a, author = {Faro, S and Lecroq, T}, title = {2001-2010 : ten years of exact string matching algorithms}, booktitle = {SeqBio 2011 : Algorithmique, combinatoire du texte et applications en bio-informatique}, address = {Lille, France}, year = {2011} }
003 INV Gehanno, JF. Des indicateurs pour changer les pratiques ou des pratiques pour changer des indicateurs ?. 31èmes Journées Nationales de santé au travail dans le BTP, Versailles, France, Mai, 2011.
BibTeX: @inproceedings{Gehanno2011c, author = {Gehanno, JF}, title = {Des indicateurs pour changer les pratiques ou des pratiques pour changer des indicateurs ?}, booktitle = {31èmes Journées Nationales de santé au travail dans le BTP}, address = {Versailles, France}, month = {Mai}, year = {2011} }
003 INV Gehanno, JF. Accès à la connaissance par l'utilisation des bases de données via Internet. 26èmes Journées Internationales Méditerranéennes de Médecine du Travail, Rennes, France, Mai, 2011.
BibTeX: @inproceedings{Gehanno2012d, author = {Gehanno, JF}, title = {Accès à la connaissance par l'utilisation des bases de données via Internet}, booktitle = {26èmes Journées Internationales Méditerranéennes de Médecine du Travail}, address = {Rennes, France}, month = {Mai}, year = {2011} }
004 ACTI Abdoune, H; Merabti, T; Darmoni SJ & Joubert, M. Assisting the translation of the CORE Subset of SNOMED CT into French. User Centred Networked Health Care - Proceedings of MIE 2011, Studies in Health Technology and Informatics, Volume 169, Pages 819-823, 2011.
Abstract: Background: the Core Subset of SNOMED CT is part of the UMLS-Core Project dedicated to study problem list vocabularies. SNOMED CT is not yet translated into French. Objective: to propose an automated method to assist the translation of the CORE Subset of SNOMED CT into French. Material: the 2009 AA versions of the CORE Subset of SNOMED CT and UMLS; use of four French-language terminologies integrated into the UMLS Metathesaurus: SNOMED International, ICD10, MedDRA, and MeSH. Method: an exact mapping completed by a close mapping between preferred terms of the CORE Subset of SNOMED CT and those of the four terminologies. Results: 89% of the preferred terms of the CORE Subset of SNOMED CT are mapped with at least one preferred term in one of the four terminologies. Discussion: if needed, synonymous terms could be added by the means of synonyms in the terminologies; the proposed method is independent from French and could be applied to other natural languages.
BibTeX: @inproceedings{Abdoune2011, author = {Abdoune, H and Merabti, T and Darmoni SJ and Joubert, M}, title = {Assisting the translation of the CORE Subset of SNOMED CT into French}, booktitle = {User Centred Networked Health Care - Proceedings of MIE 2011}, year = {2011}, series = {Studies in Health Technology and Informatics}, volume = {169}, pages = {819-823}, doi = {10.3233/978-1-60750-806-9-819} }
004 ACTI Ammenwerth, E; Hackl, WO; Massari, P & Darmoni, SJ. Validation of Completeness, Correctness, Relevance and Understandability of the PSIP CDSS for Medication Safety. Patient Safety Informatics - Adverse Drug Events, Human Factors and IT Tools for Patient Medication Safety, Studies in Health Technology and Informatics, Volume 166, Pages 254-259, 2011. PSIP.
BibTeX: @inproceedings{Ammenwerth2011, author = {Ammenwerth, E and Hackl, WO and Massari, P and Darmoni, SJ}, title = {Validation of Completeness, Correctness, Relevance and Understandability of the PSIP CDSS for Medication Safety}, booktitle = {Patient Safety Informatics - Adverse Drug Events, Human Factors and IT Tools for Patient Medication Safety}, year = {2011}, series = {Studies in Health Technology and Informatics}, volume = {166}, pages = {254-259}, note = {PSIP}, url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=19731}, doi = {10.3233/978-1-60750-740-6-254} }
004 ACTI Bouhamed, H; Lecroq, T; Rebai, A & Jaoua, M. Improving algorithms for knowledge discovery in genetics databases. 2nd International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD 2011), Toulouse, France, 2011.
BibTeX: @inproceedings{Bouhamed2011, author = {Bouhamed, H and Lecroq, T and Rebai, A and Jaoua, M}, title = {Improving algorithms for knowledge discovery in genetics databases}, booktitle = {2nd International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD 2011)}, address = {Toulouse, France}, year = {2011}, doi = {10.1109/DEXA.2011.41} }
004 ACTI Bouhamed, H; Lecroq, T; Rebai, A & Jaoua, M. Data-organization before learning Multi-Entity Bayesian Networks structure. Proceedings of The International Conference on Pattern Recognition and Computer Vision, Amsterdam, Pays-Bas, Volume 78, Pages 305-308, World Academy of Science, Engineering and Technology, 2011.
BibTeX: @inproceedings{Bouhamed2011a, author = {Bouhamed, H and Lecroq, T and Rebai, A and Jaoua, M}, title = {Data-organization before learning Multi-Entity Bayesian Networks structure}, booktitle = {Proceedings of The International Conference on Pattern Recognition and Computer Vision}, address = {Amsterdam, Pays-Bas}, publisher = {World Academy of Science, Engineering and Technology}, year = {2011}, volume = {78}, pages = {305-308}, url = {http://www.waset.org/journals/waset/v54/v54-60.pdf} }
004 ACTI Coutant, S; Lefebvre, A; Léonard, M; Prieur-Gaston, E; Campion, D; Lecroq, T & Dauchel, H. EVA: Exome Variation Analyzer, a convivial tool for filtering strategies. Proccedings of NETTAB'11(Network Tools and Applications in Biology), Pavia, Italy, 2011.
BibTeX: @inproceedings{Coutant2011, author = {Coutant, S and Lefebvre, A and Léonard, M and Prieur-Gaston, E and Campion, D and Lecroq, T and Dauchel, H}, title = {EVA: Exome Variation Analyzer, a convivial tool for filtering strategies}, booktitle = {Proccedings of NETTAB'11(Network Tools and Applications in Biology)}, address = {Pavia, Italy}, year = {2011}, url = {http://f1000.com/posters/browse/summary/1089452} }
004 ACTI El Falah, T; Lecroq, T & Elloumi, M. Experimental Evaluation of Fast Solution Algorithms for the Simple Motif Problem. Proceedings of the First International Conference on Computer Science, Engineering and Information Technology, Tirunelveli, Inde, Communications in Computer and Information Science, Volume 204, Pages 601-610, Springer-Verlag, 2011.
BibTeX: @inproceedings{El2011, author = {El Falah, T and Lecroq, T and Elloumi, M}, title = {Experimental Evaluation of Fast Solution Algorithms for the Simple Motif Problem}, booktitle = {Proceedings of the First International Conference on Computer Science, Engineering and Information Technology}, address = {Tirunelveli, Inde}, publisher = {Springer-Verlag}, year = {2011}, series = {Communications in Computer and Information Science}, volume = {204}, pages = {601-610}, url = {http://hal.archives-ouvertes.fr/hal-00627213} }
004 ACTI El Falah, Tarek; Lecroq, Thierry & Elloumi, Mourad. An Efficient Motif Search Algorithm Based on a Minimal Forbidden Patterns Approach. 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011), Advances in Intelligent and Soft Computing, Volume 93, Pages 175-182, Springer Berlin / Heidelberg, 2011.
BibTeX: @incollection{ElFalah2011, author = {El Falah, Tarek and Lecroq, Thierry and Elloumi, Mourad}, title = {An Efficient Motif Search Algorithm Based on a Minimal Forbidden Patterns Approach}, booktitle = {5th International Conference on Practical Applications of Computational Biology \& Bioinformatics (PACBB 2011)}, publisher = {Springer Berlin / Heidelberg}, year = {2011}, series = {Advances in Intelligent and Soft Computing}, volume = {93}, pages = {175-182}, doi = {10.1007/978-3-642-19914-1_24} }
004 ACTI Fici, G.; Lecroq, T.; Lefebvre, A. & Prieur-Gaston, E.. Computing Abelian periods in words. Proceedings of the Prague Stringology Conference 2011, Prague, Tcheque Republic, Pages 184-196, 2011.
BibTeX: @inproceedings{Fici2011a, author = {{F}ici, {G}. and {L}ecroq, {T}. and {L}efebvre, {A}. and {P}rieur-{G}aston, {E}.}, title = { {C}omputing {A}belian periods in words}, booktitle = {Proceedings of the Prague Stringology Conference 2011}, address = {Prague, Tcheque Republic}, year = {2011}, pages = {184-196} }
004 ACTI Golbreich, C; Grosjean, J & Darmoni SJ. The FMA in OWL 2. AIME, Volume 6747, Pages 204-214, Springer-Verlag, 2011.
BibTeX: @inproceedings{Golbreich2011, author = {Golbreich, C and Grosjean, J and Darmoni SJ}, title = {The FMA in OWL 2}, booktitle = {AIME}, publisher = {Springer-Verlag}, year = {2011}, volume = {6747}, pages = {204-214}, url = {http://www.springer.com/computer/ai/book/978-3-642-22217-7}, doi = {10.1007/978-3-642-22218-4_25} }
004 ACTI Griffon, N; Soualmia LF; Névéol, A; Massari P; Thirion B; Dahamna, B & Darmoni, SJ. Evaluation of Multi-Terminology Super-Concepts for Information Retrieval. User Centred Networked Health Care - Proceedings of MIE 2011, Studies in Health Technology and Informatics, Volume 169, Pages 492-496, 2011.
Abstract: Background: 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®. Objective: To evaluate precision and recall of super-concepts for information retrieval in a multi-terminology paradigm compared to MeSH-only. Methods: We evaluate the relevance of resources retrieved by multi-terminology super-concepts and MeSH-only super-concepts queries. Results: 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). Conclusion: 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.
BibTeX: @inproceedings{Griffon2011, author = {Griffon, N and Soualmia LF and Névéol, A and Massari P and Thirion B and Dahamna, B and Darmoni, SJ}, title = {Evaluation of Multi-Terminology Super-Concepts for Information Retrieval}, booktitle = {User Centred Networked Health Care - Proceedings of MIE 2011}, year = {2011}, series = {Studies in Health Technology and Informatics}, volume = {169}, pages = {492-496}, doi = {10.3233/978-1-60750-806-9-492} }
004 ACTI Grosjean, J; Merabti, T; Dahamna, B; Kergourlay, I; Thirion B; Soualmia LF & Darmoni, SJ. Health Multi-Terminology Portal: a semantics added-value for patient safety. Patient Safety Informatics - Adverse Drug Events, Human Factors and IT Tools for Patient Medication Safety, Studies in Health Technology and Informatics, Volume 166, Pages 129-138, 2011. PSIP.
BibTeX: @inproceedings{Grosjean2011a, author = {Grosjean, J and Merabti, T and Dahamna, B and Kergourlay, I and Thirion B and Soualmia LF and Darmoni, SJ}, title = {Health Multi-Terminology Portal: a semantics added-value for patient safety}, booktitle = {Patient Safety Informatics - Adverse Drug Events, Human Factors and IT Tools for Patient Medication Safety}, year = {2011}, series = {Studies in Health Technology and Informatics}, volume = {166}, pages = {129-138}, note = {PSIP}, url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=19716}, doi = {10.3233/978-1-60750-740-6-129} }
004 ACTI Grosjean, J; Merabti, T; Griffon, N; Dahamna, B & Darmoni SJ. Multiterminology cross-lingual model to create the European Health Terminology/Ontology Portal. Short papers of the 9th International Conference on Terminology and Artificial Intelligence, TIA, Paris, November, Pages 119-122, 2011.
BibTeX: @inproceedings{Grosjean2011b, author = {Grosjean, J and Merabti, T and Griffon, N and Dahamna, B and Darmoni SJ}, title = {Multiterminology cross-lingual model to create the European Health Terminology/Ontology Portal}, booktitle = {Short papers of the 9th International Conference on Terminology and Artificial Intelligence, TIA}, address = {Paris}, month = {November}, year = {2011}, pages = {119-122}, url = {http://tia2011.crim.fr/Proceedings/pdf/TIA20.pdf} }
004 ACTI Hagège, C; Marchal, P; Gicquel, Q; Darmoni, SJ; Pereira, S & Metzger, MH. Linguistic and Temporal Processing for Discovering Hospital Acquired Infection from Patient Records. Knowledge Representation for Health-Care, Lisbon, Portugal, August, Lecture Notes in Computer Science, Volume 6512, Pages 70-84, Springer Berlin / Heidelberg, 2011. The 2nd International Workshop on Knowledge Representation for Health Care (KR4HC-2010) - Workshop ECAI 2010.
Abstract: This paper describes the first steps of development of a rule-based system that automatically processes medical records in order to discover possible cases of hospital acquired infections (HAI). The system takes as input a set of patient records in electronic format and gives as output, for each document, information regarding HAI. In order to achieve this goal, a temporal processing together with a deep syntactic and semantic analysis of the patient records is performed. Medical knowledge used by the rules is derived from a set of documents that have been annotated by medical doctors. After a brief description of the context of this work, we present the general architecture of our document processing chain and explain how we perform our temporal and linguistic analysis. Finally, we report our preliminary results and we lay out the next steps of the project.
BibTeX: @inproceedings{Hagege2010, author = {Hagège, C and Marchal, P and Gicquel, Q and Darmoni, SJ and Pereira, S and Metzger, MH}, title = {Linguistic and Temporal Processing for Discovering Hospital Acquired Infection from Patient Records}, booktitle = {Knowledge Representation for Health-Care}, address = {Lisbon, Portugal}, month = {August}, publisher = {Springer Berlin / Heidelberg}, year = {2011}, series = {Lecture Notes in Computer Science}, volume = {6512}, pages = {70--84}, note = {The 2nd International Workshop on Knowledge Representation for Health Care (KR4HC-2010) - Workshop ECAI 2010}, doi = {10.1007/978-3-642-18050-7_6} }
004 ACTI Soualmia LF; Griffon, N; Grosjean, J & Darmoni SJ. Improving Information Retrieval by Meta-Modelling Medical Terminologies. 13th conference on Artificial Intelligence in MEdicine (AIME), Lectures Notes in ArtificiaI Intelligence, Pages pp. 215-219, Springer, Heidelberg, 2011.
BibTeX: @inproceedings{LF2011, author = {Soualmia LF and Griffon, N and Grosjean, J and Darmoni SJ}, title = {Improving Information Retrieval by Meta-Modelling Medical Terminologies}, booktitle = {13th conference on Artificial Intelligence in MEdicine (AIME)}, publisher = {Springer, Heidelberg}, year = {2011}, series = {Lectures Notes in ArtificiaI Intelligence}, pages = {pp. 215--219}, doi = {10.1007/978-3-642-22218-4_26} }
004 ACTI Merabti, T; Abdoune, H; Letord, C; Sakji, S; Joubert, M & Darmoni SJ. Mapping the ATC classification to the UMLS Metathesaurus: some pragmatic applications. Patient Safety Informatics - Adverse Drug Events, Human Factors and IT Tools for Patient Medication Safety, Studies in Health Technology and Informatics, Volume 166, Pages 206-213, 2011. PSIP.
BibTeX: @inproceedings{Merabti2011a, author = {Merabti, T and Abdoune, H and Letord, C and Sakji, S and Joubert, M and Darmoni SJ}, title = {Mapping the ATC classification to the UMLS Metathesaurus: some pragmatic applications}, booktitle = {Patient Safety Informatics - Adverse Drug Events, Human Factors and IT Tools for Patient Medication Safety}, year = {2011}, series = {Studies in Health Technology and Informatics}, volume = {166}, pages = {206-213}, note = {PSIP}, url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=19725}, doi = {10.3233/978-1-60750-740-6-206} }
004 ACTI Moalla, Z; Soualmia, LF; Prieur-Gaston, E; Lecroq, T & Darmoni, SJ. Spell-checking queries by combining Levenshtein and Stoilos distances. Proccedings of NETTAB'11(Network Tools and Applications in Biology), Pavia, Italy, October, 2011.
BibTeX: @inproceedings{Moalla2011a, author = {Moalla, Z and Soualmia, LF and Prieur-Gaston, E and Lecroq, T and Darmoni, SJ}, title = {Spell-checking queries by combining Levenshtein and Stoilos distances}, booktitle = {Proccedings of NETTAB'11(Network Tools and Applications in Biology)}, address = {Pavia, Italy}, month = {October}, year = {2011}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/nettab2011-dis.pdf} }
004 ACTI Proux, D; Hagège, C; Gicquel, Q; Pereira, S; Darmoni, SJ; Segond, F & Metzger, MH. Architecture and Systems for Monitoring Hospital Acquired Infections inside Hospital Information Workflows. Proceedings of the Workshop on Biomedical Natural Language Processing, Hissar, Bulgaria, Pages 43-48, Association for Computational Linguistics, 2011.
Abstract: This paper describes the latest developments in the design of a tool to monitor Patient Discharge Summaries to detected pieces of evidences related to Hospital Acquired Infections. Anonymization, Named Entity detection, Temporal Expressions analysis and Causality detection methods have been developed and evaluated. They are embedded in a tool designed to work in a Hospital Information Workflow.
BibTeX: @inproceedings{Proux2011, author = {Proux, D and Hagège, C and Gicquel, Q and Pereira, S and Darmoni, SJ and Segond, F and Metzger, MH}, title = {Architecture and Systems for Monitoring Hospital Acquired Infections inside Hospital Information Workflows}, booktitle = {Proceedings of the Workshop on Biomedical Natural Language Processing}, address = {Hissar, Bulgaria}, publisher = {Association for Computational Linguistics}, year = {2011}, pages = {43-48}, url = {http://aclweb.org/anthology/W11-4207} }
005 ACTN Gicquel, Q; Proux, D; Marchal, P; Hagège, C; Berrouane, Y; Darmoni, SJ; Pereira, S; Segond, F & Metzger, MH. Evaluation d'un outil d'aide à l'anonymisation des documents médicaux basé sur le traitement automatique du langage naturel.. Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM)., Tunis, Septembre, Informatique et Santé, Pages 165-176, Springer, 2011.
BibTeX: @inproceedings{Gicquel2011, author = {Gicquel, Q and Proux, D and Marchal, P and Hagège, C and Berrouane, Y and Darmoni, SJ and Pereira, S and Segond, F and Metzger, MH}, title = {Evaluation d'un outil d'aide à l'anonymisation des documents médicaux basé sur le traitement automatique du langage naturel.}, booktitle = {Systèmes d'information pour l'amélioration de la qualité en santé. Comptes rendus des quatorzièmes Journées francophones d'informatique médicale (JFIM).}, address = {Tunis}, month = {Septembre}, publisher = {Springer}, year = {2011}, series = {Informatique et Santé}, pages = {165-176}, url = {http://www.springerlink.com/content/vr3338x017671826/}, doi = {10.1007/978-2-8178-0285-5_15} }
005 ACTN Hagège, C; Proux, D; Gicquel, Q; Darmoni, SJ; Pereira, S; Segond, F & Metzger, MH. Développement d'un système de détection des infections associées aux soins à partir de l'analyse de comptes-rendus d'hospitalisation. Traitement Automatique des Langues Naturelles (TALN), Montpellier, France, Juin-Juillet, 2011.
BibTeX: @inproceedings{Hagege2011a, author = {Hagège, C and Proux, D and Gicquel, Q and Darmoni, SJ and Pereira, S and Segond, F and Metzger, MH}, title = {Développement d'un système de détection des infections associées aux soins à partir de l'analyse de comptes-rendus d'hospitalisation}, booktitle = {Traitement Automatique des Langues Naturelles (TALN)}, address = {Montpellier, France}, month = {Juin-Juillet}, year = {2011}, url = {http://www.lirmm.fr/~lopez/RECITAL/PDF_court/Hagege_taln11_submission_136.pdf} }
005 ACTN Merabti, T; Grosjean, J; Abdoune, H; Joubert, M & Darmoni SJ. Automatic methods for mapping Biomedical terminologies in a Health Multi-Terminology Portal. EGC 2011 : atelier Extraction de Connaissances et Santé, 2011.
BibTeX: @inproceedings{Merabti2011, author = {Merabti, T and Grosjean, J and Abdoune, H and Joubert, M and Darmoni SJ}, title = {Automatic methods for mapping Biomedical terminologies in a Health Multi-Terminology Portal}, booktitle = {EGC 2011 : atelier Extraction de Connaissances et Santé}, year = {2011} }
006 COM Coutant, S. Développement de l'outil bioinformatique EVA (Exome Variation Analyzer) pour l'aide à l'interprétation des données de séquençage haut debit.. Atelier du réseau des laboratoires de diagnostic moléculaire des maladies génétiques neurologiques, musculaires, neurosensorielles et retards mentaux, Cochin, Paris, France, 2011.
BibTeX: @inproceedings{Coutant2011a, author = {Coutant, S}, title = {Développement de l'outil bioinformatique EVA (Exome Variation Analyzer) pour l'aide à l'interprétation des données de séquençage haut debit.}, booktitle = {Atelier du réseau des laboratoires de diagnostic moléculaire des maladies génétiques neurologiques, musculaires, neurosensorielles et retards mentaux}, address = {Cochin, Paris, France}, year = {2011} }
006 COM Coutant, S. Exome Variations Analyzer. Bioinformatics and High Throughput Sequencing, Institut Pasteur, Paris, France, 2011.
BibTeX: @inproceedings{Coutant2011b, author = {Coutant, S}, title = {Exome Variations Analyzer}, booktitle = {Bioinformatics and High Throughput Sequencing}, address = {Institut Pasteur, Paris, France}, year = {2011} }
006 COM Falah, TE; Lecroq, T & Elloumi, M. An efficient motif search algorithm based on a minimal forbidden patterns approach. 10e anniversaire du Séminaire MaMuX, IRCAM, Paris, France, 2011.
BibTeX: @inproceedings{Falah2011, author = {Falah, TE and Lecroq, T and Elloumi, M}, title = {An efficient motif search algorithm based on a minimal forbidden patterns approach}, booktitle = {10e anniversaire du Séminaire MaMuX}, address = {IRCAM, Paris, France}, year = {2011} }
006 COM Fici, G; Lecroq, T; Lefebvre, A & Prieur Gaston, E. Computing Abelian Periods in Words. 10e anniversaire du Séminaire MaMuX, IRCAM, Paris, France, 2011.
BibTeX: @inproceedings{Fici2011, author = {Fici, G and Lecroq, T and Lefebvre, A and Prieur Gaston, E}, title = {Computing Abelian Periods in Words}, booktitle = {10e anniversaire du Séminaire MaMuX}, address = {IRCAM, Paris, France}, year = {2011} }
006 COM Fici, G.; Lecroq, T.; Lefebvre, A. & Prieur-Gaston, E.. Computing Abelian Periods in Words. SeqBi11 - Workshop Algorithmique, combinatoire du texte et applications en bio-informatique , Rennes France , 2011.
BibTeX: @inproceedings{FICI:2011:HAL-00560414:1, author = {{F}ici, {G}. and {L}ecroq, {T}. and {L}efebvre, {A}. and {P}rieur-{G}aston, {E}.}, title = {{C}omputing {A}belian {P}eriods in {W}ords}, booktitle = {{S}eq{B}i11 - {W}orkshop {A}lgorithmique, combinatoire du texte et applications en bio-informatique }, address = {{R}ennes {F}rance }, year = {2011}, url = {http://hal.archives-ouvertes.fr/hal-00560414/en/} }
006 COM Fici, G.; Lecroq, T.; Lefebvre, A. & Prieur-Gaston, E.. Computing abelian periods in words. London Stringology Days/London Algorithmic Workshop 2011 , Londres Royaume-Uni , Pages 184-196, 2011.
BibTeX: @inproceedings{FICI:2011:HAL-00569139:1, author = {{F}ici, {G}. and {L}ecroq, {T}. and {L}efebvre, {A}. and {P}rieur-{G}aston, {E}.}, title = {{C}omputing abelian periods in words}, booktitle = {{L}ondon {S}tringology {D}ays/{L}ondon {A}lgorithmic {W}orkshop 2011 }, address = {{L}ondres {R}oyaume-{U}ni }, year = {2011}, pages = {184--196}, url = {http://hal.archives-ouvertes.fr/hal-00569139} }
006 COM Gehanno, J.-F.. Epidémiologie des maladies infectieuses chez les professionnels de santé. XXIIème congrès de la Société Française d'Hygiène Hospitalière, Lyon, June, 2011.
BibTeX: @inproceedings{Gehanno2011a, author = {Gehanno, J.-F.}, title = {Epidémiologie des maladies infectieuses chez les professionnels de santé}, booktitle = {{XXIIème} congrès de la Société Française {d'Hygiène} Hospitalière}, address = {Lyon}, month = {June}, year = {2011} }
006 COM Gehanno, J.-F.. Les principaux risques infectieux et leurs modes de transmission. JISSSP, Aix en Provence, June, 2011.
BibTeX: @inproceedings{Gehanno2011b, author = {Gehanno, J.-F.}, title = {Les principaux risques infectieux et leurs modes de transmission}, booktitle = {{JISSSP}}, address = {Aix en Provence}, month = {June}, year = {2011} }
006 COM Grosjean, J; Merabti, T & Darmoni SJ. Health Multi-Terminology Portal. RITS Recherche en Imagerie et Technologie pour la Santé, Rennes, 2011.
BibTeX: @inproceedings{Grosjean2011, author = {Grosjean, J and Merabti, T and Darmoni SJ}, title = {Health Multi-Terminology Portal}, booktitle = {RITS Recherche en Imagerie et Technologie pour la Santé}, address = {Rennes}, year = {2011} }
006 COM Philippe, N.; Salson, M.; Lecroq, T.; Léonard, M.; Commes, T. & Rivals, E.. A solution to index large set of short reads. seqBi11 - Workshop Algorithmique, combinatoire du texte et applications en bio-informatique , Rennes France , 2011.
BibTeX: @inproceedings{PHILIPPE:2011:HAL-00560731:1, author = {{P}hilippe, {N}. and {S}alson, {M}. and {L}ecroq, {T}. and {L}{\'e}onard, {M}. and {C}ommes, {T}. and {R}ivals, {E}.}, title = { {A} solution to index large set of short reads}, booktitle = {seq{B}i11 - {W}orkshop {A}lgorithmique, combinatoire du texte et applications en bio-informatique }, address = {{R}ennes {F}rance }, year = {2011}, url = {http://hal.archives-ouvertes.fr/hal-00560731/en/} }
007 AFF Berrouane, Y; Hagège, C; Gicquel, Q; Kergoulay, I; Pereira, S; Proux, D; Darmoni SJ; Segond, F & Metzger, MH. Preliminary evaluation of an automated detection tool for healthcare-associated infections, based on screening natural language medical reports. ECCMID European Congress of Clinical Microbiology and Infectious Diseases, 2011.
BibTeX: @inproceedings{Berrouane2011, author = {Berrouane, Y and Hagège, C and Gicquel, Q and Kergoulay, I and Pereira, S and Proux, D and Darmoni SJ and Segond, F and Metzger, MH}, title = {Preliminary evaluation of an automated detection tool for healthcare-associated infections, based on screening natural language medical reports}, booktitle = {ECCMID European Congress of Clinical Microbiology and Infectious Diseases}, year = {2011}, url = {http://www.eccmid-icc2011.org/} }
007 AFF Bouhamed, H; Rebai, A; Lecroq, T & Jaoua, M. A novel knowledge-discovering approach from massive data. 7th International Conference on Data Mining (DMIN 2011), Las Vegas, Nevada, USA, 2011. Poster.
BibTeX: @inproceedings{Bouhamed2011b, author = {Bouhamed, H and Rebai, A and Lecroq, T and Jaoua, M}, title = {A novel knowledge-discovering approach from massive data}, booktitle = {7th International Conference on Data Mining (DMIN 2011)}, address = {Las Vegas, Nevada, USA}, year = {2011}, note = {Poster} }
007 AFF Bousquet, C; Souvignet, J; Merabti, T; Sadou, E; Trombert, B & Rodrigues, JM. Method for mapping the French CCAM terminology to the UMLS metathesaurus. #Stud##Health##Technol##Inform# MIE, Volume 180, Pages 164-68, 2011.
BibTeX: @inproceedings{Bousquet2011, author = {Bousquet, C and Souvignet, J and Merabti, T and Sadou, E and Trombert, B and Rodrigues, JM}, title = {Method for mapping the French CCAM terminology to the UMLS metathesaurus}, booktitle = {MIE}, journal = {#Stud##Health##Technol##Inform#}, year = {2011}, volume = {180}, pages = {164-68}, doi = {10.3233/978-1-61499-101-4-164} }
007 AFF Dirieh Dibad, AD et al.. Information Retrieval in Electronic Health Record: a feasibility study. MIE, 2011.
BibTeX: @inproceedings{Dirieh2011a, author = {Dirieh Dibad, AD et al.}, title = {Information Retrieval in Electronic Health Record: a feasibility study}, booktitle = {MIE}, year = {2011}, url = {http://person.hst.aau.dk/ska/mie2011/CD/MIE_2011_Content/Posters/026_or_submission_136_3_am_sm_ok.pdf} }
007 AFF Kerdelhue, G & Gehanno, JF. Tools and organization of a current awareness service. Eahil, 2011. One of 10 best posters..
BibTeX: @inproceedings{Kerdelhue2011, author = {Kerdelhue, G and Gehanno, JF}, title = {Tools and organization of a current awareness service}, booktitle = {Eahil}, year = {2011}, note = {One of 10 best posters.} }
008 OS El Falah, T.; Lecroq, T. & Elloumi, M.. Motif finding algorithms in biological sequences. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications , Pages 387-398 , Wiley , 2011.
BibTeX: @incollection{ELFALAH:2011:HAL-00560398:1, author = {{E}l {F}alah, {T}. and {L}ecroq, {T}. and {E}lloumi, {M}.}, title = { {M}otif finding algorithms in biological sequences}, booktitle = {{A}lgorithms in {C}omputational {M}olecular {B}iology: {T}echniques, {A}pproaches and {A}pplications }, publisher = {{W}iley }, year = {2011}, pages = {387-398 }, url = {http://hal.archives-ouvertes.fr/hal-00560398/en/} }
008 OS Soualmia, LF; Dahamna, B & Darmoni SJ. Extracting and Evaluating Knowledge from e-Health Documents : a Contribution to Information Retrieval and Indexing in : Information Extraction from Internet. , Pages 89-108, CreateSpace, 2011.
BibTeX: @inbook{Soualmia2011, author = {Soualmia, LF and Dahamna, B and Darmoni SJ}, title = {Information Extraction from Internet}, publisher = {CreateSpace}, year = {2011}, pages = {89-108}, url = {http://www.iconceptpress.com/www/site/download.paper.php?paperID=100619153747} }
010 AP Fici, G; lecroq, T; Lefebvre, A & Prieur Gaston, E. Computing Abelian periods in words. , 2011. Report ISRN I3S/RR-2011-01-FR.
BibTeX: @techreport{Fici2011b, author = {Fici, G and lecroq, T and Lefebvre, A and Prieur Gaston, E}, title = {Computing Abelian periods in words}, year = {2011}, note = {Report ISRN I3S/RR-2011-01-FR} }
010 AP Golbreich, C; Grosjean, J & Darmoni, SJ. The Foundational Model of Anatomy in the Health Multi-Terminology Portal. , 2011. Technical report.
BibTeX: @techreport{Golbreich2011a, author = {Golbreich, C and Grosjean, J and Darmoni, SJ}, title = {The Foundational Model of Anatomy in the Health Multi-Terminology Portal}, year = {2011}, note = {Technical report} }
010 AP Lefebvre, A. Des mots et des tableaux - Mais à qui est ce tableau ?. Ecole Jeunes Chercheurs du GDR Informatique Mathématiques, Amiens, 2011.
BibTeX: @inproceedings{Lefebvre2011a, author = {Lefebvre, A}, title = {Des mots et des tableaux - Mais à qui est ce tableau ?}, booktitle = {Ecole Jeunes Chercheurs du GDR Informatique Mathématiques}, address = {Amiens}, year = {2011} }
010 AP Merabti, Tayeb. Le CISMeF agrège ses terminologies pour une meilleure recherche dans ses fonds. Documentaliste - Sciences de l'information , Number 4, 2011.
Abstract: Le Cismef intègre désormais plusieurs terminologies au service de l'indexation et de l'interrogation de ses ressources. Un chantier mené à bien grâce à l'emploi de standards du web sémantique tels que RDF et Owl.
BibTeX: @article{Merabti2011c, author = {Merabti, Tayeb}, title = {Le CISMeF agrège ses terminologies pour une meilleure recherche dans ses fonds}, journal = {Documentaliste - Sciences de l'information}, year = {2011}, number = {4}, url = {http://www.adbs.fr/web-semantique-web-de-donnees-pole-2-le-cismef-agrege-ses-terminologies-pour-une-meilleure-recherche-dans-ses-fonds-112553.htm?RH=REVUE} }
2010 001 ACL-int Groult, Richard; Prieur, Elise & Richomme, Gwénaël. Counting distinct palindromes in a word in linear time. Information Processing Letters , September, Volume 110, Number 20, Pages 908-912, 2010.
Abstract: textlessptextgreatertextlessbr/textgreaterWe design an algorithm to count the number of distinct palindromes in a word w in time O(w), by adapting an algorithm to detect all occurrences of maximal palindromes in a given word and using the longest previous factor array. As a direct consequence, this shows that the palindromic richness (or fullness) of a word can be checked in linear time.textless/ptextgreater
BibTeX: @article{groult_counting_2010, author = {Groult, Richard and Prieur, Elise and Richomme, Gwénaël}, title = {Counting distinct palindromes in a word in linear time}, month = {September}, journal = {Information Processing Letters}, year = {2010}, volume = {110}, number = {20}, pages = {908--912}, url = {http://www.sciencedirect.com/science/article/pii/S002001901000236X}, doi = {16/j.ipl.2010.07.018} }
001 ACL-int Laetitia Rollin; Stefan Darmoni; Jean-François Caillard & Jean-François Gehanno. Searching for high-quality articles about intervention studies in occupational health - what is really missed when using only the Medline database?. Scand J Work Environ Health , Aug, 2010.
Abstract: OBJECTIVE: Most occupational health physicians access electronic databases to obtain reliable medical information. Although it is demonstrated that the use of Medline alone does not ensure comprehensiveness, many experts rely solely on this database. Our study aimed to discover to what extent the physician who limits his/her search to Medline misses studies of high quality. METHODS: We constructed a "gold standard" database of high-quality intervention studies gathering all the references included in the systematic reviews of the Cochrane Library and indexed under the topic "occupational health field". We then searched all these references, one by one, in Medline. RESULTS: Overall, 88.8% [95% confidence interval (95% CI) 86.1-91.5] of the high quality studies included in our gold standard database were indexed in Medline. References included in reviews on psychiatric or psychological topics were significantly less often indexed in Medline [81.7% (95% CI 75.9-88.5)] than references included in reviews on other topics [92.2% (95% CI 89.5-95.0)] (P=0.001). CONCLUSION: The recall ratio of Medline for high-quality intervention studies is close to 90 For occupational health practitioners who aim to find reliable answers to their daily practice questions, searching Medline only is more cost-effective than previously thought.
BibTeX: @article{Rollin2010, author = {Laetitia Rollin and Stefan Darmoni and Jean-François Caillard and Jean-François Gehanno}, title = {Searching for high-quality articles about intervention studies in occupational health - what is really missed when using only the Medline database?}, month = {Aug}, journal = {Scand J Work Environ Health}, year = {2010}, url = {http://www.sjweh.fi/show_abstract.php?abstract_id=3082} }
001 ACL-int Salson, M; Lecroq, T; Léonard, M & Mouchard, L. Dynamic Extended Suffix Arrays. Journal of Discrete Algorithms , Volume 8, Number 2, Pages 241-257, 2010.
BibTeX: @article{Salson2009a, author = {Salson, M and Lecroq, T and Léonard, M and Mouchard, L}, title = {Dynamic Extended Suffix Arrays}, journal = {Journal of Discrete Algorithms}, year = {2010}, volume = {8}, number = {2}, pages = {241--257}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/jda2009.pdf}, doi = {10.1016/j.jda.2009.02.007} }
001 ACL-int de Vendômois, Joël Spiroux; Cellier, Dominique; Vélot, Christian; Clair, Emilie; Mesnage, Robin & Séralini, Gilles-Eric. Debate on GMOs health risks after statistical findings in regulatory tests. International Journal of Biological Sciences , Volume 6, Number 6, Pages 590-598, 2010.
Abstract: We summarize the major points of international debate on health risk studies for the main commercialized edible GMOs. These GMOs are soy, maize and oilseed rape designed to contain new pesticide residues since they have been modified to be herbicide-tolerant (mostly to Roundup) or to produce mutated Bt toxins. The debated alimentary chronic risks may come from unpredictable insertional mutagenesis effects, metabolic effects, or from the new pesticide residues. The most detailed regulatory tests on the GMOs are three-month long feeding trials of laboratory rats, which are biochemically assessed. The tests are not compulsory, and are not independently conducted. The test data and the corresponding results are kept in secret by the companies. Our previous analyses of regulatory raw data at these levels, taking the representative examples of three GM maize NK 603, MON 810, and MON 863 led us to conclude that hepatorenal toxicities were possible, and that longer testing was necessary. Our study was criticized by the company developing the GMOs in question and the regulatory bodies, mainly on the divergent biological interpretations of statistically significant biochemical and physiological effects. We present the scientific reasons for the crucially different biological interpretations and also highlight the shortcomings in the experimental protocols designed by the company. The debate implies an enormous responsibility towards public health and is essential due to nonexistent traceability or epidemiological studies in the GMO-producing countries.
BibTeX: @article{de_vendomois_debate_2010, author = {de Vendômois, Joël Spiroux and Cellier, Dominique and Vélot, Christian and Clair, Emilie and Mesnage, Robin and Séralini, {Gilles-Eric}}, title = {Debate on {GMOs} health risks after statistical findings in regulatory tests}, journal = {International Journal of Biological Sciences}, year = {2010}, volume = {6}, number = {6}, pages = {590--598}, url = {http://www.biolsci.org/v06p0590.htm}, doi = {10.7150/ijbs.6.590} }
002 ACL-nat Darmoni, SJ; Merabti, T; Joubert, M; Lecroq, T & Rath, A. Mapping biomedical terminologies using natural language processing tools and UMLS: mapping the Orphanet thesaurus to the MeSH. Ingénierie et Recherche Biomédicale / BioMedical Engineering and Research , Volume 31, Number 4, Pages 221-225, 2010.
Abstract: Background: Orphanet aims to provide rare disease information to healthcare professionals, patients, and their relatives. Objective: The objective of this work is to evaluate two methodologies (UMLS and manual Orphanet-ICD-10 link-based mapping & String Based matching) used to map Orphanet thesaurus to the MeSH thesaurus. Results: On a corpus of 375 mappings, the string based matching provides significantly better results than the UMLS and manual Orphanet-ICD-10 link-based mapping. Conclusion: String based matching could be applied to any biomedical terminology in French not yet included into UMLS.
BibTeX: @article{Darmoni2010, author = {Darmoni, SJ and Merabti, T and Joubert, M and Lecroq, T and Rath, A}, title = {Mapping biomedical terminologies using natural language processing tools and UMLS: mapping the Orphanet thesaurus to the MeSH}, journal = {Ingénierie et Recherche Biomédicale / BioMedical Engineering and Research}, year = {2010}, volume = {31}, number = {4}, pages = {221-225}, doi = {10.1016/j.irbm.2010.04.003} }
002 ACL-nat Gaston, Benoist; Groult, Richard; Lefebvre, Arnaud; Léonard, Martine & Prieur-Gaston, Elise. Multiplions et divisons avec des bâtons : Les réglettes de Genaille et Lucas.. Bulletin Vert de l'APMEP , May, Number 488, Pages p. 339-348, 2010.
Abstract: Les réglettes de Genaille et Lucas ont été inventées par l'ingénieur Henri Genaille en 1885 sur une proposition du mathématicien Édouard Lucas. Il existe des réglettes pour les multiplications et pour les divisions entières. Ces réglettes furent beaucoup utilisées jusque dans les années 1920, période d'apparition des règles à calcul qui précédèrent les calculatrices. Les réglettes présentées dans ce document permettent d'effectuer rapidement de grandes multiplications ou divisions sans calculer de tête. Nous expliquons comment les manipuler et les construire.
BibTeX: @article{Gaston2010, author = {Gaston, Benoist and Groult, Richard and Lefebvre, Arnaud and L{\'e}onard, Martine and Prieur-Gaston, Elise}, title = {{Multiplions et divisons avec des b{\^a}tons : Les r{\'e}glettes de Genaille et Lucas.}}, month = {May}, journal = {Bulletin Vert de l'APMEP}, year = {2010}, number = {488}, pages = {p. 339-348}, url = {http://hal.archives-ouvertes.fr/hal-00488540/en/} }
002 ACL-nat Goullé, Jean-Pierre; Gehanno, Jean-François; Mahieu, Loic; Saunier, Florence; Saussereau, Élodie; Guerbet, Michel & Lacroix, Christian. Intérêt de la mesure des isotopes du plomb dans un cas d'intoxication familiale par un plat à tajine. Annales de Toxicologie Analytique , October, Volume 22, Number 3, Pages 153-157, 2010.
BibTeX: @article{Goulle2010a, author = {Goullé, Jean-Pierre and Gehanno, Jean-François and Mahieu, Loic and Saunier, Florence and Saussereau, Élodie and Guerbet, Michel and Lacroix, Christian}, title = {Intérêt de la mesure des isotopes du plomb dans un cas d'intoxication familiale par un plat à tajine}, month = {October}, journal = {Annales de Toxicologie Analytique}, year = {2010}, volume = {22}, number = {3}, pages = {153--157}, url = {http://www.ata-journal.org/index.php?option=com_article&access=standard&Itemid=129&url=/articles/ata/abs/2010/03/ata09063/ata09063.html}, doi = {10.1051/ata/2010020} }
003 INV Gehanno, JF. Référentiels et évaluation des pratiques professionnelles. 47èmes journées Santé-Travail du CISME, Paris, France, Octobre, 2010.
BibTeX: @inproceedings{Gehanno2010, author = {Gehanno, JF}, title = {Référentiels et évaluation des pratiques professionnelles}, booktitle = {47èmes journées Santé-Travail du CISME}, address = {Paris, France}, month = {Octobre}, year = {2010} }
003 INV Lecroq, T.. Alignments in 2D and experimentscientcient matching on encoded binary strings. Optimization and Learning: Theory, Algorithms and Applications 2010 , Metz France , 2010.
BibTeX: @inproceedings{LECROQ:2010:HAL-00504103:1, author = {{L}ecroq, {T}.}, title = { {A}lignments in 2{D} and experimentscientcient matching on encoded binary strings}, booktitle = {{O}ptimization and {L}earning: {T}heory, {A}lgorithms and {A}pplications 2010 }, address = {{M}etz {F}rance }, year = {2010}, url = {http://hal.archives-ouvertes.fr/hal-00504103/en/} }
003 INV Lecroq, T.. Indexing Structures and Next Generation Sequencing (NGS). Journées Montoises d'Informatique Théorique/ Mons Theoretical Computer Science Days , Amiens France , 2010.
BibTeX: @inproceedings{LECROQ:2010:HAL-00563117:1, author = {{L}ecroq, {T}.}, title = { {I}ndexing {S}tructures and {N}ext {G}eneration {S}equencing ({NGS})}, booktitle = {{J}ourn{\'e}es {M}ontoises d'{I}nformatique {T}h{\'e}orique/ {M}ons {T}heoretical {C}omputer {S}cience {D}ays }, address = {{A}miens {F}rance }, year = {2010}, url = {http://hal.archives-ouvertes.fr/hal-00563117/en/} }
004 ACTI Déleger, L; Merabti, T; Lecroq, T; Joubert, M; Zweigenbaum, P & Darmoni, SJ. A Twofold Strategy for Translating a Medical Terminology into French. AMIA, Pages 152-156, 2010. Distinguished paper award.
BibTeX: @inproceedings{Deleger2010, author = {Déleger, L and Merabti, T and Lecroq, T and Joubert, M and Zweigenbaum, P and Darmoni, SJ}, title = {A Twofold Strategy for Translating a Medical Terminology into French}, booktitle = {AMIA}, year = {2010}, pages = {152-156}, note = {Distinguished paper award} }
004 ACTI T. El Falah; T. Lecroq & M. Elloumi. SMS-Forbid: an efficient algorithm for Simple Motif Problem. #proct#ISCA 2nd International Conference on Bioinformatics and Computational Biology, Honolulu, Hawai, Pages 121-126, The International Society for Computers and their Applications, 2010.
BibTeX: @inproceedings{Falah2010, author = {T. El Falah and T. Lecroq and M. Elloumi}, title = {SMS-Forbid: an efficient algorithm for Simple Motif Problem}, booktitle = {#proct#ISCA 2nd International Conference on Bioinformatics and Computational Biology}, address = {Honolulu, Hawai}, publisher = {The International Society for Computers and their Applications}, year = {2010}, pages = {121--126}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/bicob2010.pdf} }
004 ACTI Lamy, JB; Duclos, C; Hamek, S; Beuscart, MC; Kerdelhué, G; Darmoni, SJ; Favre, M; Falcoff, H; Simon, C; Pereira, S; Serrot, E; Mitouard, T; Hardouin, E; Kergosien, Y & Venot, A. Towards iconic language for patient records, drug monographs, guidelines and medical search engines. Stud Health Technol Inform MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics, Cape Town, South Africa, Volume 160, Number pt 1, Pages 156-160, 2010.
BibTeX: @inproceedings{Lamy2010, author = {Lamy, JB and Duclos, C and Hamek, S and Beuscart, MC and Kerdelhué, G and Darmoni, SJ and Favre, M and Falcoff, H and Simon, C and Pereira, S and Serrot, E and Mitouard, T and Hardouin, E and Kergosien, Y and Venot, A}, title = {Towards iconic language for patient records, drug monographs, guidelines and medical search engines}, booktitle = {MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics}, address = {Cape Town, South Africa}, journal = {Stud Health Technol Inform}, year = {2010}, volume = {160}, number = {pt 1}, pages = {156--160} }
004 ACTI Tayeb Merabti; Philipe Massari; Michel Joubert; Eric Sadou; Thierry Lecroq; Hocine Abdoune; Jean-Marie Rodrigues & Stefan J Darmoni. An Automated Approach to map a French terminology to UMLS.. Stud Health Technol Inform MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics, Cape Town, South Africa, Volume 160, Number pt 1, Pages 1040-1044, 2010.
Abstract: Background: CCAM is a French terminology for coding clinical procedures. CCAM is a multi-hierarchical structured classification for procedures used in France for reimbursement in health care, which is external to UMLS. Objective: The objective of this work is to describe a French lexical approach allowing mapping CCAM procedures to the UMLS Metathesaurus to achieve interoperability to multiple international terminologies. This approach used a preliminary step intended to take only the significant characters used to code CCAM corresponding to anatomical and actions axes. Results: According to the 7,926 CCAM codes used in this study, 5,212 possible matches (exact matching, single to multiple matching, partial matching) are found using the French CCAM to UMLS based mapping, 65% of the corresponding anatomical terms in the CCAM code are mapped to at least one UMLS Concept and 37% of the corresponding action terms in the CCAM code are mapped to at least one UMLS Concept. For all the exact matches found (n=200), 91% were rated by a human expert as narrower than the mapped UMLS Concepts, while only 3% were irrelevant.
BibTeX: @inproceedings{Merabti2010, author = {Tayeb Merabti and Philipe Massari and Michel Joubert and Eric Sadou and Thierry Lecroq and Hocine Abdoune and Jean-Marie Rodrigues and Stefan J Darmoni}, title = {An Automated Approach to map a French terminology to UMLS.}, booktitle = {MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics}, address = {Cape Town, South Africa}, journal = {Stud Health Technol Inform}, year = {2010}, volume = {160}, number = {pt 1}, pages = {1040--1044}, url = {http://hal.archives-ouvertes.fr/hal-00563123/en/} }
004 ACTI Merlin, B; Chazard, E; Pereira, S; Serrot, E; Sakji, S; Beuscart, R & Darmoni, SJ. Can F-MTI semantic-mined drug codes be used for Adverse Drug Events detection when no CPOE is available?. Stud Health Technol Inform MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics, Cape Town, South Africa, Volume 160, Number pt 1, Pages 1025-1029, 2010.
BibTeX: @inproceedings{Merlin2010, author = {Merlin, B and Chazard, E and Pereira, S and Serrot, E and Sakji, S and Beuscart, R and Darmoni, SJ}, title = {Can F-MTI semantic-mined drug codes be used for Adverse Drug Events detection when no CPOE is available?}, booktitle = {MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics}, address = {Cape Town, South Africa}, journal = {Stud Health Technol Inform}, year = {2010}, volume = {160}, number = {pt 1}, pages = {1025-1029} }
004 ACTI Proux, D; Marchal, P; Segond, F; Kergourlay, I; Pereira, S; Gicquel, Q; Darmoni, SJ & Metzger, MH. Improving Hospital Document workflow with a Risk Patterns Detection tool to detect potential Hospital Acquired Infections. Biomedical Information Extraction, RANLP conference, 2010. ALADIN..
BibTeX: @inproceedings{Proux2010, author = {Proux, D and Marchal, P and Segond, F and Kergourlay, I and Pereira, S and Gicquel, Q and Darmoni, SJ and Metzger, MH}, title = {Improving Hospital Document workflow with a Risk Patterns Detection tool to detect potential Hospital Acquired Infections}, booktitle = {Biomedical Information Extraction, RANLP conference}, year = {2010}, note = {ALADIN.}, url = {http://www.lml.bas.bg/ranlp2009/biomedicalIE/} }
004 ACTI Sakji, S; Gicquel, Q; Pereira, S; Kergoulay, I; Proux, D; Darmoni SJ & Metzger, MH. Evaluation of a French Medical Multi-Terminology Indexer for the Manual Annotation of Natural Language Medical Reports of Healthcare-Associated Infections. Stud Health Technol Inform MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics, Cape Town, South Africa, Volume 160, Number Pt 1, Pages 252-256, 2010.
BibTeX: @inproceedings{Sakji2010, author = {Sakji, S and Gicquel, Q and Pereira, S and Kergoulay, I and Proux, D and Darmoni SJ and Metzger, MH}, title = {Evaluation of a French Medical Multi-Terminology Indexer for the Manual Annotation of Natural Language Medical Reports of Healthcare-Associated Infections}, booktitle = {MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics}, address = {Cape Town, South Africa}, journal = {Stud Health Technol Inform}, year = {2010}, volume = {160}, number = {Pt 1}, pages = {252--256} }
004 ACTI Soula, G; Darmoni, SJ; Le Beux, P; Renard, JM; Dahamna, B & Fieschi, M. An open repositories network development for medical teaching resources.. Stud Health Technol Inform MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics, Cape Town, South Africa, Volume 160, Number Pt 1, Pages 610-614, 2010.
Abstract: The lack of interoperability between repositories of heterogeneous and geographically widespread data is an obstacle to the diffusion, sharing and reutilization of those data. We present the development of an open repositories network taking into account both the syntactic and semantic interoperability of the different repositories and based on international standards in this field. The network is used by the medical community in France for the diffusion and sharing of digital teaching resources. The syntactic interoperability of the repositories is managed using the OAI-PMH protocol for the exchange of metadata describing the resources. Semantic interoperability is based, on one hand, on the LOM standard for the description of resources and on MESH for the indexing of the latter and, on the other hand, on semantic interoperability management designed to optimize compliance with standards and the quality of the metadata.
BibTeX: @inproceedings{Soula2010, author = {Soula, G and Darmoni, SJ and Le Beux, P and Renard, JM and Dahamna, B and Fieschi, M}, title = {An open repositories network development for medical teaching resources.}, booktitle = {MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics}, address = {Cape Town, South Africa}, journal = {Stud Health Technol Inform}, year = {2010}, volume = {160}, number = {Pt 1}, pages = {610--614} }
005 ACTN Gicquel, Q; Kergoulay, I; Pereira, S; Grandbastien, B; Berrouane, Y; Tavolacci, MP; Segond, F; Darmoni SJ & Metzger, MH. L'apport d'un serveur multi-terminologique de santé pour un codage standardisé de données épidémiologiques - Exemple d'application en épidémiologie hospitalière. Revue d'Épidemiologie et de Santé Publique Actes ADELF-EMOIS, Volume 58, Number S1, Pages S25, 2010. ALADIN-DTH.
BibTeX: @article{Gicquel2010, author = {Gicquel, Q and Kergoulay, I and Pereira, S and Grandbastien, B and Berrouane, Y and Tavolacci, MP and Segond, F and Darmoni SJ and Metzger, MH}, title = {L'apport d'un serveur multi-terminologique de santé pour un codage standardisé de données épidémiologiques - Exemple d'application en épidémiologie hospitalière}, booktitle = {Actes ADELF-EMOIS}, journal = {Revue d'Épidemiologie et de Santé Publique}, year = {2010}, volume = {58}, number = {S1}, pages = {S25}, note = {ALADIN-DTH}, url = {http://www.em-consulte.com/article/248607}, doi = {10.1016/j.respe.2010.02.065} }
006 COM Groult, R; Prieur, E & Richomme, G. Counting different palindromes in a word in linear time. Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, Montpellier, France, 2010.
BibTeX: @inproceedings{Groult2010, author = {Groult, R and Prieur, E and Richomme, G}, title = {Counting different palindromes in a word in linear time}, booktitle = {Workshop Algorithmique, combinatoire du texte et applications en bio-informatique}, address = {Montpellier, France}, year = {2010} }
006 COM Léonard, M; Mouchard, L & Salson, M. Coût d'une mise à jour de la table des suffixes. Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, Montpellier, France, 2010.
BibTeX: @inproceedings{Leonard2010, author = {Léonard, M and Mouchard, L and Salson, M}, title = {Coût d'une mise à jour de la table des suffixes}, booktitle = {Workshop Algorithmique, combinatoire du texte et applications en bio-informatique}, address = {Montpellier, France}, year = {2010} }
007 AFF Ammenwerth, E; Hackl, W; Bjoern, B; Koutkias, V; Massari, P; Pechlaner, C; Riedmann, D; Saboor, S & Darmoni, SJ. Validation of a knowledge base for advanced CPOE systems based on test cases. MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics, Cape Town, South Africa, 2010.
BibTeX: @inproceedings{Ammenwerth2010, author = {Ammenwerth, E and Hackl, W and Bjoern, B and Koutkias, V and Massari, P and Pechlaner, C and Riedmann, D and Saboor, S and Darmoni, SJ}, title = {Validation of a knowledge base for advanced CPOE systems based on test cases}, booktitle = {MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics}, address = {Cape Town, South Africa}, year = {2010} }
007 AFF Bousquet, C; Sadou, E; Merabti, T; Trombert, B; Kumar, A; Darmoni, SJ & Rodrigues, JM. Multiaxial description of the French CCAM terminology for clinical procedures and mapping on the UMLS metathesaurus. MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics, Cape Town, South Africa, 2010.
BibTeX: @inproceedings{Bousquet2010, author = {Bousquet, C and Sadou, E and Merabti, T and Trombert, B and Kumar, A and Darmoni, SJ and Rodrigues, JM}, title = {Multiaxial description of the French CCAM terminology for clinical procedures and mapping on the UMLS metathesaurus}, booktitle = {MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics}, address = {Cape Town, South Africa}, year = {2010} }
007 AFF Goullé, J.P; Lacroix, C; Perreard, T; Spiroux, J; Cellier, D & Guerbet, M. Rejets de médicaments dans les eaux usées de l'agglomération de Rouen. 48ème CONGRES DE LA SOCIETE DE TOXICOLOGIE CLINIQUE, MARSEILLE, FRANCE, May, 2010.
BibTeX: @inproceedings{Goulle2010, author = {Goullé, J.P and Lacroix, C and Perreard, T and Spiroux, J and Cellier, D and Guerbet, M}, title = {Rejets de médicaments dans les eaux usées de l'agglomération de Rouen}, booktitle = {48ème CONGRES DE LA SOCIETE DE TOXICOLOGIE CLINIQUE}, address = {MARSEILLE, FRANCE}, month = {May}, year = {2010} }
007 AFF Joubert, M; Merabti, T; Vandenbussche, PY; Abdoune, H; Dahamna, B; Fieschi, M & Darmoni, SJ. Modeling and Integrating Terminologies into a French Multi-terminology Server. MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics, Cape Town, South Africa, 2010.
BibTeX: @inproceedings{Joubert2010, author = {Joubert, M and Merabti, T and Vandenbussche, PY and Abdoune, H and Dahamna, B and Fieschi, M and Darmoni, SJ}, title = {Modeling and Integrating Terminologies into a French Multi-terminology Server}, booktitle = {MEDINFO 2010 - Proceedings of the 13th World Congress on Medical Informatics}, address = {Cape Town, South Africa}, year = {2010} }
007 AFF Kerdelhué, G; Lamy, JB; Venot, A; Duclos, C & Darmoni, SJ. An iconic language for the "CISMeF Bonnes pratiques" website. EAHIL, 2010.
BibTeX: @inproceedings{Kerdelhue2010, author = {Kerdelhué, G and Lamy, JB and Venot, A and Duclos, C and Darmoni, SJ}, title = {An iconic language for the "CISMeF Bonnes pratiques" website}, booktitle = {EAHIL}, year = {2010} }
007 AFF Merabti, T & Darmoni SJ. ATC to PubMed: a bibliographic tool for drugs. AMIA, Pages 1174, 2010.
BibTeX: @inproceedings{Merabti2010a, author = {Merabti, T and Darmoni SJ}, title = {ATC to PubMed: a bibliographic tool for drugs}, booktitle = {AMIA}, year = {2010}, pages = {1174} }
010 AP Faro, S. & Lecroq, T.. The Exact String Matching Problem: a Comprehensive Experimental Evaluation. , 2010.
BibTeX: @techreport{FARO:2010:HAL-00560411:1, author = {{F}aro, {S}. and {L}ecroq, {T}.}, title = { {T}he {E}xact {S}tring {M}atching {P}roblem: a {C}omprehensive {E}xperimental {E}valuation}, year = {2010}, url = {http://hal.archives-ouvertes.fr/hal-00560411/en/} }
010 AP Golbreich, C; Grosjean, J & Darmoni, SJ. Pushing the FMA-OWL Enveloppe Further. , 2010. Technical report.
Abstract: Representing the Foundational Model of Anatomy (FMA) in OWL 2 W3C standard, is essential for its interoperability with other biomedical ontologies, its design, maintenance, and quality insurance. The paper describes the method and 'FMA-OWLizer' tool that moves the FMA to OWL 2. One main strength of the approach is to leverage OWL expressiveness to explicit some implicit semantics and naming conventions of the FMA, meanwhile improving its ontological model and fixing some FMA errors. Another originality is the flexibility and versatility of the conversion: many options allow for producing several FMA-OWL variants customized to users, e.g., choosing a frame or OWL source, generating an OWL DL or OWL 2, a full or reduced FMA target, configuring the classes definitions etc. Thus several new FMA-OWL ontologies are available. To the best of our knowledge, no complete representation of the entire FMA in OWL DL or OWL 2 existed so far.
BibTeX: @techreport{Golbreich2010, author = {Golbreich, C and Grosjean, J and Darmoni, SJ}, title = {Pushing the FMA-OWL Enveloppe Further}, year = {2010}, note = {Technical report}, url = {http://hal-lirmm.ccsd.cnrs.fr/lirmm-00495056/fr/} }
010 AP Golbreich, C; Grosjean J & Darmoni, SJ. FMA and HMTP Portal in OWL: Reconciling Ontology with Terminology in Life Sciences via Metamodeling. , June, 2010.
Abstract: The aim is to highlight how it is possible to reconcile ontologies and terminologies in Life Sciences via metamodeling. The paper focuses on the Foundational Model of Anatomy (FMA). The first part describes the FMA ontology formalization in OWL 2. The second part presents the Health Multi-Terminologies Portal (HMTP) of French terminologies implemented in OWL. It explains how its FMA terminology was obtained from the FMA ontology by reification. The FMA ontology and terminology illustrate how ontologies and terminologies can be made compatible via metamodeling. Advantages and possible means to bind the two views even more closely are discussed in conclusion. To the best of our knowledge, no complete representation of the FMA ontology and terminology in OWL 2 existed so far.
BibTeX: @techreport{Golbreich2010a, author = {Golbreich, C and Grosjean J and Darmoni, SJ}, title = {FMA and HMTP Portal in OWL: Reconciling Ontology with Terminology in Life Sciences via Metamodeling}, month = {June}, year = {2010}, url = {http://hal-lirmm.ccsd.cnrs.fr/lirmm-00534124/fr/} }
010 AP Kerdelhué, G. CISMeF : un catalogue et index des sites médicaux de langue française. La Santé de l'Homme , Novembre-Décembre, Number 410, Pages 36, 2010.
BibTeX: @article{Kedelhue2010, author = {Kerdelhué, G}, title = {CISMeF : un catalogue et index des sites médicaux de langue française}, month = {Novembre-Décembre}, journal = {La Santé de l'Homme}, year = {2010}, number = {410}, pages = {36}, url = {http://www.inpes.sante.fr/SLH/pdf/sante-homme-410.pdf} }
011 TH Griffon, N. Modélisation et évaluation d'un outil de recherche d'informations au sein des dossiers patients informatisés. School: University of Rouen, France, 2010. MD thesis.
BibTeX: @mastersthesis{Griffon2010, author = {Griffon, N}, title = {Modélisation et évaluation d'un outil de recherche d'informations au sein des dossiers patients informatisés}, school = {University of Rouen, France}, year = {2010}, note = {MD thesis}, url = {http://www.chu-rouen.fr/tibs/wp-content/uploads/vff.pdf} }
011 TH Merabti, T. Méthodes pour la mise en relations des terminologies médicales : contribution à l'interopérabilité sémantique Inter et Intra terminologique. School: University of Rouen, France, 2010.
BibTeX: @phdthesis{Merabti2010b, author = {Merabti, T}, title = {Méthodes pour la mise en relations des terminologies médicales : contribution à l'interopérabilité sémantique Inter et Intra terminologique}, school = {University of Rouen, France}, year = {2010}, url = {http://www.chu-rouen.fr/tibs/wp-content/uploads/th%C3%A8se_version_finale_TM.pdf} }
011 TH Sakji, S. Recherche d'information et indexation automatique des médicaments à l'aide de plusieurs terminologies de santé. School: University of Rouen, France, 2010.
BibTeX: @phdthesis{Sakji2010a, author = {Sakji, S}, title = {Recherche d'information et indexation automatique des médicaments à l'aide de plusieurs terminologies de santé}, school = {University of Rouen, France}, year = {2010}, url = {http://www.chu-rouen.fr/tibs/wp-content/uploads/Th%C3%A8se_Saoussen_SAKJI.pdf} }
2009 1 Publication internationale Crochemore, M & Lecroq, T. Suffix tree. Encyclopedia of Database Systems, Pages 2876-2880, Springer Verlag, 2009.
BibTeX: @incollection{Crochemore2009, author = {Crochemore, M and Lecroq, T}, title = {Suffix tree}, booktitle = {Encyclopedia of Database Systems}, publisher = {Springer Verlag}, year = {2009}, pages = {2876--2880}, doi = {10.1007/978-0-387-39940-9_1142} }
1 Publication internationale Crochemore, M & Lecroq, T. Trie. Encyclopedia of Database Systems, Pages 3179-3182, Springer Verlag, 2009.
BibTeX: @incollection{Crochemore2009a, author = {Crochemore, M and Lecroq, T}, title = {Trie}, booktitle = {Encyclopedia of Database Systems}, publisher = {Springer Verlag}, year = {2009}, pages = {3179--3182}, doi = {10.1007/978-0-387-39940-9_1143} }
1 Publication internationale Crochemore, M & Lecroq, T. Text data compression algorithms. Algorithms and Theory of Computation Handbook, Second Edition, Volume 1: General Concepts and Techniques, Boca Raton, FL, Pages 14.1-14.25, CRC Press Inc., 2009.
BibTeX: @incollection{Crochemore2009b, author = {Crochemore, M and Lecroq, T}, title = {Text data compression algorithms}, booktitle = {Algorithms and Theory of Computation Handbook, Second Edition, Volume 1: General Concepts and Techniques}, address = {Boca Raton, FL}, publisher = {CRC Press Inc.}, year = {2009}, pages = {14.1-14.25}, url = {http://208.254.79.11/product/isbn/9781584888222} }
1 Publication internationale Duval, JP; Lecroq, T & Lefebvre, A. Efficient validation and construction of border arrays and validation of string matching automata. RAIRO-Theoretical Informatics and Applications , Volume 43, Pages 281-297, 2009.
BibTeX: @article{Duval2009, author = {Duval, JP and Lecroq, T and Lefebvre, A}, title = {Efficient validation and construction of border arrays and validation of string matching automata}, journal = {RAIRO-Theoretical Informatics and Applications}, year = {2009}, volume = {43}, pages = {281-297}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/rairo2009.pdf}, doi = {10.1051/ita:2008030} }
1 Publication internationale Faro, S & Lecroq, T. Efficient Variants of the Backward-Oracle-Matching Algorithm. International Journal of Foundations of Computer Science , Volume 20, Pages 967-984, 2009.
BibTeX: @article{Faro2009a, author = {Faro, S and Lecroq, T}, title = {Efficient Variants of the Backward-Oracle-Matching Algorithm}, journal = {International Journal of Foundations of Computer Science}, year = {2009}, volume = {20}, pages = {967-984}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/ijfcs2009.pdf}, doi = {10.1142/S0129054109006991} }
1 Publication internationale Jean-François Gehanno; Laetitia Rollin; Tony Le Jean; Alexandre Louvel; Stefan Darmoni & William Shaw. Precision and Recall of Search Strategies for Identifying Studies on Return-To-Work in Medline.. J Occup Rehabil , Apr, Volume 19, Number 3, Pages 223-230, 2009.
Abstract: Introduction The purpose of this study was to report on the qualities of various search strategies and keywords to find return to work (RTW) studies in the Medline bibliographic database. Methods We searched Medline for articles on RTW published in 2003, using multiple search strings, and hand searched 16 major periodicals of rehabilitation or occupational medicine. Among the retrieved articles, those considered to be relevant, were pooled in a Gold Standard Database. From this database, we identified candidate text words or MeSH terms for search strategies using a word frequency analysis of the abstracts and a MEDLINE categorization algorithm. According to the frequency of identified terms, searches were run for each term independently and in combination. We computed Recall, Precision, and number needed to read (NNR = 1/Precision) of each keyword or combination of keywords. Results Among the 8,073 articles examined, 314 (3.9 were considered relevant and included in the Gold Standard Database. The search strings ("Rehabilitation, Vocational" [MeSH]), ("Return to work"[All]) and ("Back to work"[All]) had Recall/Precision ratio of 30.46/19.11, 59.55/87.38 and 3.18/90.91 respectively. Their combination with the Boolean operator OR yielded to a Recall/Precision ratio of 73.89/58.44% and a NNR of 1.7. For the end user requiring comprehensive literature search, the best string was ("Return to work" OR "Back to work" OR "Rehabilitation, vocational"[MeSH] OR "rehabilitation"[Subheading]), with a Recall of 88.22% and a NNR of 18. Conclusions No single MeSH term is available to help the physician to identify relevant studies on RTW in Medline. Locating these types of studies requires the use of various MeSH and non-MeSH terms in combination to obtain a satisfactory Recall. Nevertheless, enhancing the Recall of search strategies may lead to lower Precision, and higher NNR, although with a non linear trend. This factor must be taken into consideration by the end user in order to improve the cost-effectiveness ratio of the search in Medline.
BibTeX: @article{Gehanno2009, author = {Jean-François Gehanno and Laetitia Rollin and Tony Le Jean and Alexandre Louvel and Stefan Darmoni and William Shaw}, title = {Precision and Recall of Search Strategies for Identifying Studies on Return-To-Work in Medline.}, month = {Apr}, journal = {J Occup Rehabil}, year = {2009}, volume = {19}, number = {3}, pages = {223-230}, url = {http://dx.doi.org/10.1007/s10926-009-9177-0}, doi = {10.1007/s10926-009-9177-0} }
1 Publication internationale Humphrey, S; Névéol, A; Gobeil J; Ruch P; Darmoni SJ & Browne A. Comparing a Rule Based vs. Statistical System for Automatic Categorization of MEDLINE Documents According to Biomedical Specialty. Journal of the American Society for Information Science and Technology , july, Volume 60, Number 12, Pages 2530-2539, 2009.
BibTeX: @article{Humphrey2009, author = {Humphrey, S and Névéol, A and Gobeil J and Ruch P and Darmoni SJ and Browne A}, title = {Comparing a Rule Based vs. Statistical System for Automatic Categorization of MEDLINE Documents According to Biomedical Specialty}, month = {july}, journal = {Journal of the American Society for Information Science and Technology}, year = {2009}, volume = {60}, number = {12}, pages = {2530-2539}, doi = {10.1002/asi.21170} }
1 Publication internationale Raaf, H; Abdeddaïm, S & Messabih, B. Petri Nets for Modelling and Decomposition of Metabolic Network. International Review on Computers and Software , May, 2009.
Abstract: One model to present the metabolic networks is defined. This model based on Petri Nets (PNs), represents the metabolic network in qualitative manner and offers an appropriate expression to the structural analysis. The related previous works consist in using the PNs for simulating. A detailed qualitative analysis should be done before a quantitative (kinetic) analysis is made. This paper firstly extend construction strategy of Petri net model in considering data types in places( internal or external metabolite) and the types of transitions(reversible or irreversible reaction) to allow pathway analysis. Secondly, as pathway analysis of large metabolic networks meets with the problem of combinatorial explosion of pathways we propose to deconstruct metabolic networks into subnetworks based on the global network structure. So we propose to use a centrality measure based on shortest paths linking. To do this we give a new definition of reactions graph as a depending graph.
BibTeX: @article{Raaf2009, author = {Raaf, H and Abdeddaïm, S and Messabih, B}, title = {Petri Nets for Modelling and Decomposition of Metabolic Network}, month = {May}, journal = {International Review on Computers and Software}, year = {2009}, url = {http://www.praiseworthyprize.com/IRECOS_latest.html#Petri_Nets_for_Modelling_and__Decomposition_of_Metabolic_Network} }
1 Publication internationale Rollin, L; Darmoni, SJ; Caillard, JF & Gehanno, JF. Fate of abstracts presented at the ICOH International Meeting: are they followed by publication in peer-reviewed journals?. Scandinavian Journal of Work, Environment & Health , Volume 35, Number 6, Pages 461-465, 2009.
BibTeX: @article{Rollin2009a, author = {Rollin, L and Darmoni, SJ and Caillard, JF and Gehanno, JF}, title = {Fate of abstracts presented at the ICOH International Meeting: are they followed by publication in peer-reviewed journals?}, journal = {Scandinavian Journal of Work, Environment \& Health}, year = {2009}, volume = {35}, number = {6}, pages = {461-465}, url = {http://www.sjweh.fi/show_abstract.php?abstract_id=1362}, doi = {10.5271/sjweh.1362} }
1 Publication internationale Salson, M; Lecroq, T; Léonard, M & Mouchard, L. Dynamic Burrows-Wheeler Transform. Theoretical Computer Science , Volume 410, Number 43, Pages 4350-4359, 2009.
BibTeX: @article{Salson2009, author = {Salson, M and Lecroq, T and Léonard, M and Mouchard, L}, title = {Dynamic Burrows-Wheeler Transform}, journal = {Theoretical Computer Science}, year = {2009}, volume = {410}, number = {43}, pages = {4350-4359}, doi = {10.1016/j.tcs.2009.07.016} }
1 Publication internationale Sibert, L; Giorgi, R; Dahamna, B; Doucet, J; Charlin, B & Darmoni, SJ. Is a Web-based Concordance test feasible to assess therapeutic decision-making skills in a French context?. Medical Teacher , April, Volume 31, Number 4, Pages 162-8, 2009.
BibTeX: @article{Sibert2009, author = {Sibert, L and Giorgi, R and Dahamna, B and Doucet, J and Charlin, B and Darmoni, SJ}, title = {Is a Web-based Concordance test feasible to assess therapeutic decision-making skills in a French context?}, month = {April}, journal = {Medical Teacher}, year = {2009}, volume = {31}, number = {4}, pages = {162-8}, doi = {10.1080/01421590802572783} }
1 Publication internationale Séralini, Gilles-Eric; de Vendômois, Joël Spiroux; Cellier, Dominique; Sultan, Charles; Buiatti, Marcello; Gallagher, Lou; Antoniou, Michael & Dronamraju, Krishna R. How subchronic and chronic health effects can be neglected for GMOs, pesticides or chemicals. International Journal of Biological Sciences , Volume 5, Number 5, Pages 438-443, 2009.
Abstract: Chronic health effects are increasing in the world such as cancers, hormonal, reproductive, nervous, or immune diseases, even in young people. During regulatory toxicological subchronic tests to prevent these on mammalian health, prior commercialization of chemicals, including pesticides and drugs, or GMOs, some statistically significant findings may be revealed. This discussion is about the need to investigate the relevant criteria to consider those as biologically significant. The sex differences and the non linear dose or time related effects should be considered in contrast to the claims of a Monsanto-supported expert panel about a GMO, the MON 863 Bt maize, but also for pesticides or drugs, in particular to reveal hormone-dependent diseases and first signs of toxicities.
BibTeX: @article{seralini_how_2009, author = {Séralini, {Gilles-Eric} and de Vendômois, Joël Spiroux and Cellier, Dominique and Sultan, Charles and Buiatti, Marcello and Gallagher, Lou and Antoniou, Michael and Dronamraju, Krishna R}, title = {How subchronic and chronic health effects can be neglected for {GMOs}, pesticides or chemicals}, journal = {International Journal of Biological Sciences}, year = {2009}, volume = {5}, number = {5}, pages = {438--443}, url = {http://www.biolsci.org/v05p0438.htm}, doi = {10.7150/ijbs.5.438} }
1 Publication internationale de Vendômois, Joël Spiroux; Roullier, François; Cellier, Dominique & Séralini, Gilles-Eric. A comparison of the effects of three GM corn varieties on mammalian health. International Journal of Biological Sciences , Volume 5, Number 7, Pages 706-726, 2009.
Abstract: We present for the first time a comparative analysis of blood and organ system data from trials with rats fed three main commercialized genetically modified (GM) maize (NK 603, MON 810, MON 863), which are present in food and feed in the world. NK 603 has been modified to be tolerant to the broad spectrum herbicide Roundup and thus contains residues of this formulation. MON 810 and MON 863 are engineered to synthesize two different Bt toxins used as insecticides. Approximately 60 different biochemical parameters were classified per organ and measured in serum and urine after 5 and 14 weeks of feeding. GM maize-fed rats were compared first to their respective isogenic or parental non-GM equivalent control groups. This was followed by comparison to six reference groups, which had consumed various other non-GM maize varieties. We applied nonparametric methods, including multiple pairwise comparisons with a False Discovery Rate approach. Principal Component Analysis allowed the investigation of scattering of different factors (sex, weeks of feeding, diet, dose and group). Our analysis clearly reveals for the 3 GMOs new side effects linked with GM maize consumption, which were sex- and often dose-dependent. Effects were mostly associated with the kidney and liver, the dietary detoxifying organs, although different between the 3 GMOs. Other effects were also noticed in the heart, adrenal glands, spleen and haematopoietic system. We conclude that these data highlight signs of hepatorenal toxicity, possibly due to the new pesticides specific to each GM corn. In addition, unintended direct or indirect metabolic consequences of the genetic modification cannot be excluded.
BibTeX: @article{de_vendomois_comparison_2009, author = {de Vendômois, Joël Spiroux and Roullier, François and Cellier, Dominique and Séralini, {Gilles-Eric}}, title = {A comparison of the effects of three {GM} corn varieties on mammalian health}, journal = {International Journal of Biological Sciences}, year = {2009}, volume = {5}, number = {7}, pages = {706--726}, url = {http://www.biolsci.org/v05p0706.htm}, doi = {10.7150/ijbs.5.706} }
2 Publication nationale Darmoni, SJ; Ladner, J; Devos, P & Gehanno, JF. Robustesse du score SIGAPS, critère bibliométrique majeur pour l'enveloppe MERRI des CHU. Presse Med , Jul-Aug, Volume 38, Number 7-8, Pages 1056-61, 2009.
Abstract: SIGAPS is a bibliometric score that aims at making an inventory, evaluating and promoting scientific publications of hospitals that perform research. It has become a major stake in France since it is one of the most important components of the MERRI (Mission Training, Research, Reference and Innovation) founding of hospitals. This score is based on the points attributed to the authors of articles published in journals indexed in Medline, according to the rank of the authors and the Impact Factor of the journal. OBJECTIVES: to compare the reliability of the score when applying different way of computing it, and different weights for the rank or the Impact Factor. MATERIAL AND METHODS: we computed the scores of all the physicians of a University Hospital, using the rules that are actually applied at the national level. We then used 4 different scenarios, with different weight given to the rank of authors or the Impact Factor. We compared the scores obtained by each author according to the different scenarios with the Spearman's rank and Pearson's correlation coefficients. RESULTS: The score is not significantly affected when no points are given to the fourth authors and above, when the last author get more points or to change the points according to the Impact Factor of the journal. CONCLUSION: The different scenarios do not lead to significant changes for the physicians' scores, and therefore for the cumulated score of the hospital. Despite the well known limits of bibliometric indicators, the SIGAPS score appears reliable to compare the hospitals for founding decisions.
BibTeX: @article{Darmoni2009, author = {Darmoni, SJ and Ladner, J and Devos, P and Gehanno, JF}, title = {Robustesse du score SIGAPS, critère bibliométrique majeur pour l'enveloppe MERRI des CHU}, month = {Jul-Aug}, journal = {Presse Med}, year = {2009}, volume = {38}, number = {7-8}, pages = {1056-61}, url = {http://dx.doi.org/10.1016/j.lpm.2009.03.011}, doi = {10.1016/j.lpm.2009.03.011} }
2 Publication nationale Gehanno, JF; Kerdelhue, G; Darmoni, SJ; Fantoni, S; Frimat, P & Caillard, JF. Veille documentaire en santé au travail des personnels de santé. Archives des Maladies Professionnelles et de l'Environnement , Février, Volume 70, Pages 43-47, 2009.
BibTeX: @article{Gehanno2008a, author = {Gehanno, JF and Kerdelhue, G and Darmoni, SJ and Fantoni, S and Frimat, P and Caillard, JF}, title = {Veille documentaire en santé au travail des personnels de santé}, month = {Février}, journal = {Archives des Maladies Professionnelles et de l'Environnement}, year = {2009}, volume = {70}, pages = {43-47}, url = {http://www.sciencedirect.com/science/article/B8JFG-4V4M33G-1/2/0f2dccbfd9fa5b927ae379c705b567ba}, doi = {10.1016/j.admp.2008.10.020} }
2 Publication nationale Hervé Nabarette; François Romaneix; Célia Boyer; Stéphan Jacques Darmoni; Pierre-Louis Rémy & Etienne Caniard. Certification des sites dédiés à la santé en France.. Presse Med , Aug, 2009.
Abstract: The 2004 statute that created the French National Authority for Health (HAS, Haute Autorité de Santé) required it to establish a procedure for the certification of health-related web sites. The HAS established a procedure based on the HONcode certification scheme set up by the Health On the Net Foundation, with which HAS has a partnership agreement. The HONcode includes eight principles that govern the quality of online heath information and its presentation (quality of the production process). The collaboration between HAS and HON has already led to improvements in a large number of web sites in France and to their certification. The main advantages of certification for site publishers are better site quality and enhanced credibility rather than a larger audience. Quality certification has little impact on the choice of site by Internet users as they tend to use search engines to find health-related information. Future development of the procedure should work to increase the value of certification both by improving the quality of sites and in signaling quality to Internet users.
BibTeX: @article{Nabarette2009, author = {Hervé Nabarette and François Romaneix and Célia Boyer and Stéphan Jacques Darmoni and Pierre-Louis Rémy and Etienne Caniard}, title = {Certification des sites dédiés à la santé en France.}, month = {Aug}, journal = {Presse Med}, year = {2009}, url = {http://www.hon.ch/Conf/Docs/PresseMedicale_10/Article10.pdf}, doi = {10.1016/j.lpm.2009.06.008} }
2 Publication nationale Pauchet, A; El Abed, M; Merabti, T; Prieur, E; Lecroq, T & Darmoni, SJ. Identification de répétitions dans les navigations au sein d'un catalogue de santé. RIA (Revue d'Intelligence Artificielle) , Volume 23, Number 1, Pages 113-132, 2009.
BibTeX: @article{Pauchet, author = {Pauchet, A and El Abed, M and Merabti, T and Prieur, E and Lecroq, T and Darmoni, SJ}, title = {Identification de répétitions dans les navigations au sein d'un catalogue de santé}, journal = {RIA (Revue d'Intelligence Artificielle)}, year = {2009}, volume = {23}, number = {1}, pages = {113-132}, url = {http://ria.revuesonline.com/article.jsp?articleId=12858}, doi = {10.3166/ria.23.113-132} }
2 Publication nationale Sakji, S; Thirion, B; Dahamna, B & Darmoni, SJ. Recherche des sources d'information institutionnelle de santé françaises Le site Internet CISMeF. Presse Médicale , Octobre, Volume 38, Number 10, Pages 1443-1450, 2009.
BibTeX: @article{Sakji2009a, author = {Sakji, S and Thirion, B and Dahamna, B and Darmoni, SJ}, title = {Recherche des sources d'information institutionnelle de santé françaises Le site Internet CISMeF}, month = {Octobre}, journal = {Presse Médicale}, year = {2009}, volume = {38}, number = {10}, pages = {1443-1450}, doi = {10.1016/j.lpm.2009.05.014} }
2 Publication nationale Salson, M. Structures d'indexation compressées et dynamiques pour le texte. School: Université de Rouen, France, 2009.
BibTeX: @phdthesis{Salson2009b, author = {Salson, M}, title = {Structures d'indexation compressées et dynamiques pour le texte}, school = {Université de Rouen, France}, year = {2009} }
3 Communication internationale Beuscart, R; McNair, P; Darmoni, SJ; Koutkia, V; Maglaveras, N; Beuscart-Zephir, MC & Nohr, C. Patient safety: detection and prevention of adverse drug events.. Stud Health Technol Inform MIE2009, Volume 150, Pages 968-971, IOS Press, 2009.
Abstract: Adverse Drug Events (ADE) represent a key problem in Public Health. The detection and prevention of ADE is a real challenge for hospitals and healthcare professionals. Healthcare Information and Communication Technologies can contribute to reduce the incidence of preventable ADE. During this workshop, we will discuss the various aspects of detection of ADE through methods like data and semantic mining in medical databases; the possibility of preventing ADE by using clinical decision support systems; the importance of Human Factors Engineering and the contextualization of knowledge. Examples and demonstrations will come from the European Project PSIP, devoted to the detection and prevention of ADE in Hospitals.
BibTeX: @inproceedings{Beuscart2009, author = {Beuscart, R and McNair, P and Darmoni, SJ and Koutkia, V and Maglaveras, N and Beuscart-Zephir, MC and Nohr, C}, title = {Patient safety: detection and prevention of adverse drug events.}, booktitle = {MIE2009}, journal = {Stud Health Technol Inform}, publisher = {IOS Press}, year = {2009}, volume = {150}, pages = {968--971}, doi = {10.3233/978-1-60750-044-5-968} }
3 Communication internationale Darmoni, SJ; Joubert, M; Dahamna, B; Delahousse, J & Fieschi, M. SMTS: a French Health Multi-terminology Server. AMIA symp., Pages 808, IOS Press, 2009. InterSTIS.
BibTeX: @inproceedings{Darmoni2009b, author = {Darmoni, SJ and Joubert, M and Dahamna, B and Delahousse, J and Fieschi, M}, title = {SMTS: a French Health Multi-terminology Server}, booktitle = {AMIA symp.}, publisher = {IOS Press}, year = {2009}, pages = {808}, note = {InterSTIS} }
3 Communication internationale Darmoni, SJ; Sakji, S; Pereira, S; Merabti T; Prieur E; Joubert M & Thirion B. Multiple terminologies in an health portal: automatic indexing and information retrieval. Artificial Intelligence in Medicine, Verona, Italy, July, Lecture Notes in Computer Science, Pages 255-259, Springer, 2009. PSIP. InterSTIS.
Abstract: Background: In the specific context of developing quality-controlled health gateways, several standards must be respected (e.g. Dublin Core for metadata element set; thesaurus MeSH as the controlled vocabulary to index Internet resources; HON code to accredit quality of health Web sites). These standards were applied to create the CISMeF Web site (French acronym for Catalog & Index of Health Internet resources in French). Objective: In this work, the strategic shift of the CISMeF team is intended to index and retrieve French resources not anymore with a single terminology (MeSH thesaurus) but with the main health terminologies available in French (ICD 10, SNOMED International, CCAM, ATC). Methods & Results: Since 2005, we have developed the French Multi-Terminology Indexer (F-MTI), using a multi-terminology approach and mappings between health terminologies. This tool is used for automatic indexing and information retrieval. Conclusion: Since the last quarter of 2008, F-MTI is daily used in the CISMeF production environment and is connected to a French Health Multi-Terminology Server.
BibTeX: @inproceedings{Darmoni2009a, author = {Darmoni, SJ and Sakji, S and Pereira, S and Merabti T and Prieur E and Joubert M and Thirion B}, title = {Multiple terminologies in an health portal: automatic indexing and information retrieval}, booktitle = {Artificial Intelligence in Medicine}, address = {Verona, Italy}, month = {July}, publisher = {Springer}, year = {2009}, series = {Lecture Notes in Computer Science}, pages = {255-259}, note = {PSIP. InterSTIS}, doi = {10.1007/978-3-642-02976-9_37} }
3 Communication internationale Durieux, V & Kerdelhué, G. Access to health information on the Internet: can social bookmarking systems replace expert gateways?. Workshop EAHIL, Dublin, Ireland, June, 2009.
BibTeX: @inproceedings{Durieux2009, author = {Durieux, V and Kerdelhué, G}, title = {Access to health information on the Internet: can social bookmarking systems replace expert gateways?}, booktitle = {Workshop EAHIL}, address = {Dublin, Ireland}, month = {June}, year = {2009}, url = {http://www.eahil2009.ie/images/Eahil/Images/papers/fri8/durieux_paper.pdf} }
3 Communication internationale Gehanno, JF, Kerdelhué, G Darmoni, SJ. Relevance of Google Customized Search Engine vs. CISMeF Quality-Controlled Health Gateway. Stud Health Technol Inform MIE2009, Volume 150, Pages 312-6, 2009.
BibTeX: @inproceedings{Gehanno2009a, author = {Gehanno, JF, Kerdelhué, G Darmoni, SJ}, title = {Relevance of Google Customized Search Engine vs. CISMeF Quality-Controlled Health Gateway}, booktitle = {MIE2009}, journal = {Stud Health Technol Inform}, year = {2009}, volume = {150}, pages = {312-6}, doi = {10.3233/978-1-60750-044-5-312} }
3 Communication internationale Joubert, M; Abdoune, H; Merabti, T; Darmoni, SJ & Fieschi, M. Assisting the Translation of SNOMED CT into French using UMLS and four Representative French-language Terminologies. AMIA symp., Pages 291-295, IOS Press, 2009. InterSTIS.
BibTeX: @inproceedings{Joubert2009a, author = {Joubert, M and Abdoune, H and Merabti, T and Darmoni, SJ and Fieschi, M}, title = {Assisting the Translation of SNOMED CT into French using UMLS and four Representative French-language Terminologies}, booktitle = {AMIA symp.}, publisher = {IOS Press}, year = {2009}, pages = {291-295}, note = {InterSTIS} }
3 Communication internationale Merabti, Tand Letord, C; Abdoune, H; Lecroq, T; Joubert, M & Darmoni, SJ. Projection and inheritance of SNOMED CT Relations between MeSH Terms. Stud Health Technol Inform MIE2009, Volume 150, Pages 233-7, IOS Press, 2009. InterSTIS.
BibTeX: @inproceedings{Merabti2009a, author = {Merabti, Tand Letord, C and Abdoune, H and Lecroq, T and Joubert, M and Darmoni, SJ}, title = {Projection and inheritance of SNOMED CT Relations between MeSH Terms}, booktitle = {MIE2009}, journal = {Stud Health Technol Inform}, publisher = {IOS Press}, year = {2009}, volume = {150}, pages = {233-7}, note = {InterSTIS}, doi = {10.3233/978-1-60750-044-5-233} }
3 Communication internationale Pereira, S; Plaisantin, B; Korchi, M; Rozanes, N; Serrot, E; Joubert, M & Darmoni, SJ. Automatic construction of dictionnaries, application to product characteristics indexing. Stud Health Technol Inform MIE2009, Volume 150, Pages 512-6, IOS Press, 2009.
Abstract: Summary of Product Characteristics (SPC) indexing enables to extract all the information needed to analyze a prescription and find some inappropriate medications. We evaluate a French Multi-Terminology Indexer tool (F-MTI) for SPC automatic indexing. This tool uses a dictionary containing the textual forms that are likely to appear in natural language text for the drug clinical particular terms contained in the Vidal thesaurus (TUV). We developed a method to automatically generate this dictionary. The evaluation showed a precision of 52.9% and a recall of 46.2%. F-MTI will be integrated in a semi-automatic indexing tool.
BibTeX: @inproceedings{Pereira2009a, author = {Pereira, S and Plaisantin, B and Korchi, M and Rozanes, N and Serrot, E and Joubert, M and Darmoni, SJ}, title = {Automatic construction of dictionnaries, application to product characteristics indexing}, booktitle = {MIE2009}, journal = {Stud Health Technol Inform}, publisher = {IOS Press}, year = {2009}, volume = {150}, pages = {512-6}, doi = {10.3233/978-1-60750-044-5-512} }
3 Communication internationale Pereira, S; Sakji, S; Névéol, A; Kergoulay, I; Kerdelhué, G; Serrot, E; Joubert, M & Darmoni SJ. Multi-terminology indexing for the assignment of MeSH descriptors to medical abstracts in French. AMIA symp., Pages 521-525, IOS Press, 2009. PSIP.
BibTeX: @inproceedings{Pereira2009b, author = {Pereira, S and Sakji, S and Névéol, A and Kergoulay, I and Kerdelhué, G and Serrot, E and Joubert, M and Darmoni SJ}, title = {Multi-terminology indexing for the assignment of MeSH descriptors to medical abstracts in French}, booktitle = {AMIA symp.}, publisher = {IOS Press}, year = {2009}, pages = {521-525}, note = {PSIP} }
3 Communication internationale Proux, Denys; Marchal, Pierre; Segond, Frédérique; Kergourlay, Ivan; Darmoni, Stéfan; Pereira, Suzanne; Gicquel, Quentin & Metzger, Marie Hélène. Natural Language Processing to Detect Risk Patterns Related to Hospital Acquired Infections. Proceedings of the Workshop on Biomedical Information Extraction, Borovets, Bulgaria, September, Pages 35-41, Association for Computational Linguistics, 2009.
BibTeX: @inproceedings{proux-EtAl:2009:BiomedicalIE, author = {Proux, Denys and Marchal, Pierre and Segond, Fr\'{e}d\'{e}rique and Kergourlay, Ivan and Darmoni, St\'{e}fan and Pereira, Suzanne and Gicquel, Quentin and Metzger, Marie H\'{e}l\`{e}ne}, title = {Natural Language Processing to Detect Risk Patterns Related to Hospital Acquired Infections}, booktitle = {Proceedings of the Workshop on Biomedical Information Extraction}, address = {Borovets, Bulgaria}, month = {September}, publisher = {Association for Computational Linguistics}, year = {2009}, pages = {35--41}, url = {http://www.aclweb.org/anthology/W09-4506} }
3 Communication internationale Sakji, S; Dirieh Dibad, AD; Kergourlay, I; Joubert, M & Darmoni, SJ. Information Retrieval in Context Using Various Health Terminologies. RCIS, International Conference on Research Challenges in Information Science, Fez, Morocco, April, Pages 453-458, IEEE, 2009. PSIP.
BibTeX: @inproceedings{Sakji2009, author = {Sakji, S and Dirieh Dibad, AD and Kergourlay, I and Joubert, M and Darmoni, SJ}, title = {Information Retrieval in Context Using Various Health Terminologies}, booktitle = {RCIS, International Conference on Research Challenges in Information Science}, address = {Fez, Morocco}, month = {April}, publisher = {IEEE}, year = {2009}, pages = {453-458}, note = {PSIP}, doi = {10.1109/RCIS.2009.5089310} }
3 Communication internationale Sakji, S; Letord, C; Dahamna, B; Kergourlay, I; Pereira, S; Joubert, M & Darmoni, SJ. Automatic indexing in a drug information portal.. Stud Health Technol Inform , Volume 148, Pages 112-122, IOS Press, 2009. PSIP.
Abstract: Objective: The objective of this work is to create a bilingual (French/English) Drug Information Portal (DIP), in a multi-terminological context and to emphasize its exploitation by an ATC automatic indexing allowing having more pertinent information about substances, organs or systems on which drugs act and their therapeutic and chemical characteristics. Methods: 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 and uses specific drugs terminologies such as the ATC classification which used to automatic index the DIP resources. Results: DIP is the result of collaboration between the CISMeF team and the VIDAL Company, specialized in drug information. DIP is conceived to facilitate the user information retrieval. The ATC automatic indexing provided relevant results in 76% of cases. Conclusion: Using multi-terminological context and in the framework of the drug field, indexing drugs with the appropriate codes or/and terms revealed to be very important to have the appropriate information storage and retrieval. The main challenge in the coming year is to increase the accuracy of the approach.
BibTeX: @inproceedings{Sakji2009c, author = {Sakji, S and Letord, C and Dahamna, B and Kergourlay, I and Pereira, S and Joubert, M and Darmoni, SJ}, title = {Automatic indexing in a drug information portal.}, journal = {Stud Health Technol Inform}, publisher = {IOS Press}, year = {2009}, volume = {148}, pages = {112--122}, note = {PSIP}, doi = {10.3233/978-1-60750-043-8-112} }
3 Communication internationale Sakji, S; Letord, C; Pereira , S; Dahamna, B; Joubert, M & Darmoni, SJ. Drug Information Portal in Europe: information retrieval with multiple health terminologies. Stud Health Technol Inform MIE2009, Volume 150, Pages 497-501, IOS Press, 2009. PSIP..
BibTeX: @inproceedings{Sakji2009b, author = {Sakji, S and Letord, C and Pereira , S and Dahamna, B and Joubert, M and Darmoni, SJ}, title = {Drug Information Portal in Europe: information retrieval with multiple health terminologies}, booktitle = {MIE2009}, journal = {Stud Health Technol Inform}, publisher = {IOS Press}, year = {2009}, volume = {150}, pages = {497-501}, note = {PSIP.}, doi = {10.3233/978-1-60750-044-5-497} }
3 Communication internationale Thirion, B; Robu, I & Darmoni, SJ. Optimization of the PubMed Automatic Term Mapping. Stud Health Technol Inform MIE2009, Volume 150, Pages 238-42, 2009.
BibTeX: @inproceedings{Thirion2009, author = {Thirion, B and Robu, I and Darmoni, SJ}, title = {Optimization of the PubMed Automatic Term Mapping}, booktitle = {MIE2009}, journal = {Stud Health Technol Inform}, year = {2009}, volume = {150}, pages = {238-42}, doi = {10.3233/978-1-60750-044-5-238} }
4 Communication nationale Chanoni, E; Lecroq, T & Pauchet, A. Extraction de motifs dans des dialogues annotés par programmation dynamique. Actes des Cinquièmes Journées Francophones Modèles Formels de l'Interaction, Lannion, France, Pages 101-112, 2009.
BibTeX: @inproceedings{Chanoni2009, author = {Chanoni, E and Lecroq, T and Pauchet, A}, title = {Extraction de motifs dans des dialogues annotés par programmation dynamique}, booktitle = {Actes des Cinquièmes Journées Francophones Modèles Formels de l'Interaction}, address = {Lannion, France}, year = {2009}, pages = {101--112} }
4 Communication nationale Dirieh Dibad, AD; Sakji, S; Prieur, E; Pereira, S; Joubert, M & Darmoni, SJ. Recherche d'information multi-terminologique en contexte : Etude préliminaire. Risques, technologies de l'information pour les pratiques médicales : comptes rendus des treizièmes journées francophones d'informatique médicale (JFIM), Nice, France, Avril, Informatique et santé, Volume 17, Pages 101-112, Springer, 2009. PSIP.
BibTeX: @inproceedings{Dirieh2009, author = {Dirieh Dibad, AD and Sakji, S and Prieur, E and Pereira, S and Joubert, M and Darmoni, SJ}, title = {Recherche d'information multi-terminologique en contexte : Etude préliminaire}, booktitle = {Risques, technologies de l'information pour les pratiques médicales : comptes rendus des treizièmes journées francophones d'informatique médicale (JFIM)}, address = {Nice, France}, month = {Avril}, publisher = {Springer}, year = {2009}, series = {Informatique et santé}, volume = {17}, pages = {101-112}, note = {PSIP}, url = {http://www.springerlink.com/content/p582765854143840/}, doi = {10.1007/978-2-287-99305-3_10} }
4 Communication nationale Faro, S & Lecroq, T. An efficient matching algorithm for encoded DNA sequences and binary strings. Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching CPM'09, Lille, France, Lecture Notes in Computer Science, Number 5577, Pages 106-155, Springer-Verlag, 2009.
Abstract: We present a new efficient algorithm for exact matching in encoded DNA sequences and on binary strings. Our algorithm combines a multi-pattern version of the Bndm algorithm and a simplified version of the Commentz-Walter algorithm. We performed also experimental comparisons with the most efficient algorithms presented in the literature. Experimental results show that the newly presented algorithm outperforms existing solutions in most cases.
BibTeX: @inproceedings{Faro2009b, author = {Faro, S and Lecroq, T}, title = {An efficient matching algorithm for encoded DNA sequences and binary strings}, booktitle = {Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching CPM'09}, address = {Lille, France}, publisher = {Springer-Verlag}, year = {2009}, series = {Lecture Notes in Computer Science}, number = {5577}, pages = {106-155}, doi = {10.1007/978-3-642-02441-2_10} }
4 Communication nationale Harris, EY; Lecroq, Y; Kucherov, G & Lonardi, S. CPM's 20th anniversary: a statistical retrospective. Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching CPM'09, Lille, France, Lecture Notes in Computer Science, Number 5577, Pages 1-11, Springer-Verlag, 2009.
Abstract: This year the Annual Symposiumon Combinatorial Pattern Matching (CPM) celebrates its 20th anniversary. Over the last two decades the Symposium has established itself as the most recognized international forum for research in combinatorial pattern matching and related applications. Contributions to the conference typically address issues of searching and matching strings and more complex patterns such as trees, regular expressions, graphs, point sets, and arrays. Advances in this field rely on the ability to expose combinatorial properties of the computational problem at hand and to exploit these properties in order to either achieve superior performance or identify conditions underwhich searches cannot be performed efficiently. The meeting also dealswith combinatorial problems in computational biology, data compression, data mining, coding, information retrieval, natural language processing and pattern recognition.
BibTeX: @inproceedings{Harris2009, author = {Harris, EY and Lecroq, Y and Kucherov, G and Lonardi, S}, title = {CPM's 20th anniversary: a statistical retrospective}, booktitle = {Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching CPM'09}, address = {Lille, France}, publisher = {Springer-Verlag}, year = {2009}, series = {Lecture Notes in Computer Science}, number = {5577}, pages = {1-11}, doi = {10.1007/978-3-642-02441-2_1} }
4 Communication nationale Joubert, M; Dahamna, B; Delahousse, J; Fieschi, M & Darmoni SJ. SMTS® : Un Serveur Multi-Terminologies de Santé. Risques, technologies de l'information pour les pratiques médicales : comptes rendus des treizièmes journées francophones d'informatique médicale (JFIM), Nice, France, Avril, Informatique et santé, Volume 17, Pages 47-56, 2009. InterSTIS.
BibTeX: @inproceedings{Joubert2009, author = {Joubert, M and Dahamna, B and Delahousse, J and Fieschi, M and Darmoni SJ}, title = {SMTS® : Un Serveur Multi-Terminologies de Santé}, booktitle = {Risques, technologies de l'information pour les pratiques médicales : comptes rendus des treizièmes journées francophones d'informatique médicale (JFIM)}, address = {Nice, France}, month = {Avril}, year = {2009}, series = {Informatique et santé}, volume = {17}, pages = {47-56}, note = {InterSTIS}, url = {http://www.springerlink.com/content/v32879v42214l1r3}, doi = {10.1007/978-2-287-99305-3_5} }
4 Communication nationale Merabti, T; Abdoune, H; Lecroq, T; Joubert, M & Darmoni, SJ. Projection des relations SNOMED CT entre les termes de deux terminologies (CIM10 et SNOMED 3.5). Risques, technologies de l'information pour les pratiques médicales : comptes rendus des treizièmes journées francophones d'informatique médicale (JFIM), Nice, France, Avril, Informatique et santé, Volume 17, Pages 79-88, 2009. InterSTIS.
BibTeX: @inproceedings{Merabti2009, author = {Merabti, T and Abdoune, H and Lecroq, T and Joubert, M and Darmoni, SJ}, title = {Projection des relations SNOMED CT entre les termes de deux terminologies (CIM10 et SNOMED 3.5)}, booktitle = {Risques, technologies de l'information pour les pratiques médicales : comptes rendus des treizièmes journées francophones d'informatique médicale (JFIM)}, address = {Nice, France}, month = {Avril}, year = {2009}, series = {Informatique et santé}, volume = {17}, pages = {79-88}, note = {InterSTIS}, url = {http://www.springerlink.com/content/g817q31010448324}, doi = {10.1007/978-2-287-99305-3_8} }
4 Communication nationale Merabti, T & Darmoni SJ. Web sémantique au sein de CISMeF. i-expo, salon de l'information numérique, Juin, 2009.
BibTeX: @inproceedings{Merabti2009b, author = {Merabti, T and Darmoni SJ}, title = {Web sémantique au sein de CISMeF}, booktitle = {i-expo, salon de l'information numérique}, month = {Juin}, year = {2009} }
4 Communication nationale Pereira, S; Massari, P; Buemi, A; Dahamna, B; Serrot, E; Joubert, M & Darmoni SJ. F-MTI : outil d'indexation multi-terminologique : application à l'indexation automatique de la SNOMED. Risques, technologies de l'information pour les pratiques médicales : comptes rendus des treizièmes journées francophones d'informatique médicale (JFIM), Nice, France, Avril, Informatique et santé, Volume 17, Pages 57-67, 2009.
BibTeX: @inproceedings{Pereira2009, author = {Pereira, S and Massari, P and Buemi, A and Dahamna, B and Serrot, E and Joubert, M and Darmoni SJ}, title = {F-MTI : outil d'indexation multi-terminologique : application à l'indexation automatique de la SNOMED}, booktitle = {Risques, technologies de l'information pour les pratiques médicales : comptes rendus des treizièmes journées francophones d'informatique médicale (JFIM)}, address = {Nice, France}, month = {Avril}, year = {2009}, series = {Informatique et santé}, volume = {17}, pages = {57-67}, url = {http://www.springerlink.com/content/q673u2tp56124t63}, doi = {10.1007/978-2-287-99305-3_6} }
5 Résumé Faro, S & Lecroq, T. Efficient Pattern Matching on Binary Strings. SOFSEM, 2009.
BibTeX: @inproceedings{Faro2009, author = {Faro, S and Lecroq, T}, title = {Efficient Pattern Matching on Binary Strings}, booktitle = {SOFSEM}, year = {2009} }
5 Résumé Letord, C; Sakji, S; Pereira, S; Dahamna, B; Kergoulay, I & Darmoni, SJ. A Drug Information Portal in Europe. AMIA symp., Pages 931, IOS Press, 2009. PSIP.
BibTeX: @inproceedings{Letord2009, author = {Letord, C and Sakji, S and Pereira, S and Dahamna, B and Kergoulay, I and Darmoni, SJ}, title = {A Drug Information Portal in Europe}, booktitle = {AMIA symp.}, publisher = {IOS Press}, year = {2009}, pages = {931}, note = {PSIP} }
5 Résumé Metzger, MH; Gicquel, Q; Proux, D; Pereira, S; Kergoulay, I; Serrot, E; Segond, F & Darmoni SJ. Development of an Automated Detection Tool for Health Care-Associated Infections Based on Screening Natural Language Medical Reports.. AMIA symp., Pages 967, IOS Press, 2009. ALADIN.
BibTeX: @inproceedings{Metzger2009, author = {Metzger, MH and Gicquel, Q and Proux, D and Pereira, S and Kergoulay, I and Serrot, E and Segond, F and Darmoni SJ}, title = {Development of an Automated Detection Tool for Health Care-Associated Infections Based on Screening Natural Language Medical Reports.}, booktitle = {AMIA symp.}, publisher = {IOS Press}, year = {2009}, pages = {967}, note = {ALADIN} }
5 Résumé Rollin, L; Darmoni, S; Caillard, JF & Gehanno, JF. Fate of abstracts presented at the ICOH International Meetings: are they followed by publication in peer-reviewed journals?. ICOH 2009 congress, 2009.
BibTeX: @inproceedings{Rollin2009, author = {Rollin, L and Darmoni, S and Caillard, JF and Gehanno, JF}, title = {Fate of abstracts presented at the ICOH International Meetings: are they followed by publication in peer-reviewed journals?}, booktitle = {ICOH 2009 congress}, year = {2009} }
5 Résumé Sibert, L; Dahamna, B; Doré, B & Darmoni SJ. Le test de concordance en urologie : du format papier à l'application en ligne. Pédagogie Médicale , Volume 10, Number Suppl. 1, 2009.
BibTeX: @article{Sibert2009a, author = {Sibert, L and Dahamna, B and Doré, B and Darmoni SJ}, title = {Le test de concordance en urologie : du format papier à l'application en ligne}, journal = {Pédagogie Médicale}, year = {2009}, volume = {10}, number = {Suppl. 1}, doi = {10.1051/pmed/20099993} }
2008 1 Publication internationale Crochemore, M & Lecroq, T. Sequential Multiple String Matching. Encyclopedia of Algorithms, Pages 826-829, Springer Verlag, 2008.
BibTeX: @incollection{Crochemore2008a, author = {Crochemore, M and Lecroq, T}, title = {Sequential Multiple String Matching}, booktitle = {Encyclopedia of Algorithms}, publisher = {Springer Verlag}, year = {2008}, pages = {826--829} }
1 Publication internationale Crochemore, M & Lecroq, T. Sequential Exact String Matching. Encyclopedia of Algorithms, Pages 824-826, Springer Verlag, 2008.
BibTeX: @incollection{Crochemore2008b, author = {Crochemore, M and Lecroq, T}, title = {Sequential Exact String Matching}, booktitle = {Encyclopedia of Algorithms}, publisher = {Springer Verlag}, year = {2008}, pages = {824--826} }
1 Publication internationale Crochemore, M & T. Lecroq, T. Alignments and Approximate String Matching. New Developments in Formal Languages and Applications, Studies in Computational Intelligence, Volume 113, Pages 59-93, Springer Verlag Berlin, 2008.
BibTeX: @incollection{Crochemore2008, author = {Crochemore, M and T. Lecroq, T}, title = {Alignments and Approximate String Matching}, booktitle = {New Developments in Formal Languages and Applications}, publisher = {Springer Verlag Berlin}, year = {2008}, series = {Studies in Computational Intelligence}, volume = {113}, pages = {59--93}, url = {http://springerlink.com/content/l872835380820687/?p=7706254dc0b246918bc8109ff852f7c5&pi=2}, doi = {10.1007/978-3-540-78291-9_3} }
1 Publication internationale Faro, S & Lecroq, T. Efficient Pattern Matching on Binary Strings. Rapport arXiv:0810.2390 , Oct, 2008.
Abstract: The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in telecom and computer network applications. Moreover the problem finds applications also in the field of image processing and in pattern matching on compressed texts. Recently it has been shown that adaptations of classical exact string matching algorithms are not very efficient on binary data. In this paper we present two efficient algorithms for the problem adapted to completely avoid any reference to bits allowing to process pattern and text byte by byte. Experimental results show that the new algorithms outperform existing solutions in most cases.
BibTeX: @article{Faro2008a, author = {Faro, S and Lecroq, T}, title = {Efficient Pattern Matching on Binary Strings}, month = {Oct}, journal = {Rapport arXiv:0810.2390}, year = {2008}, url = {http://arxiv.org/abs/0810.2390} }
1 Publication internationale Névéol, A; Deserno, T; Darmoni, SJ; Güld, M & Aronson, AR. Natural language processing vs. content-based image analysis for medical document retrieval. Journal of the American Society for Information Science and Technology , sep, Volume 60, Number 1, Pages 123-134, 2008.
Abstract: One of the most significant recent advances in health information systems has been the shift from paper to electronic documents. While research on automatic text and image processing has taken separate paths, there is a growing need for joint efforts, particularly for electronic health records and biomedical literature databases. This work aims at comparing text-based versus image-based access to multimodal medical documents using state-of-the-art methods of processing text and image components. A collection of 180 medical documents containing an image accompanied by a short text describing it was divided into training and test sets. Content-based image analysis and natural language processing techniques are applied individually and combined for multimodal document analysis. The evaluation consists of an indexing task and a retrieval task based on the "gold standard" codes manually assigned to corpus documents. The performance of text-based and image-based access, as well as combined document features, is compared. Image analysis proves more adequate for both the indexing and retrieval of the images. In the indexing task, multimodal analysis outperforms both independent image and text analysis. This experiment shows that text describing images can be usefully analyzed in the framework of a hybrid text/image retrieval system.
BibTeX: @article{Neveol2009, author = {Névéol, A and Deserno, T and Darmoni, SJ and Güld, M and Aronson, AR}, title = {Natural language processing vs. content-based image analysis for medical document retrieval}, month = {sep}, journal = {Journal of the American Society for Information Science and Technology}, year = {2008}, volume = {60}, number = {1}, pages = {123--134}, doi = {10.1002/asi.20955} }
1 Publication internationale Prieur, E & Lecroq, T. On-line construction of compact suffix vectors and maximal repeats. Theoretical Computer Science , Volume 407, Number 1-3, Pages 290-301, 2008.
BibTeX: @article{Prieur, author = {Prieur, E and Lecroq, T}, title = {On-line construction of compact suffix vectors and maximal repeats}, journal = {Theoretical Computer Science}, year = {2008}, volume = {407}, number = {1-3}, pages = {290-301}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/tcs2008.pdf}, doi = {10.1016/j.tcs.2008.06.017} }
1 Publication internationale SMITH, DR; GEHANNO, JF & TAKAHASHI, K. Bibliometric Research in Occupational Health. Industrial Health , Volume 46, Number 6, Pages 519-522, 2008.
BibTeX: @article{SMITH2008, author = {SMITH, DR and GEHANNO, JF and TAKAHASHI, K}, title = {Bibliometric Research in Occupational Health}, journal = {Industrial Health}, year = {2008}, volume = {46}, number = {6}, pages = {519-522}, doi = {10.2486/indhealth.46.519} }
1 Publication internationale Touyar, N; Schbath, S; Cellier, D & Dauchel, H. Poisson approximation for the number of repeats in a stationary Markov chain. Journal of Applied Probabability , Volume 45, Number 2, Pages 440-455, 2008.
BibTeX: @article{Touyar2008, author = {Touyar, N and Schbath, S and Cellier, D and Dauchel, H}, title = {Poisson approximation for the number of repeats in a stationary Markov chain}, journal = {Journal of Applied Probabability}, year = {2008}, volume = {45}, number = {2}, pages = {440--455}, doi = {10.1239/jap/1214950359} }
2 Publication nationale Florea, F; Buzuloiu, V; Rogozan, A; Cornea, V; Bensrhair, A & Darmoni, SJ. Extraction and interpretation of image-related medical knowledge from on-line health-documents. UPB Scientific Bulletin, Series C: Electrical Engineering , Volume 70, Number 2, Pages 29-40, 2008.
Abstract: Over the last decade, Internet has become a significant source of information in numerous fields, including health. The French heath -catalogue CISMeF provides medical documents indexing and searching capabilities. The images represent a significant portion of the on-line medical knowledge and a valuable component of diagnosis and teaching. To enrich the Doc'CISMeF search engine with a "search -by-image-criteria" capability, we developed the MedIC module to allow the users to search for documents using image-related criteria. To extract accurate image descriptors, the MedIC architecture takes into consideration both the image itself and the corresponding image-related textregions. In this paper we present our approach for text-region extraction and interpretation, as well as the results obtained for image medical modality extraction.
BibTeX: @article{Florea2006c, author = {Florea, F and Buzuloiu, V and Rogozan, A and Cornea, V and Bensrhair, A and Darmoni, SJ}, title = {Extraction and interpretation of image-related medical knowledge from on-line health-documents}, journal = {UPB Scientific Bulletin, Series C: Electrical Engineering}, year = {2008}, volume = {70}, number = {2}, pages = {29-40}, url = {http://www.scientificbulletin.upb.ro/rev_docs_arhiva/full96719.pdf} }
2 Publication nationale Gehanno, JF & Caillard, JF. Evidence-based medicine et évaluation des pratiques professionnelles. Archives des Maladies Professionnelles et de l'Environnement 2008 , Volume 69, Number 2, Pages 140-2, 2008.
BibTeX: @article{Gehanno2008c, author = {Gehanno, JF and Caillard, JF}, title = {Evidence-based medicine et évaluation des pratiques professionnelles}, journal = {Archives des Maladies Professionnelles et de l'Environnement 2008}, year = {2008}, volume = {69}, number = {2}, pages = {140-2}, doi = {10.1016/j.admp.2008.03.042} }
2 Publication nationale Gehanno, JF; Weber, J; Sobaszek, A; Cantineau, A; Sibert, L & Caillard, JF. Détermination des besoins éducatifs des futurs médecins du travail par une méthode de groupes de discussion dirigée. Archives des Maladies Professionnelles et de l'Environnement , Volume 69, Number 3, Pages 423-37, 2008.
BibTeX: @article{Gehanno2008b, author = {Gehanno, JF and Weber, J and Sobaszek, A and Cantineau, A and Sibert, L and Caillard, JF}, title = {Détermination des besoins éducatifs des futurs médecins du travail par une méthode de groupes de discussion dirigée}, journal = {Archives des Maladies Professionnelles et de l'Environnement}, year = {2008}, volume = {69}, number = {3}, pages = {423-37}, doi = {10.1016/j.admp.2008.05.005} }
2 Publication nationale Letord, C; Sakji, S; Pereira, S; Dahamna, B; Kergourlay, I & Darmoni, SJ. Recherche d'information multi-terminologique : application à un portail d'information sur le médicament en Europe. Ingénierie et Recherche Biomédicale / BioMedical Engineering and Research , Number 29, Pages 350-356, 2008. PSIP.
BibTeX: @article{Letord2008, author = {Letord, C and Sakji, S and Pereira, S and Dahamna, B and Kergourlay, I and Darmoni, SJ}, title = {Recherche d'information multi-terminologique : application à un portail d'information sur le médicament en Europe}, journal = {Ingénierie et Recherche Biomédicale / BioMedical Engineering and Research}, year = {2008}, number = {29}, pages = {350-356}, note = {PSIP}, doi = {10.1016/j.irbm.2008.10.001} }
2 Publication nationale Julien Mancini; Stefan Darmoni; Hervé Chaudet & Marius Fieschi. Le paradoxe de la « T2A bibliométrique » SIGAPS : un risque d'effet délétère sur la recherche française ?. Presse Med , Nov, 2008.
BibTeX: @article{Mancini2008, author = {Julien Mancini and Stefan Darmoni and Hervé Chaudet and Marius Fieschi}, title = {Le paradoxe de la « T2A bibliométrique » SIGAPS : un risque d'effet délétère sur la recherche française ?}, month = {Nov}, journal = {Presse Med}, year = {2008}, url = {http://dx.doi.org/10.1016/j.lpm.2008.10.005}, doi = {10.1016/j.lpm.2008.10.005} }
2 Publication nationale Pereira, S. Indexation multi-terminologique de concepts en santé. School: Université de Rouen, 2008.
BibTeX: @phdthesis{Pereira2008, author = {Pereira, S}, title = {Indexation multi-terminologique de concepts en santé}, school = {Université de Rouen}, year = {2008}, url = {http://suzanne.b.pereira.free.fr/Pereirathese.pdf} }
2 Publication nationale Rongère, Julie; Tavolacci, MP; Douyère, M; Thirion, B; Darmoni, SJ & Ladner, J. Utilisation et qualité des sites présentant l'offre de formations en santé publique.. Santé Publique , Volume 20, Number 5, Pages 465-474, 2008.
Abstract: The objective of this work was to study the use of the Internet and the quality of the websites for postgraduate public health courses in France, and to compare them with equivalent courses in the United States of America. Between June 2004 and January 2005, the authorized public health diplomas proposed in France and in the United States were inventoried and listed, and then all websites of these public health diplomas were systematically visited and reviewed using a standardized questionnaire. In France, 36 public health courses (7 post graduate diplomas [DEA], 13 Masters degrees [DESS] and 16 masters of public health [MPH]) were identified and selected from 53 websites. Information on student profiles, prerequisite skills, the courses' curricula and program descriptions and the potential career opportunities were more frequently available for the MPH compared to the DEA and DESS. In United States, 66 MPH and 127 Master of Science in Public Health (MSPH) programs were accredited. The target public and validation methods were more often indicated on the American sites, while the prerequisite skills were more frequently found on the French sites. The recent implementation of the LMD (Bachelor's-Masters-Doctoral degrees) education system in France has encouraged the utilisation of Internet as an information and communications tool for the presentation and marketing of these new diplomas.
BibTeX: @article{Rongere2008, author = {Rongère, Julie and Tavolacci, MP and Douyère, M and Thirion, B and Darmoni, SJ and Ladner, J}, title = {Utilisation et qualité des sites présentant l'offre de formations en santé publique.}, journal = {Santé Publique}, year = {2008}, volume = {20}, number = {5}, pages = {465--474}, doi = {10.3917/spub.085.0465} }
2 Publication nationale Sabourin, JC & Darmoni, SJ. Avec le score SIGAPS : c'est le moment de publier dans les Annales de pathologie !. Annales de Pathologie , April, Volume 28, Pages 77-78, 2008.
BibTeX: @article{Sabourin2008, author = {Sabourin, JC and Darmoni, SJ}, title = {Avec le score SIGAPS : c'est le moment de publier dans les Annales de pathologie !}, month = {April}, journal = {Annales de Pathologie}, year = {2008}, volume = {28}, pages = {77-78}, doi = {10.1016/j.annpat.2008.05.001} }
2 Publication nationale Thirion, B. L'Europe des bibliothèques de santé. BBF , Volume 53, Number 1, Pages 38-40, 2008.
BibTeX: @article{Thirion2008, author = {Thirion, B}, title = {L'Europe des bibliothèques de santé}, journal = {BBF}, year = {2008}, volume = {53}, number = {1}, pages = {38-40}, url = {http://bbf.enssib.fr/sdx/BBF/frontoffice/2008/01/document.xsp?id=bbf-2008-01-0038-007/2008/01/fam-dossier/dossier&statutMaitre=non&statutFils=non} }
3 Communication internationale Faro, S & Lecroq, T. Efficient Variants of the Backward-Oracle-Matching Algorithm. Proceedings of the Prague Stringology conference, #ctu#, Pages 146-160, 2008.
BibTeX: @inproceedings{Faro2008, author = {Faro, S and Lecroq, T}, title = {Efficient Variants of the Backward-Oracle-Matching Algorithm}, booktitle = {Proceedings of the Prague Stringology conference}, address = {#ctu#}, year = {2008}, pages = {146--160}, url = {http://www.stringology.org/event/2008/p14.html} }
3 Communication internationale Gehanno, JF. Teaching Evidence Based Medicine in Occupational Health.. EASOM Summer School, Amsterdam, Netherland, August, 2008.
BibTeX: @inproceedings{Gehanno2008d, author = {Gehanno, JF}, title = {Teaching Evidence Based Medicine in Occupational Health.}, booktitle = {EASOM Summer School}, address = {Amsterdam, Netherland}, month = {August}, year = {2008} }
3 Communication internationale Gehanno, JF; Kerdelhue, G; Letord, C; Fantoni, S & Frimat, P. A web site to follow-up literature in occupational health for healthcare workers. 8th International Conference on Education and Training in Occupational Health, Glasgow, UK, April, 2008.
BibTeX: @inproceedings{Gehanno2008, author = {Gehanno, JF and Kerdelhue, G and Letord, C and Fantoni, S and Frimat, P}, title = {A web site to follow-up literature in occupational health for healthcare workers}, booktitle = {8th International Conference on Education and Training in Occupational Health}, address = {Glasgow, UK}, month = {April}, year = {2008}, url = {http://www.gla.ac.uk/icoh2008/} }
3 Communication internationale Joubert, M; Darmoni, SJ; Avillach, P; Dahamna, B & Fieschi, M. Using Knowledge for Indexing Health Web Resources in a Quality-Controlled Gateway. eHealth Beyond the Horizon - Get IT There - Proceedings of MIE2008 - The XXIst International Congress of the European Federation for Medical Informatics, Göteborg, Sweden, May, Studies in Health Technology and Informatics, Volume 136, Pages 205 - 210, 2008.
Abstract: Objectives: 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. Material and methods: 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. Results: 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. Discussion: 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 removal by using statistical knowledge of nonstatistically significant associations of terms. Conclusion: This method can assist effectively indexers in their daily work and will be soon applied in the CISMeF system.
BibTeX: @inproceedings{Michel2008, author = {Joubert, M and Darmoni, SJ and Avillach, P and Dahamna, B and Fieschi, M}, title = {Using Knowledge for Indexing Health Web Resources in a Quality-Controlled Gateway}, booktitle = {eHealth Beyond the Horizon - Get IT There - Proceedings of MIE2008 - The XXIst International Congress of the European Federation for Medical Informatics}, address = {Göteborg, Sweden}, month = {May}, year = {2008}, series = {Studies in Health Technology and Informatics}, volume = {136}, pages = {205 - 210}, url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=8724} }
3 Communication internationale Kerdelhué, G; Thirion, B; Dahamna, B & Darmoni, SJ. Cataloguing and displaying Web feeds from French language health sites: a Web 2.0 add-on to a health gateway. eHealth Beyond the Horizon - Get IT There - Proceedings of MIE2008 - The XXIst International Congress of the European Federation for Medical Informatics, Göteborg, Sweden, May, Studies in Health Technology and Informatics, Volume 136, Pages 33 - 38, 2008.
Abstract: 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 how the aggregator was put online and the features of this news gateway. CISMeF actualités was built accordingly to the editorial policy of CISMeF. Only a part of the Web feeds of the catalogue were included to display the most authoritative sources. Web feeds were also grouped by medical specialties and by countries using the prior indexing of websites with MeSH terms and the so-called metaterms. CISMeF actualités now displays 131 Web feeds across 40 different medical specialities, coming from 5 different countries. It is one example, among many, that static hypertext links can now easily and beneficially be completed, or replaced, by dynamic display of Web content using syndication feeds.
BibTeX: @inproceedings{Kerdelhue2008, author = {Kerdelhué, G and Thirion, B and Dahamna, B and Darmoni, SJ}, title = {Cataloguing and displaying Web feeds from French language health sites: a Web 2.0 add-on to a health gateway}, booktitle = {eHealth Beyond the Horizon - Get IT There - Proceedings of MIE2008 - The XXIst International Congress of the European Federation for Medical Informatics}, address = {Göteborg, Sweden}, month = {May}, year = {2008}, series = {Studies in Health Technology and Informatics}, volume = {136}, pages = {33 - 38}, url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=8694} }
3 Communication internationale Massari, P; Pereira, S; Thirion, B; Derville, A & Darmoni, SJ. Use of super-concepts to customize electronic medical records data display. eHealth Beyond the Horizon - Get IT There - Proceedings of MIE2008 - The XXIst International Congress of the European Federation for Medical Informatics, Göteborg, Sweden, May, Studies in Health Technology and Informatics, Volume 136, Pages 845 - 850, 2008.
Abstract: Patient medical record systems (MRS) merely offer static applications, in which mostly unstructured text is linked to coded data. In these applications the more common presentation is a time oriented one, which does not allow easily for data and information retrieval. Concept oriented views based on supper-concepts (metaterms) initially defined in CISMeF to optimize Web medical search, was implemented in our MRS as specialties views. This work shows that these terminological tools are able to facilitate information retrieval.
BibTeX: @inproceedings{Massari2008, author = {Massari, P and Pereira, S and Thirion, B and Derville, A and Darmoni, SJ}, title = {Use of super-concepts to customize electronic medical records data display}, booktitle = {eHealth Beyond the Horizon - Get IT There - Proceedings of MIE2008 - The XXIst International Congress of the European Federation for Medical Informatics}, address = {Göteborg, Sweden}, month = {May}, year = {2008}, series = {Studies in Health Technology and Informatics}, volume = {136}, pages = {845 - 850}, url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=8836} }
3 Communication internationale Merabti, T; Pereira, S; Letord, C; Lecroq, T; Dahamna, B; Joubert, M & Darmoni, SJ. Searching Related Resources in a Quality Controlled Health Gateway: a Feasibility Study. eHealth Beyond the Horizon - Get IT There - Proceedings of MIE2008 - The XXIst International Congress of the European Federation for Medical Informatics, Göteborg, Sweden, May, Studies in Health Technology and Informatics, Volume 136, Pages 235 - 240, 2008.
Abstract: Objective: 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. Method: CISMeF-RRA is inspired by the PubMed Related Citations Articles. CISMeF-RRA combines statistical distances with a semantic distance using MeSH terms/qualifiers. Material: In this feasibility study an evaluation was performed using 50 CISMeF resources randomly chosen. Results: Overall, 49% of the related documents were ranked as relevant. Conclusion: if this feasibility study is confirmed by another evaluation of more resources, CISMeF-RRA will be implemented in the CISMeF catalog.
BibTeX: @inproceedings{Tayeb2008a, author = {Merabti, T and Pereira, S and Letord, C and Lecroq, T and Dahamna, B and Joubert, M and Darmoni, SJ}, title = {Searching Related Resources in a Quality Controlled Health Gateway: a Feasibility Study}, booktitle = {eHealth Beyond the Horizon - Get IT There - Proceedings of MIE2008 - The XXIst International Congress of the European Federation for Medical Informatics}, address = {Göteborg, Sweden}, month = {May}, year = {2008}, series = {Studies in Health Technology and Informatics}, volume = {136}, pages = {235 - 240}, url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=8729} }
3 Communication internationale Pereira, S; Massari, P; Joubert, M; Serrot, E & Darmoni, SJ. Exploring Multi-terminology Indexing of Discharge Summaries. , May, 2008. (Poster) MIE 2008 eHealth beyond the horizon ? get IT there Göteborg, Sweden May 25-28, 2008.
BibTeX: @inproceedings{Suzanne2008a, author = {Pereira, S and Massari, P and Joubert, M and Serrot, E and Darmoni, SJ}, title = {Exploring Multi-terminology Indexing of Discharge Summaries}, month = {May}, year = {2008}, note = {(Poster) MIE 2008 eHealth beyond the horizon ? get IT there Göteborg, Sweden May 25-28, 2008} }
3 Communication internationale Pereira, S; Névéol, A; Kerdelhué, G; Serrot, E; Joubert, M & Darmoni, SJ. Using multi-terminology indexing for the assignment of MeSH descriptors to health resources in a French online catalogue. AMIA symp., Pages 586-590, IOS Press, 2008.
Abstract: Background: In the specific context of French MeSH indexing in an Internet quality-controlled health gateway, we implemented a MeSH automatic indexing tool, the French Multi-Terminology Indexer (F-MTI). It implements a multi-terminology approach using four main medical terminologies in French and the mappings between them. Objective: In this paper, we attempt to determine which of lemmatization or stemming is better to be integrated in F-MTI, and to evaluate an approach using multi-terminologies. Methods: The algorithm was evaluated on a CISMeF corpus comprising 18,814 resources indexed manually. Results: Precision and recall are very close comparing lemmatization and stemming, and mono-terminology and multi-terminology. Conclusion: F-MTI will soon be used in the CISMeF production environment and in a Health MultiTerminology Server in French.
BibTeX: @inproceedings{Suzanne2008b, author = {Pereira, S and Névéol, A and Kerdelhué, G and Serrot, E and Joubert, M and Darmoni, SJ}, title = {Using multi-terminology indexing for the assignment of MeSH descriptors to health resources in a French online catalogue}, booktitle = {AMIA symp.}, publisher = {IOS Press}, year = {2008}, pages = {586-590} }
3 Communication internationale Salson, M; Lecroq, T; Léonard, M & Mouchard, L. Dynamic Burrows-Wheeler Transform. Proceedings of the Prague Stringology conference, #ctu#, Pages 13-25, 2008.
BibTeX: @inproceedings{Salson2008, author = {Salson, M and Lecroq, T and Léonard, M and Mouchard, L}, title = {Dynamic Burrows-Wheeler Transform}, booktitle = {Proceedings of the Prague Stringology conference}, address = {#ctu#}, year = {2008}, pages = {13--25}, url = {http://www.stringology.org/event/2008/p02.html} }
3 Communication internationale Soualmia, LF; Dahamna, B & Darmoni, SJ. Mining knowledge from Corpora: an Application to Retrieval and Indexing. eHealth Beyond the Horizon - Get IT There - Proceedings of MIE2008 - The XXIst International Congress of the European Federation for Medical Informatics, Göteborg, Sweden, May, Studies in Health Technology and Informatics, Volume 136, Pages 467-472, 2008.
Abstract: The present work aims at discovering new associations between medical concepts to be exploited as input in retrieval and indexing. Material and Methods: 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. Results: 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. Conclusions: Association rules bear out existing relations, produce new knowledge and support users and indexers in document retrieval and indexing.
BibTeX: @inproceedings{Soualmia2008, author = {Soualmia, LF and Dahamna, B and Darmoni, SJ}, title = {Mining knowledge from Corpora: an Application to Retrieval and Indexing}, booktitle = {eHealth Beyond the Horizon - Get IT There - Proceedings of MIE2008 - The XXIst International Congress of the European Federation for Medical Informatics}, address = {Göteborg, Sweden}, month = {May}, year = {2008}, series = {Studies in Health Technology and Informatics}, volume = {136}, pages = {467-472}, url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=8769} }
4 Communication nationale Chanoni, E; Lecroq, T & Pauchet, A. Une nouvelle heuristique pour l'alignement de motifs 2D par programmation dynamique. Actes des Journées Francophones de Planification, Décision et Apprentissage pour la conduite de systèmes, Metz, France, Pages 83-91, 2008.
BibTeX: @inproceedings{Chanoni2008, author = {Chanoni, E and Lecroq, T and Pauchet, A}, title = {Une nouvelle heuristique pour l'alignement de motifs 2D par programmation dynamique}, booktitle = {Actes des Journées Francophones de Planification, Décision et Apprentissage pour la conduite de systèmes}, address = {Metz, France}, year = {2008}, pages = {83--91} }
4 Communication nationale Sakji, S. Recherche multi-terminologique de l'information de santé sur l'Internet.. CORIA (cinquième édition de la COnférence en Recherche d'Information et Applications), Tregastel, France, Mars, 2008. PSIP.
BibTeX: @inproceedings{SAKJI2008, author = {Sakji, S}, title = {Recherche multi-terminologique de l'information de santé sur l'Internet.}, booktitle = {CORIA (cinquième édition de la COnférence en Recherche d'Information et Applications)}, address = {Tregastel, France}, month = {Mars}, year = {2008}, note = {PSIP}, url = {http://coria08.irisa.fr} }
5 Résumé Darmoni, SJ; Pereira, S; Névéol, A; Massari, P; Dahamna, B; Letord, C; Kedelhué, G; Piot, J; Derville, A & Thirion, B. French Infobutton: an academic and... business perspective. AMIA Symp., Pages 920, IOS Press, 2008.
Abstract: Infobuttons are context-specific links between clinical information systems and other online information resources. The objective of this study is to describe a French Infobutton, which will be sold in the Frenchspeaking Health Information market.
BibTeX: @inproceedings{SJ.2008, author = {Darmoni, SJ and Pereira, S and Névéol, A and Massari, P and Dahamna, B and Letord, C and Kedelhué, G and Piot, J and Derville, A and Thirion, B}, title = {French Infobutton: an academic and... business perspective}, booktitle = {AMIA Symp.}, publisher = {IOS Press}, year = {2008}, pages = {920} }
5 Résumé Merabti, T; Pereira, S; Lecroq, T; Joubert, M & Darmoni, SJ. Inheritance of SNOMED CT Relations between Concepts by two Health Terminologies (SNOMED International and ICD-10). KR-MED 2008 - Representing and sharing knowledge using SNOMED International Conference, Phoenix, AZ, USA, June, 2008. InterSTIS.
BibTeX: @inproceedings{Tayeb2008, author = {Merabti, T and Pereira, S and Lecroq, T and Joubert, M and Darmoni, SJ}, title = {Inheritance of SNOMED CT Relations between Concepts by two Health Terminologies (SNOMED International and ICD-10)}, booktitle = {KR-MED 2008 - Representing and sharing knowledge using SNOMED International Conference}, address = {Phoenix, AZ, USA}, month = {June}, year = {2008}, note = {InterSTIS} }
5 Résumé Suzanne Pereira, Philippe Massari,, Antoine Buemi, Badisse Dahamna, Elisabeth Serrot, Michel Joubert, Stéfan J. Darmoni. Evaluation of two French SNOMED indexing systems with a parallel corpus. KR-MED 2008 - Representing and sharing knowledge using SNOMED International Conference, Phoenix, AZ, USA, June, 2008.
BibTeX: @inproceedings{Suzanne2008, author = {Suzanne Pereira, Philippe Massari,, Antoine Buemi, Badisse Dahamna, Elisabeth Serrot, Michel Joubert, Stéfan J. Darmoni}, title = {Evaluation of two French SNOMED indexing systems with a parallel corpus}, booktitle = {KR-MED 2008 - Representing and sharing knowledge using SNOMED International Conference}, address = {Phoenix, AZ, USA}, month = {June}, year = {2008} }
2007 1 Publication internationale Crochemore, M; Hancart, C & Lecroq, T. Algorithms on strings. , Cambridge University Press, 2007.
BibTeX: @book{Crochemore2007, author = {Crochemore, M and Hancart, C and Lecroq, T}, title = {Algorithms on strings}, publisher = {Cambridge University Press}, year = {2007} }
1 Publication internationale Cuggia, M; Darmoni, SJ; Garcelon, N; Soualmia, L & Bourde, A. Doc'UMVF: two search tools to provide quality-controlled teaching resources in French to students and teachers.. Int J Med Inform , Volume 76, Number 5-6, Pages 357-362, 2007.
Abstract: The UMVF project is a federation of medical teaching resources covering 32 medical schools in France. Today, the indexing of these resources is carried out manually by the CISMeF team at the University Hospital of Rouen. This indexing is based on MeSH thesaurus. We use a subset of SCORM metadata standard. This choice was defined in collaboration with the French Medical Virtual University consortium (French acronym: UMVF). Currently, with the UMVF searching tool (called Doc'UMVF), medical students can reach more than 3300 resources useful in their curriculum. Doc'UMVF is developed in close collaboration between the medical informatics laboratories of Rennes and Rouen. In this paper we present two complementary searching tools based on different methods and which are integrated and used to improve both the relevance and the coverage rate of the answers. A specific searching module has been built to retrieve specific resources concerning the National Medical Exam ENC ("Examen National Classant") is also available. Nevertheless, due to lack of time, numerous resources are not yet indexed. Therefore we have decided to use also automatic indexing method (Nomindex). This approach will be improved by further research works, resulting from Rouen and Geneva teams. After having built a searching meta-motor, our objective is to develop a meta-tool intended to index the whole set of digital pedagogical resources produced by the UMVF framework. This manual re-indexing will be carried out only for the most important resources (national references), with a more or less fine granularity.
BibTeX: @article{Cuggia2007, author = {Cuggia, M and Darmoni, SJ and Garcelon, N and Soualmia, L and Bourde, A}, title = {Doc'UMVF: two search tools to provide quality-controlled teaching resources in French to students and teachers.}, journal = {Int J Med Inform}, year = {2007}, volume = {76}, number = {5-6}, pages = {357--362}, doi = {10.1016/j.ijmedinf.2007.01.001} }
1 Publication internationale Duval, JP; Lecroq, T & Lefebvre, A. Efficient validation and construction of border arrays. London Algorithmics and Stringology 2006, Texts in Algorithms, Volume 8, Pages 135-147, King's College London Publications, 2007.
BibTeX: @incollection{Duval2007, author = {Duval, JP and Lecroq, T and Lefebvre, A}, title = {Efficient validation and construction of border arrays}, booktitle = {London Algorithmics and Stringology 2006}, publisher = {King's College London Publications}, year = {2007}, series = {Texts in Algorithms}, volume = {8}, pages = {135--147} }
1 Publication internationale Gehanno, JF; Takahashi, K; Darmoni, SJ & Weber, J. Citation classics in occupational medicine journals.. Scand J Work Environ Health , Aug, Volume 33, Number 4, Pages 245-251, 2007.
Abstract: OBJECTIVES: The number of citations an article receives after its publication not only reflects its impact on the scientific community, but also the impact of the institutions or countries in the field studied. In 1987, Garfield introduced the concept of "citation classics" for the best-cited articles. An analysis of top-cited articles coming from journals in the field of occupational medicine (eg, Occupational and Environmental Medicine, Scandinavian Journal of Work, Environment & Health) has not yet been reported. The purpose of this study was to assess whether or not such citation classics exist in this field and to analyze their characteristics. METHODS: The most frequently cited articles published in the five major journals in occupational medicine were identified using the database of Science Citation Index Expanded. The data were obtained by searching one year and one journal at a time. All of the articles cited more than 100 times were collected and analyzed. RESULTS: Among the 15 553 articles published by the five journals since 1949, only 85 articles had been cited more than 100 times. The oldest had been published in 1950 and the latest in 1997. The United Kingdom contributed 28% of the citation classics and the United States or Sweden produced 19 The most cited article had been cited 979 times. The main topics of articles were metabolism, occupational neoplasms, and work-related musculoskeletal disorders. CONCLUSIONS: Since the 1980s, Scandinavia and the United States have taken the leadership in the publication of citation classic papers. Nevertheless, according to the level of citations, the influence of literature published in occupational medicine journals remains limited.
BibTeX: @article{Gehanno2007, author = {Gehanno, JF and Takahashi, K and Darmoni, SJ and Weber, J}, title = {Citation classics in occupational medicine journals.}, month = {Aug}, journal = {Scand J Work Environ Health}, year = {2007}, volume = {33}, number = {4}, pages = {245--251} }
1 Publication internationale Gehanno, JF; Vu, T; Choudat, D & Conso, F. Devenir des internes de medecine du travail formes en France entre 2002 et 2004. Archives des Maladies Professionnelles et de l'Environnement , April, Volume 68, Pages 110-118, 2007.
BibTeX: @article{Gehanno2007b, author = {Gehanno, JF and Vu, T and Choudat, D and Conso, F}, title = {Devenir des internes de medecine du travail formes en France entre 2002 et 2004}, month = {April}, journal = {Archives des Maladies Professionnelles et de l'Environnement}, year = {2007}, volume = {68}, pages = {110-118}, url = {http://www.sciencedirect.com/science/article/B8JFG-4R0CFRC-2/2/ce5acd7798f06412549571cc53f5a9e1}, doi = {10.1016/S1775-8785(07)88908-9} }
1 Publication internationale T. Lecroq. Fast exact string matching algorithms. Information Processing Letters , Volume 102, Number 6, Pages 229-235, 2007.
BibTeX: @article{Lecroq2007, author = {T. Lecroq}, title = {Fast exact string matching algorithms}, journal = {Information Processing Letters}, year = {2007}, volume = {102}, number = {6}, pages = {229--235}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/tcs2008.pdf}, doi = {10.1016/j.ipl.2007.01.002} }
1 Publication internationale Renard, JM; Bourde, A; Cuggia, M; Garcelon, N; Souf, N; Darmoni, SJ; Beuscart, R & Brunetaud, JM. An Internet supported workflow for the publication process in UMVF (French Virtual Medical University).. Int J Med Inform , Volume 76, Number 5-6, Pages 363-368, 2007.
Abstract: The " Université Médicale Virtuelle Francophone" (UMVF) is a federation of French medical schools. Its main goal is to share the production and use of pedagogic medical resources generated by academic medical teachers. We developed an Open-Source application based upon a workflow system, which provides an improved publication process for the UMVF. For teachers, the tool permits easy and efficient upload of new educational resources. For web masters it provides a mechanism to easily locate and validate the resources. For librarian it provide a way to improve the efficiency of indexation. For all, the utility provides a workflow system to control the publication process. On the students side, the application improves the value of the UMVF repository by facilitating the publication of new resources and by providing an easy way to find a detailed description of a resource and to check any resource from the UMVF to ascertain its quality and integrity, even if the resource is an old deprecated version. The server tier of the application is used to implement the main workflow functionalities and is deployed on certified UMVF servers using the PHP language, an LDAP directory and an SQL database. The client tier of the application provides both the workflow and the search and check functionalities. A unique signature for each resource, was needed to provide security functionality and is implemented using a Digest algorithm. The testing performed by Rennes and Lille verified the functionality and conformity with our specifications.
BibTeX: @article{Renard2007, author = {Renard, JM and Bourde, A and Cuggia, M and Garcelon, N and Souf, N and Darmoni, SJ and Beuscart, R and Brunetaud, JM}, title = {An Internet supported workflow for the publication process in UMVF (French Virtual Medical University).}, journal = {Int J Med Inform}, year = {2007}, volume = {76}, number = {5-6}, pages = {363--368}, doi = {10.1016/j.ijmedinf.2007.01.010} }
1 Publication internationale Séralini, GE; Cellier, D & de Vendomois, JS. New analysis of a rat feeding study with a genetically modified maize reveals signs of hepatorenal toxicity. Arch. Environ. Contam. Toxicol , Volume 52, Pages 596-602, 2007.
BibTeX: @article{Seralini2007, author = {Séralini, GE and Cellier, D and de Vendomois, JS}, title = {New analysis of a rat feeding study with a genetically modified maize reveals signs of hepatorenal toxicity}, journal = {Arch. Environ. Contam. Toxicol}, year = {2007}, volume = {52}, pages = {596--602}, doi = {10.1007/s00244-006-0149-5} }
2 Publication nationale Florea, F. Indexation et recherche d'information combinée texte et image dans le catalogue de santé CISMeF. School: INSA de Rouen, 2007.
BibTeX: @phdthesis{Florea2007c, author = {Florea, F}, title = {Indexation et recherche d'information combinée texte et image dans le catalogue de santé CISMeF}, school = {INSA de Rouen}, year = {2007} }
2 Publication nationale Kerdelhué, G. Utilisation du thésaurus MeSH dans le site CISMeF.. Documentaliste - Sciences de l'information , Volume 44, Number 1, 2007.
BibTeX: @article{Kerdelhue2007, author = {Kerdelhué, G}, title = {Utilisation du thésaurus MeSH dans le site CISMeF.}, journal = {Documentaliste - Sciences de l'information}, year = {2007}, volume = {44}, number = {1}, url = {http://www.adbs.fr/utilisation-du-thesaurus-mesh-dans-le-site-cismef-15472.htm} }
2 Publication nationale Meslin, C. Utilisation de la table des suffixes pour la détection des répétitions. School: Université de Rouen, France, 2007.
BibTeX: @phdthesis{Meslin2007, author = {Meslin, C}, title = {Utilisation de la table des suffixes pour la d\'etection des r\'ep\'etitions}, school = {Universit\'e de Rouen, France}, year = {2007} }
2 Publication nationale Prieur, E. Méthodes et structures de données pour l'indexation et la détection de répétitions dans les séquences biologiques : les vecteurs de suffixes. School: Université de Rouen, France, 2007.
BibTeX: @phdthesis{Prieur2007, author = {Prieur, E}, title = {M\'ethodes et structures de donn\'ees pour l'indexation et la d\'etection de r\'ep\'etitions dans les s\'equences biologiques : les vecteurs de suffixes}, school = {Universit\'e de Rouen, France}, year = {2007} }
3 Communication internationale Darmoni, SJ. Information and Communication Technologies in Modern Health Library.. EAHIL Workshop, Cracovie, Pologne, September, 2007.
BibTeX: @inproceedings{SJ.2007, author = {Darmoni, SJ}, title = {Information and Communication Technologies in Modern Health Library.}, booktitle = {EAHIL Workshop}, address = {Cracovie, Pologne}, month = {September}, year = {2007}, url = {http://www.bm.cm-uj.krakow.pl/eahil/proceedings/oral/Darmoni.pdf} }
3 Communication internationale Florea, F; Buzuloiu, V; Rogozan, A; Bensrhair, A & Darmoni, SJ. Automatic Image Annotation Combining the Content and the Context of Medical Images. Proc. International Symposium on Signals, Circuits and Systems ISSCS 2007, Volume 1, Pages 1-4, 2007.
BibTeX: @inproceedings{Florea2007, author = {Florea, F and Buzuloiu, V and Rogozan, A and Bensrhair, A and Darmoni, SJ}, title = {Automatic Image Annotation Combining the Content and the Context of Medical Images}, booktitle = {Proc. International Symposium on Signals, Circuits and Systems ISSCS 2007}, year = {2007}, volume = {1}, pages = {1--4}, doi = {10.1109/ISSCS.2007.4292712} }
3 Communication internationale Florea, F; Rogozan, A; Barbu, E; Bensrhair, A & Darmoni, SJ. MedIC at ImageCLEF 2006: Automatic Image Categorization and Annotation using Combined Visual Representations. Lecture Notes in Computer Science , Alicante, Spain, Number 4730, Pages 670-677, 2007.
BibTeX: @inproceedings{Florea2007a, author = {Florea, F and Rogozan, A and Barbu, E and Bensrhair, A and Darmoni, SJ}, title = {MedIC at ImageCLEF 2006: Automatic Image Categorization and Annotation using Combined Visual Representations}, address = {Alicante, Spain}, journal = {Lecture Notes in Computer Science}, year = {2007}, number = {4730}, pages = {670-677}, url = {http://www.springerlink.com/content/w4832362m341/?k=florea}, doi = {10.1007/978-3-540-74999-8_82} }
3 Communication internationale Gehanno, JF; Thirion, B & Darmoni, SJ. Evaluation of Meta-concepts for Information Retrieval in a Quality-Controlled Health Gateway.. AMIA Symp., Pages 269-73, IOS Press, 2007.
Abstract: Background: CISMeF is a French quality-controlled health gateway that uses the MeSH thesaurus. We introduced two new concepts, metaterms (medical specialty which has semantic links with one or more MeSH terms, subheadings and resource types) and resource types. Objective: evaluate precision and recall of metaterms. Methods: We created 16 pairs of queries. Each pair concerned the same topic, but one used metaterms and one MeSH terms. To assess precision, each document retrieved by the query was classified as irrelevant, partly relevant or fully relevant. Results: the 16 queries yielded 943 documents for metaterm queries and 139 for MeSH term queries. The recall of MeSH term queries was 0.44 (compared to 1 for metaterm queries) and the precision were identical for MeSH term and metaterm queries. Conclusion: Metaconcept such as CISMeF metaterms allows a better recall with a similar precision that MeSH terms in a quality controlled health gateway.
BibTeX: @inproceedings{Gehanno2007a, author = {Gehanno, JF and Thirion, B and Darmoni, SJ}, title = {Evaluation of Meta-concepts for Information Retrieval in a Quality-Controlled Health Gateway.}, booktitle = {AMIA Symp.}, publisher = {IOS Press}, year = {2007}, pages = {269-73}, url = {http://telemedicina.unifesp.br/pub/AMIA/2007%20AMIA%20Proceedings/data/papers/papers/AMIA-0085-S2007.pdf} }
3 Communication internationale Loisel, A.; Loisel, A.; Chaignaud, N. & Kotowicz, J-Ph.. Designing a Human-Computer Dialog System for Medical Information Search. Proc. IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology Workshops, Pages 350-353, 2007.
Abstract: This article presents the Cogni-CISMeF project, which aims at improving medical information search in the CISMeF system by including a conversational agent to interact with the user in natural language. To study the cognitive processes involved during the information search, a bottom-up methodology was adopted. Experiments have been set up to obtain human dialogs dealing with medical information search. The analysis of these dialogs underlined the establishment of a common ground and accommodation effects to the user. A model of artificial agent is proposed. It leads the user in its information search by proposing to him examples, assistance and choices.
BibTeX: @inproceedings{Loisel2007, author = {Loisel, A. and Loisel, A. and Chaignaud, N. and Kotowicz, J-Ph.}, title = {Designing a Human-Computer Dialog System for Medical Information Search}, booktitle = {Proc. IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology Workshops}, year = {2007}, pages = {350--353}, doi = {10.1109/WIIATW.2007.4427605} }
3 Communication internationale Névéol, A.; Pereira, S.; Kerdelhué, G.; Dahamna, B.; Joubert, M. & Darmoni, SJ. Evaluation of a Simple Method for the Automatic Assignment of MeSH Descriptors to Health Resources in a French Online Catalogue.. Stud Health Technol Inform , U.S. National Library of Medicine, National Institutes of Health, Bethesda, USA., Volume 129, Pages 407-411, 2007.
Abstract: Background: 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. Objective: To develop a simple automatic tool that retrieves MeSH descriptors from documents titles. Methods: 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. Results: 58% of the major main headings were retrieved by the bag-of-words algorithm and the precision on main heading retrieval was 69%. Conclusion: 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.
BibTeX: @article{Neveol2007, author = {Névéol, A. and Pereira, S. and Kerdelhué, G. and Dahamna, B. and Joubert, M. and Darmoni, SJ}, title = {Evaluation of a Simple Method for the Automatic Assignment of MeSH Descriptors to Health Resources in a French Online Catalogue.}, address = {U.S. National Library of Medicine, National Institutes of Health, Bethesda, USA.}, journal = {Stud Health Technol Inform}, year = {2007}, volume = {129}, pages = {407--411} }
3 Communication internationale Névéol, A; Shooshan, S; Humphrey, S; Rindflesh, T & Aronson, AR. Multiple approaches to fine-grained indexing of the biomedical literature.. Pac Symp Biocomput , Pages 292-303, 2007.
Abstract: The number of articles in the MEDLINE database is expected to increase tremendously in the coming years. To ensure that all these documents are indexed with continuing high quality, it is necessary to develop tools and methods that help the indexers in their daily task. We present three methods addressing a novel aspect of automatic indexing of the biomedical literature, namely producing MeSH main heading/subheading pair recommendations. The methods, (dictionary-based, post- processing rules and Natural Language Processing rules) are described and evaluated on a genetics-related corpus. The best overall performance is obtained for the subheading genetics (70% precision and 17% recall with post-processing rules, 48% precision and 37% recall with the dictionary-based method). Future work will address extending this work to all MeSH subheadings and a more thorough study of method combination.
BibTeX: @inproceedings{Neveol2007a, author = {Névéol, A and Shooshan, S and Humphrey, S and Rindflesh, T and Aronson, AR}, title = {Multiple approaches to fine-grained indexing of the biomedical literature.}, journal = {Pac Symp Biocomput}, year = {2007}, pages = {292--303}, url = {http://psb.stanford.edu/psb-online/proceedings/psb07/neveol.pdf} }
3 Communication internationale Aurélie Névéol.; Suzanne Pereira; Gaëlle Lortal & Stéfan Darmoni. Using NooJ for analyzing medical texts in French. NOOJ Conference, Barcelona, Spain, june, 2007.
Abstract: The catalog of online medical resources in French (CISMeF) is a quality controlled health gateway selecting and describing major institutional medical resources in French. In order to update the catalog in a timely fashion, research efforts have addressed the development of automatic tools to process resources selected for inclusion in the catalogue. The result of the automatic processing, namely a description of resources in the form of MeSH descriptors, may be reviewed by CISMeF indexers before inclusion in the catalogue. After a brief introduction to CISMeF and the task of MeSH indexing, we review the reasons that led to chose NooJ as a text analysis tool and describe how it was integrated in a MeSH indexing system (MAIF). On-going work focuses on further development of medical text analysis material (NooJ dictionary and transducers) for MeSH indexing, to be eventually extended to multi-terminological indexing and Summary of Product Characteristics (SPC) analysis. NOOJ applications for other terminology such as ICD-10, SNOMED international, CCAM (French equivalent of US CPT) and TUV (French terminology for therapeutical and clinical notions for the use of drugs) will therefore be studied.
BibTeX: @inproceedings{Neveol2007b, author = {Aurélie Névéol. and Suzanne Pereira and Gaëlle Lortal and Stéfan Darmoni}, title = {Using NooJ for analyzing medical texts in French}, booktitle = {NOOJ Conference}, address = {Barcelona, Spain}, month = {june}, year = {2007}, url = {http://vodel.insa-rouen.fr/publications/cismef-nooj2007/} }
3 Communication internationale Soualmia, L & Dahamna, B. Knowledge Acquisition from a Medical Corpus: Use and Return on Experiences. Artificial Intelligence in Medicine Artificial Intelligence in Medicine, Lecture Notes in Computer Science, Volume 4594, Pages 160-164, Springer Berlin / Heidelberg, 2007.
Abstract: 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.
BibTeX: @inproceedings{Soualmia2007, author = {Soualmia, L and Dahamna, B}, title = {Knowledge Acquisition from a Medical Corpus: Use and Return on Experiences}, booktitle = {Artificial Intelligence in Medicine}, journal = {Artificial Intelligence in Medicine}, publisher = {Springer Berlin / Heidelberg}, year = {2007}, series = {Lecture Notes in Computer Science}, volume = {4594}, pages = {160-164}, url = {http://www.springerlink.com/index/j165732mqm231012.pdf}, doi = {10.1007/978-3-540-73599-1\_19} }
4 Communication nationale Darmoni, SJ. Recherche documentaire. Internet et Pédagogie Médicale (IPM), Strasbourg, France, Octobre, 2007.
Abstract: L'objectif est de couvrir le maximun des cours concernant la recherche documentaire par une mutualisation de ces cours. Expérience de Rouen.
BibTeX: @inproceedings{Darmoni2007a, author = {Darmoni, SJ}, title = {Recherche documentaire}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Strasbourg, France}, month = {Octobre}, year = {2007}, url = {http://www.canal-u.fr/index.php/canalu/producteurs/canal_u_medecine/dossier_programmes/pedagogie_des_sciences_medicales/colloque_et_evenement/internet_et_pedagogie_medicale_strasbourg_2007/ipm_2007} }
4 Communication nationale Duval, JP; Lecroq, T & Lefebvre, A. Efficient validation and construction of Knuth-Morris-Pratt arrays. , 2007. Conference in honor of Donald E. Knuth, Bordeaux, France, 2007.
BibTeX: @misc{Duval, author = {Duval, JP and Lecroq, T and Lefebvre, A}, title = {Efficient validation and construction of Knuth-Morris-Pratt arrays}, year = {2007}, note = {Conference in honor of Donald E. Knuth, Bordeaux, France, 2007} }
4 Communication nationale Florea, F; Cornea, V; Rogozan, A; Bensrhair, A & Darmoni, SJ. Fusion des approches visuelles et contextuelles pour l'annotation des images médicales. Extraction et Gestion des Connaissances (EGC), Namur, Belgique, 23-26 Janvier, Volume 2, Pages 421-426, 2007.
BibTeX: @inproceedings{Florea2007b, author = {Florea, F and Cornea, V and Rogozan, A and Bensrhair, A and Darmoni, SJ}, title = {Fusion des approches visuelles et contextuelles pour l'annotation des images m{\'e}dicales}, booktitle = {Extraction et Gestion des Connaissances (EGC)}, address = {Namur, Belgique}, month = {23-26 Janvier}, year = {2007}, volume = {2}, pages = {421-426} }
4 Communication nationale Kotowicz, JP.; Chaignaud, N.; Pecuchet, JP.; Loisel, A; Holzem, M.; Delavigne, V. & Darmoni, SJ.. Cogni-CISMeF : étude des processus cognitifs lors de la construction d'une requête dans un syste?me de gestion des connaissances me?dicales (CISMeF). Atelier Traitement des Connaissances, Apprentissage et NTIC, Plate-forme AFIA'07, Grenoble, 2-6 juillet, Pages 155-174, 2007.
BibTeX: @inproceedings{Kotowicz2007, author = {Kotowicz, JP. and Chaignaud, N. and Pecuchet, JP. and Loisel, A and Holzem, M. and Delavigne, V. and Darmoni, SJ.}, title = {Cogni-CISMeF : étude des processus cognitifs lors de la construction d'une requête dans un syste?me de gestion des connaissances me?dicales (CISMeF)}, booktitle = {Atelier Traitement des Connaissances, Apprentissage et NTIC, Plate-forme AFIA'07}, address = {Grenoble}, month = {2-6 juillet}, year = {2007}, pages = {155-174} }
4 Communication nationale Pereira, S; Massari, P; Joubert, M & Darmoni, SJ. Utilisation de métatermes pour la recherche d'information dans les dossiers médicaux.. JFIM, Bamako, Mali, Janvier, 2007.
BibTeX: @inproceedings{Pereira2007, author = {Pereira, S and Massari, P and Joubert, M and Darmoni, SJ}, title = {Utilisation de métatermes pour la recherche d'information dans les dossiers médicaux.}, booktitle = {JFIM}, address = {Bamako, Mali}, month = {Janvier}, year = {2007} }
4 Communication nationale Raaf, H; Abdeddaïm, S & Messabih, B. Beetweeness centrality of metabolic network using Elementary Net Systems. Actes du Quatrième Colloque sur l'Optimisation et les Systèmes d'Information COSI'2007, Oran, Algérie, Pages 567-577, 2007.
BibTeX: @inproceedings{Raaf2007, author = {Raaf, H and Abdeddaïm, S and Messabih, B}, title = {Beetweeness centrality of metabolic network using Elementary Net Systems}, booktitle = {Actes du Quatrième Colloque sur l'Optimisation et les Systèmes d'Information COSI'2007}, address = {Oran, Algérie}, year = {2007}, pages = {567--577} }
5 Résumé Caulin, C; Autret-Leca, E; Baumelou, A; Trémolières, F; German, C; Darmoni, SJ; Thirion B & Forget, JF. The therapeutic guidelines database, an original new tool. Fundamental & Clinical Pharmacology , Volume 21, Number s1, Pages 1-99, 2007.
Abstract: Introduction: Physicians are expected to prescribe according to current scientific data and evidence-based medicine, as embodied by official treatment guidelines. In order to apply these, physicians should be aware of ways to access them, and smoothly integrate their content into their daily practice. Our objectives were to provide validated summaries of treatment guidelines, to facilitate access to original documents, and to keep physicians informed on updates and related news. Methods: For one hundred most frequently encountered diseases, expert writers (GPs and specialists) were chosen to produce a summary of current validated treatment guidelines. The outline and content of these summaries were harmonized in order to increase user-friendliness. Tree-shaped decision algorithms constitute the core of each summary. They are completed with disease and diagnosis information, specific clinical situations, patient information as well as drug and non drug treatment information (all available medicinal products are listed). Whenever possible, these summaries are weighed with grades of recommendation corresponding to scientific levels of evidence, as defined by the HAS (high autority of health). Results: The therapeutic guidelines database is available through: - a website which proposes therapeutic guidelines summaries and related information regarding diseases most frequently encountered by GPs. A search engine has been integrated, which allows physicians to locate French and international treatment guidelines. This engine transforms queries expressed in usual French medical terms into MeSH (medical subjects headings) - compatible queries in order to search French and international databases efficaciously. We created a watch team to update the database and inform physicians about the latest available guidelines as well as other recent guidelinerelated news. - a pocket book with one hundred treatment strategies based on guideline summaries. Conclusion: The therapeutic guidelines database is the first one for Frenchspeaking healthcare professionals. It allows access to validated therapeutic guidelines (summaries, full-text guidelines, as well as related news). The next step is to measure the effects of this new tool on GPs daily practice.
BibTeX: @article{C2007, author = {Caulin, C and Autret-Leca, E and Baumelou, A and Trémolières, F and German, C and Darmoni, SJ and Thirion B and Forget, JF}, title = {The therapeutic guidelines database, an original new tool}, journal = {Fundamental \& Clinical Pharmacology}, year = {2007}, volume = {21}, number = {s1}, pages = {1-99}, doi = {10.1111/j.1472-8206.2007.00481.x} }
5 Résumé Darmoni, SJ; Thirion, B; Florea, F; Rogozan, A; Letord, C; Kerdelhué, G & Dacher, JN. Affiliation of a resource type to a MeSH term in a quality-controlled health gateway. Medinfo, 2007.
BibTeX: @inproceedings{Darmoni2007, author = {Darmoni, SJ and Thirion, B and Florea, F and Rogozan, A and Letord, C and Kerdelhué, G and Dacher, JN}, title = {Affiliation of a resource type to a MeSH term in a quality-controlled health gateway}, booktitle = {Medinfo}, year = {2007}, url = {http://www.chu-rouen.fr/l@stics/affiliation_medinfo_2007.pdf} }
5 Résumé Thirion, B; Pereira, S; Névéol, A; Dahamna, B & Darmoni, SJ.. French MeSH Browser: a cross-language tool to access MEDLINE/PubMed.. AMIA symp., Pages 1132, IOS Press, 2007.
Abstract: When searching the medical literature, health professionals and lay people strongly prefer to use their native language. Therefore, Medical Subject Headings (MeSH(R)) translations would be helpful to those who are not fluent in English to access scientific papers indexed in the MEDLINE(R) bibliographic database. Furthermore, medical terminologies such as MeSH are challenging in any language. Therefore, a French MeSH Browser was developed.
BibTeX: @inproceedings{Benoit2007, author = {Thirion, B and Pereira, S and Névéol, A and Dahamna, B and Darmoni, SJ.}, title = {French MeSH Browser: a cross-language tool to access MEDLINE/PubMed.}, booktitle = {AMIA symp.}, publisher = {IOS Press}, year = {2007}, pages = {1132}, url = {http://telemedicina.unifesp.br/pub/AMIA/2007%20AMIA%20Proceedings/data/papers/posters/AMIA-0243-S2007.pdf} }
2006 1 Publication internationale Crochemore, M & Lecroq, T. Text searching and indexing. Formal Languages and Applications, Studies in Computational Intelligence, Volume 25, Pages 43-80, Springer Verlag Berlin, 2006.
BibTeX: @incollection{Crochemore2006, author = {Crochemore, M and Lecroq, T}, title = {Text searching and indexing}, booktitle = {Formal Languages and Applications}, publisher = {Springer Verlag Berlin}, year = {2006}, series = {Studies in Computational Intelligence}, volume = {25}, pages = {43--80}, doi = {10.1007/978-3-540-33461-3_3} }
1 Publication internationale Darmoni, SJ; Névéol, A; Renard, JM; Gehanno, JF; Soualmia, L; Dahamna, B & Thirion, B. A MEDLINE categorization algorithm.. BMC Med Inform Decis Mak , Volume 6, Pages 7, 2006.
Abstract: 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. METHODS: The MEDLINE categorization algorithm (MCA) is based on semantic links existing between MeSH terms and metaterms on the one hand and between MeSH subheadings and metaterms on the other hand. These links are used to automatically infer a list of metaterms from any MeSH term/subheading indexing. Medical librarians manually select the semantic links. RESULTS: The MEDLINE categorization algorithm lists the medical specialties relevant to a MEDLINE file by decreasing order of their importance. The MEDLINE categorization algorithm is available on a Web site. It can run on any MEDLINE file in a batch mode. As an example, the top 3 medical specialties for the set of 60 articles published in BioMed Central Medical Informatics & Decision Making, which are currently indexed in MEDLINE are: information science, organization and administration and medical informatics. CONCLUSION: We have presented a MEDLINE categorization algorithm in order to classify the medical specialties addressed in any MEDLINE file in the form of a ranked list of relevant specialties. The categorization method introduced in this paper is based on the manual indexing of resources with MeSH (terms/subheadings) pairs by NLM indexers. This algorithm may be used as a new bibliometric tool.
BibTeX: @article{Darmoni2006, author = {Darmoni, SJ and Névéol, A and Renard, JM and Gehanno, JF and Soualmia, L and Dahamna, B and Thirion, B}, title = {A MEDLINE categorization algorithm.}, journal = {BMC Med Inform Decis Mak}, year = {2006}, volume = {6}, pages = {7}, doi = {10.1186/1472-6947-6-7} }
1 Publication internationale Ernoult, A; Tremauville, Y; Cellier, D; Margerie, P; Langlois, E & Alard, D. Potential landscape drivers of biodiversity components in a flood plain: Past or present patterns?. Biological Conservation , Volume 127, Number 1, Pages 1-17, 2006.
BibTeX: @article{Ernoult2006, author = {Ernoult, A and Tremauville, Y and Cellier, D and Margerie, P and Langlois, E and Alard, D}, title = {Potential landscape drivers of biodiversity components in a flood plain: Past or present patterns?}, journal = {Biological Conservation}, year = {2006}, volume = {127}, number = {1}, pages = {1--17}, doi = {10.1016/j.biocon.2005.07.008} }
1 Publication internationale Névéol, A; Rogozan, Aé & Darmoni, SJ. Automatic indexing of online health resources for a French quality controlled gateway. Information Processing & Management , May, Volume 42, Number 3, Pages 695-709, 2006.
Abstract: The profusion of online resources calls for tools and methods to help Internet users find precisely what they are looking for. Quality controlled gateway CISMeF provides such services for health resources. However, the human cost of maintaining and updating the catalogue are increasingly high. This paper presents the automatic indexing system currently developed in the CISMeF team to be used as such for preliminary indexing, or after human reviewing for the final indexing. The system architecture, using the INTEX platform for MeSH term extraction is detailed. The results of a first evaluation tend to indicate that the automatic indexing strategy is relevant, as it achieves a precision comparable to that of other existing operational systems. Moreover, the system presented in this paper retrieves keyword/qualifier pairs as opposed to single terms, therefore providing a significantly more precise indexing. Further development and tests will be carried out in order to improve the coverage of the dictionaries, and validate the efficiency of the system in the indexers' everyday work.
BibTeX: @article{Neveol2006b, author = {Névéol, A and Rogozan, Aé and Darmoni, SJ}, title = {Automatic indexing of online health resources for a French quality controlled gateway}, month = {May}, journal = {Information Processing \& Management}, year = {2006}, volume = {42}, number = {3}, pages = {695-709}, doi = {10.1016/j.ipm.2005.01.003} }
1 Publication internationale Robu, I; Robu, V & Thirion, B. An introduction to the Semantic Web for health sciences librarians.. J Med Libr Assoc , Apr, Volume 94, Number 2, Pages 198-205, 2006.
Abstract: OBJECTIVES: The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. METHODOLOGY: The paper is structured into two main parts. "Semantic Web Technology" provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. "Semantic Web Applications and Research Projects in the Biomedical Field" is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. DISCUSSION AND CONCLUSIONS: Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects.
BibTeX: @article{Robu2006, author = {Robu, I and Robu, V and Thirion, B}, title = {An introduction to the Semantic Web for health sciences librarians.}, month = {Apr}, journal = {J Med Libr Assoc}, year = {2006}, volume = {94}, number = {2}, pages = {198--205}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1435839} }
1 Publication internationale Sibert, L; Darmoni, SJ; Dahamna, B; Hellot, MF; Weber, J & Charlin, B. On line clinical reasoning assessment with Script Concordance test in urology: results of a French pilot study.. BMC Med Educ , Volume 6, Pages 45, 2006.
Abstract: BACKGROUND: 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. METHODS: A 97 items SC test was developed based on major educational objectives of French urology training programmes. A secure Web site was created with two sequential modules: a) The first one for the reference panel to elaborate the scoring system; b) The second for candidates with different levels of experience in urology: Board certified urologists, chief-residents, residents, medical students. All participants were recruited on a voluntary basis. Statistical analysis included descriptive statistics of the participants' scores and factorial analysis of variance (ANOVA) to study differences between groups' means. Reliability was evaluated with Cronbach's alpha coefficient. RESULTS: The on line SC test has been operational since June 2004. Twenty-six faculty members constituted the reference panel. During the following 10 months, 207 participants took the test online (124 urologists, 29 chief-residents, 38 residents, 16 students). No technical problem was encountered. Forty-five percent of the participants completed the test partially only. Differences between the means scores for the 4 groups were statistically significant (P = 0.0123). The Bonferroni post-hoc correction indicated that significant differences were present between students and chief-residents, between students and urologists. There were no differences between chief-residents and urologists. Reliability coefficient was 0.734 for the total group of participants. CONCLUSION: Feasibility of Web-based SC test was proved successful by the large number of participants who participated in a few months. This Web site has permitted to quickly confirm reliability of the SC test and develop strategy to improve construct validity of the test when applied in the field of urology. Nevertheless, optimisation of the SC test content, with a smaller number of items will be necessary. Virtual medical education initiative such as this SC test delivered on the Internet warrants consideration in the current context of national pre-residency certification examination in France.
BibTeX: @article{Sibert2006a, author = {Sibert, L and Darmoni, SJ and Dahamna, B and Hellot, MF and Weber, J and Charlin, B}, title = {On line clinical reasoning assessment with Script Concordance test in urology: results of a French pilot study.}, journal = {BMC Med Educ}, year = {2006}, volume = {6}, pages = {45}, doi = {10.1186/1472-6920-6-45} }
1 Publication internationale Sibert, L; Darmoni, SJ; Thirion, B; Douyère, M; Dahamna, B & Weber, J. A web-based teaching resource to prepare for final undergraduate examination: a French pilot study.. Med Teach , Mar, Volume 28, Number 2, Pages 158-164, 2006.
Abstract: 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' learning and should be a useful teaching resource for the preparation of the French Pre-Residency Examination.
BibTeX: @article{Sibert2006, author = {Sibert, L and Darmoni, SJ and Thirion, B and Douyère, M and Dahamna, B and Weber, J}, title = {A web-based teaching resource to prepare for final undergraduate examination: a French pilot study.}, month = {Mar}, journal = {Med Teach}, year = {2006}, volume = {28}, number = {2}, pages = {158--164}, doi = {10.1080/01421590500312920} }
2 Publication nationale Gehanno, JF; Kerdelhué, G; Darmoni, SJ; Fantoni, S; Caillard, JF & Frimat, P. Veille documentaire. Archives des Maladies Professionnelles et de l'Environnement , May, Volume 67, Pages 266-267, 2006.
BibTeX: @article{Gehanno2006, author = {Gehanno, JF and Kerdelhué, G and Darmoni, SJ and Fantoni, S and Caillard, JF and Frimat, P}, title = {Veille documentaire}, month = {May}, journal = {Archives des Maladies Professionnelles et de l'Environnement}, year = {2006}, volume = {67}, pages = {266-267}, url = {http://www.sciencedirect.com/science/article/B8JFG-4PR42F2-5G/2/1968f7b5e0022da180878cb2a4d3f887}, doi = {10.1016/S1775-8785(06)78134-6} }
2 Publication nationale Névéol, A & Darmoni, SJ. Terminologie et accès à l'information en santé.. Terminologie et accès à l'information, October, Pages 141-159, Hermes Science Publications, 2006.
BibTeX: @inproceedings{Neveol2006c, author = {Névéol, A and Darmoni, SJ}, title = {Terminologie et accès à l'information en santé.}, booktitle = {Terminologie et accès à l'information}, month = {October}, publisher = {Hermes Science Publications}, year = {2006}, pages = {141-159}, url = {http://www.lavoisier.fr/fr/livres/index.asp?texte=2746212950&select=isbn&from=Hermes} }
2 Publication nationale Paris, C & Gehanno, JF. Les apports de l'Evidence Based Medicine dans les pratiques de surveillance du médecin du travail.. Archives des Maladies Professionnelles et de l'Environnement , Volume 67, Number 2, Pages 154-7, 2006.
BibTeX: @article{Paris2006, author = {Paris, C and Gehanno, JF}, title = {Les apports de l'Evidence Based Medicine dans les pratiques de surveillance du médecin du travail.}, journal = {Archives des Maladies Professionnelles et de l'Environnement}, year = {2006}, volume = {67}, number = {2}, pages = {154-7}, doi = {ADMP-05-2006-67-2-1250-3274-101019-200517911} }
3 Communication internationale Duval, JP; Lecroq, T & Lefebvre, A. Efficient validation and construction of border arrays. Proceedings of the 11th Mons Days of Theoretical Computer Science, Rennes, France, Pages 179-189, 2006.
BibTeX: @inproceedings{Duval2006, author = {Duval, JP and Lecroq, T and Lefebvre, A}, title = {Efficient validation and construction of border arrays}, booktitle = {Proceedings of the 11th Mons Days of Theoretical Computer Science}, address = {Rennes, France}, year = {2006}, pages = {179--189}, url = {http://www.irisa.fr/JM06/Papers/duval.pdf} }
3 Communication internationale Florea, F; Barbu, E; Rogozan, A & Bensrhair, A. Using texture-based symbolic features for medical image representation. Proc. 18th International Conference on Pattern Recognition ICPR 2006, Volume 2, Pages 946-949, 2006.
BibTeX: @inproceedings{Florea2006, author = {Florea, F and Barbu, E and Rogozan, A and Bensrhair, A}, title = {Using texture-based symbolic features for medical image representation}, booktitle = {Proc. 18th International Conference on Pattern Recognition ICPR 2006}, year = {2006}, volume = {2}, pages = {946--949}, doi = {10.1109/ICPR.2006.1159} }
3 Communication internationale Florea, F; Barbu, E; Rogozan, A & Bensrhair, A. Multi-modal categorization of medical images for automatic indexing of on-line health-resources. 6th International Workshop on Pattern Recognition in Information Systems (PRIS2006), Paphos, Cyprus, 23 - 27, May 2006, Pages 48-57, 2006.
BibTeX: @inproceedings{Florea2006f, author = {Florea, F and Barbu, E and Rogozan, A and Bensrhair, A}, title = {Multi-modal categorization of medical images for automatic indexing of on-line health-resources}, booktitle = {6th International Workshop on Pattern Recognition in Information Systems (PRIS2006)}, address = {Paphos, Cyprus}, month = {23 - 27, May 2006}, year = {2006}, pages = {48-57} }
3 Communication internationale Florea, F; Barbu, E; Rogozan, A; Bensrhair, A & Buzuloiu, V. Medical Image Categorization using a Texture Based Symbolic Description. Proc. IEEE International Conference on Image Processing, Pages 1489-1492, 2006.
BibTeX: @inproceedings{Florea2006a, author = {Florea, F and Barbu, E and Rogozan, A and Bensrhair, A and Buzuloiu, V}, title = {Medical Image Categorization using a Texture Based Symbolic Description}, booktitle = {Proc. IEEE International Conference on Image Processing}, year = {2006}, pages = {1489--1492}, doi = {10.1109/ICIP.2006.312564} }
3 Communication internationale Florea, F; Rogozan, A; Bensrhair, A & Darmoni, SJ. Comparison of Feature-Selection and Classification Techniques for Medical Image Modality Categorization. 10th IEEE International Conference on Optimization of Electrical and Electronic Equipment (OPTIM2006), Brasov, Romania, May 18-19, Volume 4, Pages 161-168, 2006.
BibTeX: @inproceedings{Florea2006h, author = {Florea, F and Rogozan, A and Bensrhair, A and Darmoni, SJ}, title = {Comparison of Feature-Selection and Classification Techniques for Medical Image Modality Categorization}, booktitle = {10th IEEE International Conference on Optimization of Electrical and Electronic Equipment (OPTIM2006)}, address = {Brasov, Romania}, month = {May 18-19}, year = {2006}, volume = {4}, pages = {161-168}, url = {http://asi.insa-rouen.fr/~fflorea/documents/rapport_intern_PSI_FFI.pdf} }
3 Communication internationale Florea, F; Rogozan, A; Cornea, V; Bensrhair, A & Darmoni, SJ. MedIC/CISMeF at ImageCLEF 2006: Image Annotation and Retrieval Tasks. CLEF 2006 Workshop, Alicante, Spain, 20 - 22 September, 2006.
BibTeX: @inproceedings{Florea2006g, author = {Florea, F and Rogozan, A and Cornea, V and Bensrhair, A and Darmoni, SJ}, title = {MedIC/CISMeF at ImageCLEF 2006: Image Annotation and Retrieval Tasks}, booktitle = {CLEF 2006 Workshop}, address = {Alicante, Spain}, month = {20 - 22 September}, year = {2006}, url = {http://www.clef-campaign.org/2006/working_notes/workingnotes2006/floreaCLEF2006.pdf} }
3 Communication internationale Gehanno, JF; Darmoni, SJ; Weber, J & Caillard, JF. Citation classics in occupational medicine journals.. 28th Congress of the International Commission of Occupational Health, Milan, Italy, June, 2006.
BibTeX: @inproceedings{Gehanno2006b, author = {Gehanno, JF and Darmoni, SJ and Weber, J and Caillard, JF}, title = {Citation classics in occupational medicine journals.}, booktitle = {28th Congress of the International Commission of Occupational Health}, address = {Milan, Italy}, month = {June}, year = {2006} }
3 Communication internationale Joubert, M; Peretti, AL; Darmoni, SJ; Dahamna, B & Fieschi,M. Contribution to an automated indexing of French-language health web sites.. AMIA Annu Symp Proc , Pages 409-413, 2006.
Abstract: OBJECTIVES: to improve the indexing of French-language health web sites by emphasizing the major terms that best describe them. MATERIAL AND METHODS: this study exploits both UMLS knowledge sources and results of previous research. It proposes a method for ranking MeSH terms taken from each record in order of relevance. The method is tested on a corpus of records taken from the French-language health gateway CISMeF. RESULTS: the results of the experiment are compared to those of a preliminary study performed on a corpus taken from MEDLINE. DISCUSSION: the ultimate objective of this work is to interface the developed tools with an automated MeSH term extractor in order to propose an automated indexing engine for French-language health web sites.
BibTeX: @article{Joubert2006, author = {Joubert, M and Peretti, AL and Darmoni, SJ and Dahamna, B and Fieschi,M}, title = {Contribution to an automated indexing of French-language health web sites.}, journal = {AMIA Annu Symp Proc}, year = {2006}, pages = {409--413}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1839524} }
3 Communication internationale Neveol, A; Zeng, K & Bodenreider, O. Besides precision & recall: exploring alternative approaches to evaluating an automatic indexing tool for MEDLINE.. AMIA Annu Symp Proc , Pages 589-593, 2006.
Abstract: OBJECTIVE: This paper explores alternative approaches for the evaluation of an automatic indexing tool for MEDLINE, complementing the traditional precision and recall method. MATERIALS AND METHODS: The performance of MTI, the Medical Text Indexer used at NLM to produce MeSH recommendations for biomedical journal articles is evaluated on a random set of MEDLINE citations. The evaluation examines semantic similarity at the term level (indexing terms). In addition, the documents retrieved by queries resulting from MTI index terms for a given document are compared to the PubMed related citations for this document. RESULTS: Semantic similarity scores between sets of index terms are higher than the corresponding Dice similarity scores. Overall, 75% of the original documents and 58% of the top ten related citations are retrieved by queries based on the automatic indexing. CONCLUSIONS: The alternative measures studied in this paper confirm previous findings and may be used to select particular documents from the test set for a more thorough analysis.
BibTeX: @article{Neveol2006a, author = {Neveol, A and Zeng, K and Bodenreider, O}, title = {Besides precision \& recall: exploring alternative approaches to evaluating an automatic indexing tool for MEDLINE.}, journal = {AMIA Annu Symp Proc}, year = {2006}, pages = {589--593}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1839480} }
3 Communication internationale Névéol, A; Pereira, S; Soualmia, L; Thirion, B & Darmoni, SJ. A method of cross-lingual consumer health information retrieval.. Stud Health Technol Inform , Volume 124, Pages 601-608, 2006.
Abstract: OBJECTIVES: This paper presents a method of cross-language information retrieval aiming to make medical information available to patients in French and English, regardless of the query language they wish to use. METHODS: We describe the two MeSH-related terminologies used in this work. We show that the French patient synonyms included in CISMeF can be automatically mapped to the English consumer-oriented health topics used in MEDLINEplus, via the MeSH thesaurus. The links between French and English patient terms thus inferred can subsequently be exploited to automatically translate patient queries. RESULTS: 129 MEDLINEplus topics have been mapped to 142 CISMeF patient synonyms. Contextual links for cross-language retrieval have been added to the patient dedicated French information Gateway CISMeF. Conclusion: we have presented an efficient method for cross-lingual patient information retrieval in French and English, which may also be applied to other language pairs, subject to the availability of patient terminologies and of the MeSH thesaurus in these languages.
BibTeX: @article{Neveol2006, author = {Névéol, A and Pereira, S and Soualmia, L and Thirion, B and Darmoni, SJ}, title = {A method of cross-lingual consumer health information retrieval.}, journal = {Stud Health Technol Inform}, year = {2006}, volume = {124}, pages = {601--608} }
3 Communication internationale Pereira, S; Névéol, A; Massari, P; Joubert, M & Darmoni, SJ. Construction of a semi-automated ICD-10 coding help system to optimize medical and economic coding.. Stud Health Technol Inform , Volume 124, Pages 845-850, 2006.
Abstract: INTRODUCTION: In order to measure the medical activity in hospitals, physicians are required to code manually information concerning a patient's stay using ICD-10. This requires trained staff and a lot of time. We propose to help speed up and facilitate the tedious task of coding patient information. METHODS: we show two methods. First, we propose an automated ICD-10-based coding help system using an automated MeSH-based indexing system and a mapping between MeSH and ICD-10 extracted from the UMLS metathesaurus. Secondly, we propose the use of drug prescriptions to complete the previous coding with the use of a mapping between a given prescription drug and the relevant ICD-10 codes (in compliance with the drug approval). RESULTS: the results of a preliminary experiment indicate that the precision of the indexing system is 40% and the recall is 30% when we compare to an economic rules-based coding and to a descriptive coding. Discussion: moreover, we show that the use of prescription coding is relevant as the recall reaches 68% when the Vidal tool is used. CONCLUSION: Then, it is very interesting to complete the coding obtained automatically by the indexing/mapping system by the coding obtained from the prescriptions.
BibTeX: @article{Pereira2006, author = {Pereira, S and Névéol, A and Massari, P and Joubert, M and Darmoni, SJ}, title = {Construction of a semi-automated ICD-10 coding help system to optimize medical and economic coding.}, journal = {Stud Health Technol Inform}, year = {2006}, volume = {124}, pages = {845--850} }
3 Communication internationale Prieur, E & Lecroq, T. On-line construction of suffix vectors and maximal repeats. Proceedings of the 11th Mons Days of Theoretical Computer Science, Rennes, France, Pages 311-322, 2006.
BibTeX: @inproceedings{Prieur2006, author = {Prieur, E and Lecroq, T}, title = {On-line construction of suffix vectors and maximal repeats}, booktitle = {Proceedings of the 11th Mons Days of Theoretical Computer Science}, address = {Rennes, France}, year = {2006}, pages = {311--322}, url = {http://www.irisa.fr/JM06/Papers/prieur.pdf} }
3 Communication internationale Prieur, E & Lecroq, T. From suffix trees to suffix vectors. International Journal on Foundations of Computer Science , Volume 17, Number 6, Pages 1385-1402, 2006.
BibTeX: @article{Prieur2006a, author = {Prieur, E and Lecroq, T}, title = {From suffix trees to suffix vectors}, journal = {International Journal on Foundations of Computer Science}, year = {2006}, volume = {17}, number = {6}, pages = {1385--1402}, url = {http://www.stringology.org/cgi-bin/getfile.cgi?t=pdf&c=-&y=2005&n=3} }
3 Communication internationale Sibert, L; Darmoni, SJ; Benichou J; Dahamna, B & Weber, J. Online clinical reasoning assessment with the Script Concordance test: Results of a French pilot study.. 12th International Ottawa Conference on Medical Education, NY, USA, May, 2006.
BibTeX: @inproceedings{Sibert2006b, author = {Sibert, L and Darmoni, SJ and Benichou J and Dahamna, B and Weber, J}, title = {Online clinical reasoning assessment with the Script Concordance test: Results of a French pilot study.}, booktitle = {12th International Ottawa Conference on Medical Education}, address = {NY, USA}, month = {May}, year = {2006} }
3 Communication internationale Soualmia, L; Dahamna, B; Thirion, B & Darmoni, SJ. Strategies for health information retrieval.. Stud Health Technol Inform , Volume 124, Pages 595-600, 2006.
Abstract: BACKGROUND: 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. OBJECTIVE: 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. RESULTS: 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. CONCLUSION: The implemented heuristics contribute significantly with good results in maximising as much as possible the recall of the Doc'CISMeF search tool.
BibTeX: @article{Soualmia2006, author = {Soualmia, L and Dahamna, B and Thirion, B and Darmoni, SJ}, title = {Strategies for health information retrieval.}, journal = {Stud Health Technol Inform}, year = {2006}, volume = {124}, pages = {595--600} }
4 Communication nationale BRUNESSAUX, S; DAHAMNA, B; GALLINARI, P; KASSEL, G; MESNARD, O; PÉCUCHET, JP & SZULMAN, S. RNTL Technolangue ATONANT. Aide à l'enrichissement semi-automatique d'ontologies. TALN (Traitement automatique des langues naturelles), Leuven, France, Avril, Presses universitaires de Louvain, 2006.
BibTeX: @inproceedings{Sylvie2006, author = {BRUNESSAUX, S and DAHAMNA, B and GALLINARI, P and KASSEL, G and MESNARD, O and PÉCUCHET, JP and SZULMAN, S}, title = {RNTL Technolangue ATONANT. Aide à l'enrichissement semi-automatique d'ontologies}, booktitle = {TALN (Traitement automatique des langues naturelles)}, address = {Leuven, France}, month = {Avril}, publisher = {Presses universitaires de Louvain}, year = {2006}, edition = {Piet Mertens and Cedrick FAIRON and Anne DISTER et Patrick Watrin (Eds)}, url = {http://www.technolangue.net/IMG/pdf/Atonant-Taln06.pdf} }
4 Communication nationale Gehanno, JF; Kerdelhué, G; Darmoni, SJ; Fantoni, S; Caillard, J & Frimat, P. Veille documentaire en santé au travail.. 29eme Congrès National de Médecine et Santé au Travail, Lyon, France, Mai, 2006.
BibTeX: @inproceedings{Gehanno2006a, author = {Gehanno, JF and Kerdelhué, G and Darmoni, SJ and Fantoni, S and Caillard, J and Frimat, P}, title = {Veille documentaire en santé au travail.}, booktitle = {29eme Congrès National de Médecine et Santé au Travail}, address = {Lyon, France}, month = {Mai}, year = {2006} }
5 Résumé Burgun, A; Darmoni, SJ; Le Duff, F & Wéber, J. Problem-based learning in medical informatics for undergraduate medical students: an experiment in two medical schools.. Int J Med Inform , May, Volume 75, Number 5, Pages 396-402, 2006.
Abstract: PURPOSE: The objective of this work was to assess problem-based learning (PBL) as a method for teaching information and communication technology in medical informatics (MI) courses. A study was conducted in the Schools of Medicine of Rennes and Rouen (France) with third-year medical students. METHODS: The "PBL-in-MI" sessions included a first tutorial group meeting, then personal work, followed by a second tutorial group meeting. A problem that simulated practice and was focused on information technology was discussed. In Rouen, the students were familiar with PBL, and they enrolled on a voluntary basis, while in Rennes, the students were first-ever participants in PBL courses, and the program was mandatory. One hundred and seventy-seven students participated in the PBL-in-MI sessions and were given a questionnaire in order to evaluate qualitatively the sessions. RESULTS AND DISCUSSION: The response rate was 92.1 The overall opinion of the students was good. 69.8% responded positively to the program. In Rouen, where the students participated in PBL-in-MI sessions on a voluntary basis, the students were significantly more enthusiastic about PBL-in-MI. Moreover, attitudes and opinions of students are plausibly related to differences in previous PBL skills. The fact that the naïve group had two tutors, one trained and one naïve as the students, has been investigated. Teacher naivety was an explanatory factor for the differences between Rennes and Rouen.
BibTeX: @article{Burgun2006, author = {Burgun, A and Darmoni, SJ and Le Duff, F and Wéber, J}, title = {Problem-based learning in medical informatics for undergraduate medical students: an experiment in two medical schools.}, month = {May}, journal = {Int J Med Inform}, year = {2006}, volume = {75}, number = {5}, pages = {396--402}, doi = {10.1016/j.ijmedinf.2005.07.014} }
5 Résumé Florea, F; Müller, H; Rogozan, A; Geissbuhler, A & Darmoni, SJ. Medical image categorization with MedIC and MedGIFT. Medical Informatics Europe (MIE2006), Maastricht, Netherlands, 27-30 August, Pages 3-11, 2006.
Abstract: Images play an important role in medical diagnostics and treatment planning. Whereas medical text retrieval, analysis, and reuse have been practiced for many years, much less is known on the storage and reuse of images in a context other than a single patient, although several medical teaching files with images exist. The aim of automatic image indexing/retrieval is to provide efficient and fast access to image collections to reuse stored information. When indexing medical images, the automatic categorization provides the means of extracting otherwise unavailable information about the images. Image categorization is usually applied in a context where a large number of images needs to be treated automatically and where no or only little text is available. This study will focus on a database extracted from online resources of the CISMeF health-catalogue. The aim is to assess the performance of two medical image categorization architectures in a complex environment (10322 images, 33 classes, multiple modalities, anatomical regions, and view-angles). The image database was extracted and annotated in collaboration with an experienced radiologist. The two compared systems have very different architectures. MedIC is an architecture based on machine learning applied to several sets of image texture and grey-level statistics. It achieves a maximum accuracy of 97.24% on 32 classes (representing different modalities, anatomical regions and view angles) and 98.47% on 6 classes (representing only the medical modality), when using an SVM classifier. MedGIFT on the other hand is a visual retrieval system where the visually most similar images are used to classify new images, currently without any learning strategy. This approach reaches an accuracy of 95.25% for the 32 classes and 97.15% for detecting the modality. By including a proper learning strategy these results can be expected to increase. The results show that image categorization has reached an accuracy that can be regarded as sufficient for many automatic image categorization tasks to get information on poorly annotated image collections.
BibTeX: @inproceedings{Florea2006b, author = {Florea, F and Müller, H and Rogozan, A and Geissbuhler, A and Darmoni, SJ}, title = {Medical image categorization with MedIC and MedGIFT}, booktitle = {Medical Informatics Europe (MIE2006)}, address = {Maastricht, Netherlands}, month = {27-30 August}, year = {2006}, pages = {3-11} }
2005 1 Publication internationale Duval, JP; Lecroq, T & Lefebvre, A. Border Array on Bounded Alphabet. Journal of Automata Language and Combinatorics , Volume 10, Number 1, Pages 51-60, 2005.
BibTeX: @article{Duval2005, author = {Duval, JP and Lecroq, T and Lefebvre, A}, title = {Border Array on Bounded Alphabet}, journal = {Journal of Automata Language and Combinatorics}, year = {2005}, volume = {10}, number = {1}, pages = {51--60}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/dll.pdf} }
1 Publication internationale Gehanno, JF; Darmoni, SJ & Caillard, JF. Major inaccuracies in articles citing occupational or environmental medicine papers and their implications.. J Med Libr Assoc , Jan, Volume 93, Number 1, Pages 118-121, 2005.
BibTeX: @article{Gehanno2005, author = {Gehanno, JF and Darmoni, SJ and Caillard, JF}, title = {Major inaccuracies in articles citing occupational or environmental medicine papers and their implications.}, month = {Jan}, journal = {J Med Libr Assoc}, year = {2005}, volume = {93}, number = {1}, pages = {118--121}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=545131} }
1 Publication internationale Pelfrêne, J; Abdeddaïm, S & Alexandre, J. Extracting approximate patterns. Journal on Discrete Algorithms , Volume 3, Number 2--4, Pages 293-320, 2005.
BibTeX: @article{Pelfrene2005, author = {Pelfrêne, J and Abdeddaïm, S and Alexandre, J}, title = {Extracting approximate patterns}, journal = {Journal on Discrete Algorithms}, year = {2005}, volume = {3}, number = {2--4}, pages = {293--320}, doi = {10.1016/j.jda.2004.08.010} }
1 Publication internationale Sibert, L; Darmoni, SJ; Dahamna, B; Weber, J & Charlin, B. Online clinical reasoning assessment with the Script Concordance test: a feasibility study.. BMC Med Inform Decis Mak , Volume 5, Pages 18, 2005.
Abstract: BACKGROUND: The script concordance (SC) test is an assessment tool that measures capacity to solve ill-defined problems, that is, reasoning in context of uncertainty. This tool has been used up to now mainly in medicine. The purpose of this pilot study is to assess the feasibility of the test delivered on the Web to French urologists. METHODS: The principle of SC test construction and the development of the Web site are described. A secure Web site was created with two sequential modules: (a) The first one for the reference panel (n = 26) with two sub-tasks: to validate the content of the test and to elaborate the scoring system; (b) The second for candidates with different levels of experience in Urology: Board certified urologists, residents, medical students (5 or 6th year). Minimum expected number of participants is 150 for urologists, 100 for residents and 50 for medical students. Each candidate is provided with an individual access code to this Web site. He/she may complete the Script Concordance test several times during his/her curriculum. RESULTS: The Web site has been operational since April 2004. The reference panel validated the test in June of the same year during the annual seminar of the French Society of Urology. The Web site is available for the candidates since September 2004. In six months, 80% of the target figure for the urologists, 68% of the target figure for the residents and 20% of the target figure for the student passed the test online. During these six months, no technical problem was encountered. CONCLUSION: The feasibility of the web-based SC test is successful as two-thirds of the expected number of participants was included within six months. Psychometric properties (validity, reliability) of the test will be evaluated on a large scale (N = 300). If positive, educational impact of this assessment tool will be useful to help urologists during their curriculum for the acquisition of clinical reasoning skills, which is crucial for professional competence.
BibTeX: @article{Sibert2005, author = {Sibert, L and Darmoni, SJ and Dahamna, B and Weber, J and Charlin, B}, title = {Online clinical reasoning assessment with the Script Concordance test: a feasibility study.}, journal = {BMC Med Inform Decis Mak}, year = {2005}, volume = {5}, pages = {18}, doi = {10.1186/1472-6947-5-18} }
1 Publication internationale Soualmia, L & Darmoni, SJ. Combining different standards and different approaches for health information retrieval in a quality-controlled gateway.. Int J Med Inform , Mar, Volume 74, Number 2-4, Pages 141-150, 2005.
Abstract: Internet as source of information is increasing in preeminence in numerous fields, including health. We describe in this paper the CISMeF project (acronym of Catalogue and Index of French-speaking Medical Sites) which has been designed to help the health information consumers and health professionals to find what they are looking for among the numerous health documents available online. The catalogue is founded on two standards: a set of metadata and a terminology based on the MeSH thesaurus which has the same structure and use as an ontology of the medical domain. The structure of the catalogue allows us to place the project at an overlap between the present Web, which is informal, and the forthcoming Semantic Web. Many features of information retrieval and navigation through the catalogue were developed. These features take into account the kind of the end-user (health professional, medical student, patient). The CISMeF-patients catalogue is a sub-catalogue of CISMeF and is dedicated to the patients and the general public. It shares the same model as CISMeF whereas MEDLINE and MedlinePlus do not. We also propose to couple two approaches (morphological processing and data mining) to help the users by correcting and refining their queries.
BibTeX: @article{Soualmia2005, author = {Soualmia, L and Darmoni, SJ}, title = {Combining different standards and different approaches for health information retrieval in a quality-controlled gateway.}, month = {Mar}, journal = {Int J Med Inform}, year = {2005}, volume = {74}, number = {2-4}, pages = {141--150}, doi = {10.1016/j.ijmedinf.2004.05.012} }
1 Publication internationale Zweigenbaum, P; Baud, R; Burgun, A; Namer, F; Jarrousse, E; Grabar, N; Ruch, P; Le Duff, F; Forget, JF; Douyère, M & Darmoni, SJ. UMLF: a unified medical lexicon for French.. Int J Med Inform , Mar, Volume 74, Number 2-4, Pages 119-124, 2005.
Abstract: Medical Informatics has a constant need for basic medical language processing tasks, e.g. for coding into controlled vocabularies, free text indexing and information retrieval. Most of these tasks involve term matching and rely on lexical resources: lists of words with attached information, including inflected forms and derived words, etc. Such resources are publicly available for the English language with the UMLS Specialist Lexicon, but not in other languages. For the French language, several teams have worked on the subject and built local lexical resources. The goal of the present work is to pool and unify these resources and to add extensively to them by exploiting medical terminologies and corpora, resulting in a unified medical lexicon for French (UMLF). This paper exposes the issues raised by such an objective, describes the methods on which the project relies and illustrates them with experimental results.
BibTeX: @article{Zweigenbaum2005, author = {Zweigenbaum, P and Baud, R and Burgun, A and Namer, F and Jarrousse, E and Grabar, N and Ruch, P and Le Duff, F and Forget, JF and Douyère, M and Darmoni, SJ}, title = {UMLF: a unified medical lexicon for French.}, month = {Mar}, journal = {Int J Med Inform}, year = {2005}, volume = {74}, number = {2-4}, pages = {119--124}, doi = {10.1016/j.ijmedinf.2004.03.010} }
2 Publication nationale Névéol, A. Automatisation des tâches documentaires dans un catalogue de santé en ligne. School: INSA de Rouen, 2005.
BibTeX: @phdthesis{Neveol2005e, author = {Névéol, A}, title = {Automatisation des tâches documentaires dans un catalogue de santé en ligne}, school = {INSA de Rouen}, year = {2005}, url = {http://aurelie.neveol.free.fr/theseAN.pdf} }
2 Publication nationale Thirion, B & Bonmarchand, G. Comment trouver ou retrouver les recommandations de bonne pratique en langue francaise ou anglaise ?. Reanimation , September, Volume 14, Pages 411-415, 2005.
BibTeX: @article{Thirion2005, author = {Thirion, B and Bonmarchand, G}, title = {Comment trouver ou retrouver les recommandations de bonne pratique en langue francaise ou anglaise ?}, month = {September}, journal = {Reanimation}, year = {2005}, volume = {14}, pages = {411-415}, doi = {10.1016/j.reaurg.2005.07.001} }
3 Communication internationale Florea, F; Vertan, C; Rogozan, A; Bensrhair, A & Darmoni, SJ. Comparison of histogram-based feature sets for medical image modality categorization. Proc. International Symposium on Signals, Circuits and Systems ISSCS 2005, Iasi, Romania, 14-15 July, Volume 1, Pages 47-50 Vol. 1, 2005.
BibTeX: @inproceedings{Florea2005, author = {Florea, F and Vertan, C and Rogozan, A and Bensrhair, A and Darmoni, SJ}, title = {Comparison of histogram-based feature sets for medical image modality categorization}, booktitle = {Proc. International Symposium on Signals, Circuits and Systems ISSCS 2005}, address = {Iasi, Romania}, month = {14-15 July}, year = {2005}, volume = {1}, pages = {47--50 Vol. 1}, doi = {10.1109/ISSCS.2005.1509847} }
3 Communication internationale Gehanno, JF. Evidence Based Medicine in occupational health. Why and how to find relevant information on health screening and health surveillance in scientific literature.. CME: Health, Work & Environment, Inter-University Centre. Dubrovnik, Croatia, September, 2005.
BibTeX: @inproceedings{Gehanno2005b, author = {Gehanno, JF}, title = {Evidence Based Medicine in occupational health. Why and how to find relevant information on health screening and health surveillance in scientific literature.}, booktitle = {CME: Health, Work \& Environment}, address = {Inter-University Centre. Dubrovnik, Croatia}, month = {September}, year = {2005} }
3 Communication internationale Groult, R; Léonard, M & Mouchard, L. A Linear Algorithm for the Detection of Evolutive Tandem Repeats. Journal of Automata, Languages and Combinatorics , Volume 10, Number 5/6, Pages 671-685, 2005.
BibTeX: @article{Groult2005, author = {Groult, R and Léonard, M and Mouchard, L}, title = {A Linear Algorithm for the Detection of Evolutive Tandem Repeats}, journal = {Journal of Automata, Languages and Combinatorics}, year = {2005}, volume = {10}, number = {5/6}, pages = {671-685} }
3 Communication internationale Letellier, S; Leuraud, K; Arnaud, P & Darmoni, SJ. Usability study on two handheld computers to retrieve drug information.. Stud Health Technol Inform , Volume 116, Pages 322-327, 2005.
Abstract: Objective :Performing a usability study on two handheld computers (personal digital assistant and tablet PC), as tools for retrieving drug information.Materials and methods: A randomised crossover study was performed: 34 students in pharmacy and medicine used the two handheld tools in a randomised order, to answer a questionnaire containing 12 questions covering all the aspects of a drug database and a qualitative analysis on six different items to measure access to drug information. The availability of the drug information database Vidal on PDA and on tablet PC implied our choice of the database. Three main criteria for evaluation were chosen: success rates, time-on-task, and number of clicks.Results: There were no significant differences between the two groups neither on age, sex, medical discipline, study years nor previous computer practice. The success rate is significantly higher with the PDA for only one question. The PDA is significantly faster than the tablet PC on 7 of the 12 questions and generates fewer clicks for 3 questions. Compared to the tablet PC, it appears that the PDA is better in terms of clearness, navigability and usefulness for professional practice and it is the only tool which is significantly preferred to all other supports.Conclusion: In this study with students, the PDA is significantly more effective quantitatively and qualitatively than the tablet PC to retrieve drug information.
BibTeX: @article{Letellier2005, author = {Letellier, S and Leuraud, K and Arnaud, P and Darmoni, SJ}, title = {Usability study on two handheld computers to retrieve drug information.}, journal = {Stud Health Technol Inform}, year = {2005}, volume = {116}, pages = {322--327}, url = {http://www.magic5.unile.it/PapDoc/Article/MIE2005/TOC%20Scientific%20Contributions/Handheld%20and%20Wireless%20Computing/290.pdf} }
3 Communication internationale Névéol, A; Mary, V; Gaudinat, A; Rogozan, A & Darmoni, SJ. A Benchmark Evaluation of the French MeSH Indexing Systems. 10th Conference on Artificial Intelligence in Medicine, 2005.
BibTeX: @inproceedings{Neveol2005d, author = {Névéol, A and Mary, V and Gaudinat, A and Rogozan, A and Darmoni, SJ}, title = {A Benchmark Evaluation of the French MeSH Indexing Systems}, booktitle = {10th Conference on Artificial Intelligence in Medicine}, year = {2005}, url = {http://www.chu-rouen.fr/l@stics/NeveolAIME05long.pdf} }
3 Communication internationale Névéol, A; Mork, J; Aronson, AR & Darmoni, SJ. Evaluation of French and English MeSH indexing systems with a parallel corpus.. AMIA Annu Symp Proc , Pages 565-569, 2005.
Abstract: OBJECTIVE: This paper presents the evaluation of two MeSH indexing systems for French and English on a parallel corpus. MATERIAL AND METHODS: We describe two automatic MeSH in-dexing systems - MTI for English, and MAIF for French. The French version of the evaluation resources has been manually indexed with MeSH keyword/qualifier pairs. This professional indexing is used as our gold standard in the evaluation of both systems on keyword retrieval. RESULTS: The English system (MTI) obtains significantly better precision and recall (78% precision and 21% recall at rank 1, vs. 37 precision and 6% recall for MAIF ). Moreover, the performance of both systems can be optimised by the break-age function used by the French system (MAIF), which selects an adaptive number of descriptors for each resource indexed. CONCLUSION: MTI achieves better performance. However, both systems have features that can benefit each other.
BibTeX: @article{Neveol2005, author = {Névéol, A and Mork, J and Aronson, AR and Darmoni, SJ}, title = {Evaluation of French and English MeSH indexing systems with a parallel corpus.}, journal = {AMIA Annu Symp Proc}, year = {2005}, pages = {565--569}, url = {http://www.chu-rouen.fr/l@stics/NeveolAMIA2005.pdf} }
3 Communication internationale Prieur, E & Lecroq, T. From suffix trees to suffix vectors. Proceedings of the Prague Stringology Conference (PSC 2005), Prague, Czech Republic, Pages 37-53, 2005.
BibTeX: @inproceedings{Prieur2005a, author = {Prieur, E and Lecroq, T}, title = {From suffix trees to suffix vectors}, booktitle = {Proceedings of the Prague Stringology Conference (PSC 2005)}, address = {Prague, Czech Republic}, year = {2005}, pages = {37--53} }
3 Communication internationale Renard, JM; Brunetaud, JM; Cuggia, M; Darmoni, SJ; Lebeux, P & Beuscart, R. An Improved Publication Process for the UMVF.. Stud Health Technol Inform , Volume 116, Pages 279-283, 2005.
Abstract: The "Université Médicale Virtuelle Francophone" (UMVF) is a federation of French medical schools. Its main goal is to share the production and use of pedagogic medical resources generated by academic medical teachers. We developed an Open-Source application based upon a workflow system which provides an improved publication process for the UMVF. For teachers, the tool permits easy and efficient upload of new educational resources. For web masters it provides a mechanism to easily locate and validate the resources. For both the teachers and the web masters, the utility provides the control and communication functions that define a workflow system.For all users, students in particular, the application improves the value of the UMVF repository by providing an easy way to find a detailed description of a resource and to check any resource from the UMVF to ascertain its quality and integrity, even if the resource is an old deprecated version. The server tier of the application is used to implement the main workflow functionalities and is deployed on certified UMVF servers using the PHP language, an LDAP directory and an SQL database. The client tier of the application provides both the workflow and the search and check functionalities and is implemented using a Java applet through a W3C compliant web browser. A unique signature for each resource, was needed to provide security functionality and is implemented using the MD5 Digest algorithm. The testing performed by Rennes and Lille verified the functionality and conformity with our specifications.
BibTeX: @article{Renard2005, author = {Renard, JM and Brunetaud, JM and Cuggia, M and Darmoni, SJ and Lebeux, P and Beuscart, R}, title = {An Improved Publication Process for the UMVF.}, journal = {Stud Health Technol Inform}, year = {2005}, volume = {116}, pages = {279--283} }
4 Communication nationale Darmoni, SJ. Les sites Internet éducatifs et de prévention. Le patient au c?ur du système d?information de santé. Congrès du Graph, Marseille, France, Janvier, 2005.
BibTeX: @inproceedings{Darmoni2005, author = {Darmoni, SJ}, title = {Les sites Internet éducatifs et de prévention}, booktitle = {Le patient au c?ur du système d?information de santé. Congrès du Graph}, address = {Marseille, France}, month = {Janvier}, year = {2005}, url = {http://gestions-hospitalieres.fr/article.php?ref_article=2386} }
4 Communication nationale Florea, F; Rogozan, A; Bensrhair, A & Darmoni, SJ. Medical image retrieval by content and keyword in an on-line health-catalogue context. Computer Vision/Computer Graphics Collaboration Techniques and Applications (Mirage2005), INRIA Rocquencourt, France, Pages 229-236, 2005.
BibTeX: @inproceedings{Florea2005c, author = {Florea, F and Rogozan, A and Bensrhair, A and Darmoni, SJ}, title = {Medical image retrieval by content and keyword in an on-line health-catalogue context}, booktitle = {Computer Vision/Computer Graphics Collaboration Techniques and Applications (Mirage2005)}, address = {INRIA Rocquencourt, France}, year = {2005}, pages = {229-236} }
4 Communication nationale Florea, F; Rogozan, A; Bensrhair, A; Dacher J-N & Darmoni, SJ. Recherche des images médicales par contenu et type de ressource dans un catalogue de santé en ligne. JFIM Journées Francophones d'Informatique Médicale, Lille, France, 12-13 mai, 1-7, 2005.
BibTeX: @inproceedings{Florea2005b, author = {Florea, F and Rogozan, A and Bensrhair, A and Dacher J-N and Darmoni, SJ}, title = {Recherche des images médicales par contenu et type de ressource dans un catalogue de santé en ligne}, booktitle = {JFIM Journées Francophones d'Informatique Médicale}, address = {Lille, France}, month = {12-13 mai}, year = {2005}, series = {1-7}, url = {http://litismail.insa-rouen.fr/MnemosNet/psipubli.nsf/ce6c2c540f564a2dc125680200361b7c/96a6886bc83ef1fbc1256fd30030933d/$FILE/11-Florea-Jfim05.pdf} }
4 Communication nationale Gehanno, JF; Thirion, B; Darmoni, SJ & Caillard JF. La recherche documentaire sur le risque cancérogène par le médecin du travail.. Journées Nationales de Santé au Travail dans le BTP, Volume 28, Pages 51-53, 2005.
BibTeX: @inproceedings{Gehanno2005a, author = {Gehanno, JF and Thirion, B and Darmoni, SJ and Caillard JF}, title = {La recherche documentaire sur le risque cancérogène par le médecin du travail.}, booktitle = {Journées Nationales de Santé au Travail dans le BTP}, year = {2005}, volume = {28}, pages = {51-53}, url = {http://www.gnmbtp.org/references_documentaires/congres_2005/9.rechdocu-gehanno.pdf} }
4 Communication nationale Ladner, J; Roussel, F; Audureau, E; Girault, C; Menard, JF; Sibert, L & Darmoni, SJ. Evolution de l'utilisation d'Internet par les étudiants en médecine lors des enseignements par APP.. JFIM, 2005.
BibTeX: @inproceedings{Ladner2005, author = {Ladner, J and Roussel, F and Audureau, E and Girault, C and Menard, JF and Sibert, L and Darmoni, SJ}, title = {Evolution de l'utilisation d'Internet par les étudiants en médecine lors des enseignements par APP.}, booktitle = {JFIM}, year = {2005}, url = {http://www.univ-lille2.fr/jfim2005/papiers/48-ladner-jfim2005.pdf} }
4 Communication nationale Letellier, S; Leuraud, K & Darmoni, SJ. Etude d'utilisabilité de deux outils nomades pour accéder à une base de connaissances sur le médicament.. JFIM, 2005.
BibTeX: @inproceedings{Letellier2005a, author = {Letellier, S and Leuraud, K and Darmoni, SJ}, title = {Etude d'utilisabilité de deux outils nomades pour accéder à une base de connaissances sur le médicament.}, booktitle = {JFIM}, year = {2005}, url = {http://www.univ-lille2.fr/jfim2005/papiers/04-Letellier-JFIM2005.pdf} }
4 Communication nationale LOISEL, A; KOTOWICZ, JP; CHAIGNAUD, N & DARMONI, SJ. Un système de dialogue homme-machine pour un moteur de recherche de documents médicaux (Poster). 7ème Conférence Francophone sur l'interaction Homme-Machine, IHM'05,, Toulouse, France, septembre, Pages 31-34, 2005.
Abstract: Le projet Cogni-CISMeF vise à construire un système de dialogue Homme-Machine (DHM) en langue naturelle afin d?améliorer l?interface qui permet d?accéder à un annuaire de recherche de ressources médicales sur le Web (CISMeF). L?amorce de ce système peut s?envisager selon deux approches : ? l?analyse de dialogues recueillis entre un expert hu-main de la technologie CISMeF et des utilisateurs ; ? l?analyse de dialogues entre des utilisateurs et un système minimal de dialogue homme-machine, im-plémenté directement sur l?internet et qui évoluera progressivement. Nous réfléchissons à une modélisation informatique de la théorie de la pertinence issue des recherches en pragma-tique cognitive.
BibTeX: @inproceedings{LOISEL2005, author = {LOISEL, A and KOTOWICZ, JP and CHAIGNAUD, N and DARMONI, SJ}, title = {Un système de dialogue homme-machine pour un moteur de recherche de documents médicaux (Poster)}, booktitle = {7ème Conférence Francophone sur l'interaction Homme-Machine, IHM'05,}, address = {Toulouse, France}, month = {septembre}, year = {2005}, pages = {31-34} }
4 Communication nationale LOISEL, A; KOTOWICZ, JP; CHAIGNAUD, N & DARMONI, SJ. Un système de dialogue homme-machine pour un moteur de recherche de documents médicaux (Poster). 2èmes rencontres des Sciences et Technologies de l'Information, Clermont Ferrand, France, octobre, Pages 31-34, 2005.
Abstract: Le projet Cogni-CISMeF vise à construire un système de dialogue Homme-Machine (DHM) en langue naturelle afin d?améliorer l?interface qui permet d?accéder à un annuaire de recherche de ressources médicales sur le Web (CISMeF). L?amorce de ce système peut s?envisager selon deux approches : ? l?analyse de dialogues recueillis entre un expert hu-main de la technologie CISMeF et des utilisateurs ; ? l?analyse de dialogues entre des utilisateurs et un système minimal de dialogue homme-machine, im-plémenté directement sur l?internet et qui évoluera progressivement. Nous réfléchissons à une modélisation informatique de la théorie de la pertinence issue des recherches en pragma-tique cognitive.
BibTeX: @inproceedings{LOISEL2005a, author = {LOISEL, A and KOTOWICZ, JP and CHAIGNAUD, N and DARMONI, SJ}, title = {Un système de dialogue homme-machine pour un moteur de recherche de documents médicaux (Poster)}, booktitle = {2èmes rencontres des Sciences et Technologies de l'Information}, address = {Clermont Ferrand, France}, month = {octobre}, year = {2005}, pages = {31-34} }
4 Communication nationale Neveol, A; Florea, F; Thirion, B & Darmoni, SJ. Formalisation de règles d'indexation MeSH pour un usage automatique. Journées INTEX/NOOJ, Besançon, France, 30 May - 1 June, 2005.
BibTeX: @inproceedings{Neveol2005a, author = {Neveol, A and Florea, F and Thirion, B and Darmoni, SJ}, title = {Formalisation de règles d'indexation MeSH pour un usage automatique}, booktitle = {Journées INTEX/NOOJ}, address = {Besançon, France}, month = {30 May - 1 June}, year = {2005}, url = {http://laseldi.univ-fcomte.fr/document/colloque/nooj_2005/022NEVEOL.htm} }
4 Communication nationale Névéol, A & Ozdowska, S. Extraction de termes médicaux à partir d'un corpus parallèle anglais/français. Extraction et Gestion des Connaissances, Paris, France, Janvier, Pages 655-664, 2005.
BibTeX: @inproceedings{Neveol2005c, author = {Névéol, A and Ozdowska, S}, title = {Extraction de termes médicaux à partir d'un corpus parallèle anglais/français}, booktitle = {Extraction et Gestion des Connaissances}, address = {Paris, France}, month = {Janvier}, year = {2005}, pages = {655-664}, url = {http://w3.univ-tlse2.fr/erss/textes/pagespersos/ozdowska/publis/neveol-ozdowska-egc05.pdf} }
4 Communication nationale Névéol, A; Rogozan, A & Darmoni, SJ. Indexation automatique de ressources de santé à l'aide de paires de descripteurs MeSH.. TALN, Dourdan, France, Juin, Volume 1, Pages 475-480, 2005.
BibTeX: @inproceedings{Neveol2005b, author = {Névéol, A and Rogozan, A and Darmoni, SJ}, title = {Indexation automatique de ressources de santé à l'aide de paires de descripteurs MeSH.}, booktitle = {TALN}, address = {Dourdan, France}, month = {Juin}, year = {2005}, volume = {1}, pages = {475-480}, url = {http://taln.limsi.fr/site/talnRecital05/tome1/P54.pdf} }
4 Communication nationale Ozdowska, S; Névéol A & Thirion, B. Traduction compositionnelle automatique de bitermes dans des corpus anglais/français alignés.. 6èmes rencontres Terminologie et Intelligence Artificielle, Pages 83-94, 2005.
BibTeX: @inproceedings{Ozdowska2005, author = {Ozdowska, S and Névéol A and Thirion, B}, title = {Traduction compositionnelle automatique de bitermes dans des corpus anglais/français alignés.}, booktitle = {6èmes rencontres Terminologie et Intelligence Artificielle}, year = {2005}, pages = {83-94}, url = {http://www.loria.fr/%7Eyannick/TIA2005/doc/ozdowska.pdf} }
4 Communication nationale Pereira, S; Névéol, A; Massari, P & Darmoni, SJ. Evaluation de plusieurs terminologies médicales pour optimiser l'aide au codage médico-économique par analyse automatique de dossiers électroniques de patient. Congrès ASTI, Clermont Ferrand, France, Octobre, 2005.
BibTeX: @inproceedings{Pereira2005, author = {Pereira, S and Névéol, A and Massari, P and Darmoni, SJ}, title = {Evaluation de plusieurs terminologies médicales pour optimiser l'aide au codage médico-économique par analyse automatique de dossiers électroniques de patient}, booktitle = {Congrès ASTI}, address = {Clermont Ferrand, France}, month = {Octobre}, year = {2005} }
4 Communication nationale É. Prieur & T. Lecroq. Des arbres de suffixes aux vecteurs de suffixes. , 2005.
BibTeX: @misc{Prieur2005, author = {{\'E}. Prieur and T. Lecroq}, title = {Des arbres de suffixes aux vecteurs de suffixes}, year = {2005} }
5 Résumé Florea, F; Rogozan, A; Bensrhair, A; Dacher, J-N & Darmoni, S. Modality categorisation by textual annotations interpretation in medical imaging. Connecting Medical Informatics and Bio-Informatics, Medical Informatics Europe (MIE2005), October, Pages 1270-1275, 2005.
Abstract: Our work is concerned with the automatic indexing of medical images for image retrieval purposes inside a large on-line health-catalogue. We present, in this paper, a rule-based medical-image modality categorization approach. The modality information is important for the indexing of medical images present in on-line health documents (thus, mainly in JPEG format). In fact, contrary to the case of the DICOM images, extensively used in PACS systems, JPEG images have any attached metadata (like those present in DICOM headers). Our system is based on the automatic interpretation of textual annotations, once they are extracted from the medical image by image processing and optical character recognition techniques. The system performances were tested on a medical image database, containing six medical modalities: angiography, ultrasonography, magnetic resonance imaging, standard radiography, computer tomography, and scintigraphy. The extraction of this database from a live health environment ensures the diversity of content from the modality, anatomical region and pathological point of view. In order to determinate the medical image modality, the textual annotations have been interpreted using a set of 96 production rules defined by our expert radiologist. The high precision rate of our categorization system (~90%), proves that textual annotations present in medical images are very reliable indicators of the medical modality. Further work will concern the fusion of our rule-based system with an already implemented visual-content based system, for a robust image modality categorization.
BibTeX: @inproceedings{Florea2005d, author = {Florea, F and Rogozan, A and Bensrhair, A and Dacher, J-N and Darmoni, S}, title = {Modality categorisation by textual annotations interpretation in medical imaging}, booktitle = {Connecting Medical Informatics and Bio-Informatics, Medical Informatics Europe (MIE2005)}, month = {October}, year = {2005}, pages = {1270-1275} }
2004 1 Publication internationale Al-Qsous, S; Carpentier, E; Klein-Eude, D; Burel, C; Mareck, A; Dauchel, H; Gomord, V & A.P. Balangé. Identification and isolation of a pectin methylesterase isoform that could be involved in flax cell wall stiffening. Planta , Volume 219, Number 2, Pages 369-378., 2004.
BibTeX: @article{Al-Qsous2004, author = {Al-Qsous, S and Carpentier, E and Klein-Eude, D and Burel, C and Mareck, A and Dauchel, H and Gomord, V and A.P. Balangé}, title = {Identification and isolation of a pectin methylesterase isoform that could be involved in flax cell wall stiffening}, journal = {Planta}, year = {2004}, volume = {219}, number = {2}, pages = {369--378.}, doi = {10.1007/s00425-004-1246-1} }
1 Publication internationale Charras, C & Lecroq, T. Handbook of exact string matching algorithms. , King's College London Publications, 2004.
BibTeX: @book{Charras2004, author = {Charras, C and Lecroq, T}, title = {Handbook of exact string matching algorithms}, publisher = {King's College London Publications}, year = {2004} }
1 Publication internationale Coulouarn, C; Lefebvre, G; Derambure, C; Lequerre, T; Scotte, M; Francois, A; Cellier, D; Daveau, M & Salier, JM. Altered gene expression in acute systemic inflammation detected by complete coverage of the human liver transcriptome. Hepatology , Volume 39, Number 2, Pages 353-364, 2004.
BibTeX: @article{Coulouarn2004, author = {Coulouarn, C and Lefebvre, G and Derambure, C and Lequerre, T and Scotte, M and Francois, A and Cellier, D and Daveau, M and Salier, JM}, title = {Altered gene expression in acute systemic inflammation detected by complete coverage of the human liver transcriptome}, journal = {Hepatology}, year = {2004}, volume = {39}, number = {2}, pages = {353--364}, doi = {10.1002/hep.20052} }
1 Publication internationale Crochemore, M & Lecroq, T. 13 in : Pattern matching and text data compression algorithms. The Computer Science and Engineering Handbook, Boca Raton, FL, Pages 13-1-13-48, CRC Press Inc., 2004.
BibTeX: @incollection{Crochemore2004, author = {Crochemore, M and Lecroq, T}, title = {Pattern matching and text data compression algorithms}, booktitle = {The Computer Science and Engineering Handbook}, address = {Boca Raton, FL}, publisher = {CRC Press Inc.}, year = {2004}, pages = {13-1--13-48}, edition = {2nd} }
1 Publication internationale Darmoni, SJ; Dahamna, B & Roth-Berghofer, T. Seal of transparency heritage in the CISMeF quality-controlled health gateway.. BMC Med Inform Decis Mak , Sep, Volume 4, Pages 15, 2004.
Abstract: BACKGROUND: It is an absolute necessity to continually assess the quality of health information on the Internet. Quality-controlled subject gateways are Internet services which apply a selected set of targeted measures to support systematic resource discovery. METHODS: The CISMeF health gateway became a contributor to the MedCIRCLE project to evaluate 270 health information providers. The transparency heritage consists of using the evaluation performed on providers that are referenced in the CISMeF catalogue for evaluating the documents they publish, thus passing on the transparency label from the publishers to their documents. RESULTS: Each site rated in CISMeF has a record in the CISMeF database that generates an RDF into HTML file. The search tool Doc'CISMeF displays information originating from every publisher evaluated with a specific MedCIRCLE button, which is linked to the MedCIRCLE central repository. Starting with 270 websites, this trust heritage has led to 6,480 evaluated resources in CISMeF (49.8% of the 13,012 resources included in CISMeF). CONCLUSION: With the MedCIRCLE project and transparency heritage, CISMeF became an explicit third party.
BibTeX: @article{Darmoni2004, author = {Darmoni, SJ and Dahamna, B and Roth-Berghofer, T}, title = {Seal of transparency heritage in the CISMeF quality-controlled health gateway.}, month = {Sep}, journal = {BMC Med Inform Decis Mak}, year = {2004}, volume = {4}, pages = {15}, doi = {10.1186/1472-6947-4-15} }
1 Publication internationale Douyère, M; Soualmia, L; Névéol, A; Rogozan, A; Dahamna, B; Leroy, JP; Thirion, B & Darmoni, SJ. Enhancing the MeSH thesaurus to retrieve French online health resources in a quality-controlled gateway.. Health Info Libr J , Dec, Volume 21, Number 4, Pages 253-261, 2004.
Abstract: The amount of health information available on the Internet is considerable. In this context, several health gateways have been developed. Among them, CISMeF (Catalogue and Index of Health Resources in French) was designed to catalogue and index health resources in French. The goal of this article is to describe the various enhancements to the MeSH thesaurus developed by the CISMeF team to adapt this terminology to the broader field of health Internet resources instead of scientific articles for the medline bibliographic database. CISMeF uses two standard tools for organizing information: the MeSH thesaurus and several metadata element sets, in particular the Dublin Core metadata format. The heterogeneity of Internet health resources led the CISMeF team to enhance the MeSH thesaurus with the introduction of two new concepts, respectively, resource types and metaterms. CISMeF resource types are a generalization of the publication types of medline. A resource type describes the nature of the resource and MeSH keyword/qualifier pairs describe the subject of the resource. A metaterm is generally a medical specialty or a biological science, which has semantic links with one or more MeSH keywords, qualifiers and resource types. The CISMeF terminology is exploited for several tasks: resource indexing performed manually, resource categorization performed automatically, visualization and navigation through the concept hierarchies and information retrieval using the Doc'CISMeF search engine. The CISMeF health gateway uses several MeSH thesaurus enhancements to optimize information retrieval, hierarchy navigation and automatic indexing.
BibTeX: @article{Douyere2004, author = {Douyère, M and Soualmia, L and Névéol, A and Rogozan, A and Dahamna, B and Leroy, JP and Thirion, B and Darmoni, SJ}, title = {Enhancing the MeSH thesaurus to retrieve French online health resources in a quality-controlled gateway.}, month = {Dec}, journal = {Health Info Libr J}, year = {2004}, volume = {21}, number = {4}, pages = {253--261}, doi = {10.1111/j.1471-1842.2004.00526.x} }
1 Publication internationale Duval, JP; Kolpakov, R; Kucherov, G; Lecroq, T & Lefebvre, A. Linear-Time Computation of Local Periods. Theoretical Computer Science , Volume 326, Number 1--3, Pages 229-240, 2004.
BibTeX: @article{Duval2004, author = {Duval, JP and Kolpakov, R and Kucherov, G and Lecroq, T and Lefebvre, A}, title = {Linear-Time Computation of Local Periods}, journal = {Theoretical Computer Science}, year = {2004}, volume = {326}, number = {1--3}, pages = {229--240}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/local.pdf}, doi = {10.1016/j.tcs.2004.06.024} }
1 Publication internationale Groult, R; Léonard, M & Mouchard, L. Speeding up the detection of evolutive tandem repeats. Theoretical Computer Science , Volume 310, Number 1--3, Pages 309-328, 2004.
BibTeX: @article{Groult2004, author = {Groult, R and Léonard, M and Mouchard, L}, title = {Speeding up the detection of evolutive tandem repeats}, journal = {Theoretical Computer Science}, year = {2004}, volume = {310}, number = {1--3}, pages = {309--328}, doi = {10.1016/S0304-3975(03)00423-7} }
1 Publication internationale Groult, R; Léonard, M & Mouchard, L. Evolutive tandem repeats: a survey. String algorithmics, Pages 75-107, King's College London Publications, 2004.
BibTeX: @incollection{Groult2004a, author = {Groult, R and Léonard, M and Mouchard, L}, title = {Evolutive tandem repeats: a survey}, booktitle = {String algorithmics}, publisher = {King's College London Publications}, year = {2004}, pages = {75--107} }
1 Publication internationale Iliopoulos, CS & Lecroq, T. String algorithmics. , King's College London Publications, 2004.
BibTeX: @book{Iliopoulos2004, author = {Iliopoulos, CS and Lecroq, T}, title = {String algorithmics}, publisher = {King's College London Publications}, year = {2004} }
1 Publication internationale Lecroq, T & Lefebvre, A. Different applications of the factor oracle: an overview. String algorithmics, Pages 129-154, King's College London Publications, 2004.
BibTeX: @incollection{Lecroq2004, author = {Lecroq, T and Lefebvre, A}, title = {Different applications of the factor oracle: an overview}, booktitle = {String algorithmics}, publisher = {King's College London Publications}, year = {2004}, pages = {129--154} }
1 Publication internationale Névéol, A; Soualmia, L; Douyère, M; Rogozan, A; Thirion, B & Darmoni, SJ. Using CISMeF MeSH "Encapsulated" terminology and a categorization algorithm for health resources.. Int J Med Inform , Feb, Volume 73, Number 1, Pages 57-64, 2004.
Abstract: INTRODUCTION: CISMeF is a Quality Controlled Health Gateway using a terminology based on the Medical Subject Headings (MeSH) thesaurus that displays medical specialties (metaterms) and the relationships existing between them and MeSH terms. Objective: The need to classify the resources within the catalogue has led us to combine this type of semantic information with domain expert knowledge for health resources categorization purposes. Material and METHODS: A two-step categorization process consisting of mapping resource keywords to CISMeF metaterms and ranking metaterms by decreasing coverage in the resource has been developed. We evaluate this algorithm on a random set of 123 resources extracted from the CISMeF catalogue. Our gold standard for this evaluation is the manual classification provided by a domain expert, viz. a librarian of the team. RESULTS: The CISMeF algorithm shows 81% precision and 93% recall, and 62% of the resources were assigned a "fully relevant" or "fairly relevant" categorization according to strict standards. DISCUSSION: A thorough analysis of the results has enabled us to find gaps in the knowledge modeling of the CISMeF terminology. The necessary adjustments having been made, the algorithm is currently used in CISMeF for resource categorization.
BibTeX: @article{Neveol2004, author = {Névéol, A and Soualmia, L and Douyère, M and Rogozan, A and Thirion, B and Darmoni, SJ}, title = {Using CISMeF MeSH "Encapsulated" terminology and a categorization algorithm for health resources.}, month = {Feb}, journal = {Int J Med Inform}, year = {2004}, volume = {73}, number = {1}, pages = {57--64}, doi = {10.1016/j.ijmedinf.2003.09.004} }
2 Publication nationale Gehanno, JF; Darmoni, SJ & Caillard, JF. Erreurs dans les bibliographies des articles citant des publications de sante au travail. Une menace pour l'Evidence Based Medicine. Archives des Maladies Professionnelles et de l'Environnement , May, Volume 65, Pages 195, 2004.
BibTeX: @article{Gehanno2004, author = {Gehanno, JF and Darmoni, SJ and Caillard, JF}, title = {Erreurs dans les bibliographies des articles citant des publications de sante au travail. Une menace pour l'Evidence Based Medicine}, month = {May}, journal = {Archives des Maladies Professionnelles et de l'Environnement}, year = {2004}, volume = {65}, pages = {195}, url = {http://www.sciencedirect.com/science/article/B8JFG-4RBV0BK-7S/2/2ec8d80eb1cc603d3d3530822330d83e}, doi = {10.1016/S1775-8785(04)93253-5} }
2 Publication nationale Groult, R. Détection de répétitions en tandem avec évolution : application aux séquences biologiques. School: Université de Rouen, France, 2004.
BibTeX: @phdthesis{Groult2004b, author = {Groult, R}, title = {D\'etection de r\'ep\'etitions en tandem avec \'evolution : application aux s\'equences biologiques}, school = {Universit\'e de Rouen, France}, year = {2004} }
2 Publication nationale Pelfrêne, J. Extraction de mots approchés. School: Université de Rouen, France, 2004.
BibTeX: @phdthesis{Pelfrene2004, author = {Pelfrêne, J}, title = {Extraction de mots approch\'es}, school = {Universit\'e de Rouen, France}, year = {2004} }
2 Publication nationale Soualmia, L. Etude et Evaluation d'Approches Multiples de Projection de Requêtes pour une Recherche d'Information Intelligente. Application au domaine de la Santé sur l'Internet. Thèse d'informatique. School: INSA de Rouen, 2004.
BibTeX: @phdthesis{Soualmia2004e, author = {Soualmia, L}, title = {Etude et Evaluation d'Approches Multiples de Projection de Requêtes pour une Recherche d'Information Intelligente. Application au domaine de la Santé sur l'Internet. Thèse d'informatique}, school = {INSA de Rouen}, year = {2004}, url = {http://www.chu-rouen.fr/l@stics/Lina_Soualmia_These_Version_PDF.pdf} }
2 Publication nationale Touyar, N. Étude du nombre de répétitions maximales à gauche non chevauchantes dans les séquences d'ADN. School: Université de Rouen, France, 2004.
BibTeX: @phdthesis{Touyar2004, author = {Touyar, N}, title = {\'Etude du nombre de r\'ep\'etitions maximales \`a gauche non chevauchantes dans les s\'equences d'ADN}, school = {Universit\'e de Rouen, France}, year = {2004} }
3 Communication internationale Gehanno, JF. The Usefulness of Available Databases on Self Training.. EASOM Summer School, Belgrade, Serbia, August, 2004.
BibTeX: @inproceedings{Gehanno2004a, author = {Gehanno, JF}, title = {The Usefulness of Available Databases on Self Training.}, booktitle = {EASOM Summer School}, address = {Belgrade, Serbia}, month = {August}, year = {2004} }
3 Communication internationale Soualmia, L & Darmoni, SJ. Correcting and Refining Users QUeries: the Contribution of Morphological Knowledge and Association rules.. IPMU, Information Processing and Management of Uncertainty in Knowledge-Based Systems, Perugia, Italy, July, Pages 2059?2066, 2004.
BibTeX: @inproceedings{Soualmia2004, author = {Soualmia, L and Darmoni, SJ}, title = {Correcting and Refining Users QUeries: the Contribution of Morphological Knowledge and Association rules.}, booktitle = {IPMU, Information Processing and Management of Uncertainty in Knowledge-Based Systems}, address = {Perugia, Italy}, month = {July}, year = {2004}, pages = {2059?2066} }
3 Communication internationale Soualmia, L & Darmoni, SJ. Combining Knowledge-based Methods to Refine and Expand Queries in Medicine.. Flexible Query Answering Systems, Pages 243-255, 2004.
Abstract: Information retrieval remains problematic in spite of the numerous existing search engines. It is the same problem for health information retrieval. We propose in this paper to combine three knowledge-based methods to enhance information retrieval using query expansion in the context of the CISMeF project (Catalogue and Index of French-speaking Medical Sites) in which the resources are indexed according to a structured terminology of the medical domain and a set of metadata. The first method consists of building and using morphological knowledge of the terms. The second method consists of extracting association rules between terms by applying a data mining technique over the indexed resources. The last method consists of formalizing the terminology using the OWL-DL language to benefit from its powerful reasoning mechanisms. We describe how these methods could be used conjointly in the KnowQuE prototype (Knowledge-based Query Expansion) and we give some preliminary results.
BibTeX: @inproceedings{Soualmia2004a, author = {Soualmia, L and Darmoni, SJ}, title = {Combining Knowledge-based Methods to Refine and Expand Queries in Medicine.}, booktitle = {Flexible Query Answering Systems}, year = {2004}, pages = {243-255}, doi = {10.1007/b98090} }
3 Communication internationale Soualmia, L; Golbreich, C & Darmoni, SJ. Representing the MeSH in OWL: Towards a semi-automatic migration.. KR-MED 2004, Workshop on Knowledge Representation in Biomedicine, Whistler, BC, Canada, July, 2004.
BibTeX: @inproceedings{Soualmia2004b, author = {Soualmia, L and Golbreich, C and Darmoni, SJ}, title = {Representing the MeSH in OWL: Towards a semi-automatic migration.}, booktitle = {KR-MED 2004, Workshop on Knowledge Representation in Biomedicine}, address = {Whistler, BC, Canada}, month = {July}, year = {2004}, url = {http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-102/soualmia.pdf} }
3 Communication internationale Thirion, B; Douyère, M; Soualmia, L; Dahamna, B; Leroy, JP & Darmoni, SJ. Metadata element sets in the CISMeF Quality-Controlled Health Gateway.. International Conference on Dublin Core and Metadata Applications, Shanghai, China, October, 2004.
BibTeX: @inproceedings{Thirion2004, author = {Thirion, B and Douyère, M and Soualmia, L and Dahamna, B and Leroy, JP and Darmoni, SJ}, title = {Metadata element sets in the CISMeF Quality-Controlled Health Gateway.}, booktitle = {International Conference on Dublin Core and Metadata Applications}, address = {Shanghai, China}, month = {October}, year = {2004}, url = {http://journals.sfu.ca/dcpapers/2004/Paper_13.pdf} }
4 Communication nationale Gehanno, JF; Darmoni, SJ & Caillard, JF. Erreurs dans les bibliographies des articles citant des publications de santé au travail. Une menace pour l'Evidence Based Medicine.. 28eme Congrès National de Médecine et Santé au Travail, Bordeaux, France, Juin, 2004.
BibTeX: @inproceedings{Gehanno2004b, author = {Gehanno, JF and Darmoni, SJ and Caillard, JF}, title = {Erreurs dans les bibliographies des articles citant des publications de santé au travail. Une menace pour l'Evidence Based Medicine.}, booktitle = {28eme Congrès National de Médecine et Santé au Travail}, address = {Bordeaux, France}, month = {Juin}, year = {2004} }
4 Communication nationale Névéol, A. Indexation automatique de ressources de santé à l?aide d?un vocabulaire contrôlé. Rencontre des Etudiants Chercheurs en Informatique pour le Traitement Automatique des Langues (RECITAL), Fès, Maroc, Avril, 2004.
BibTeX: @inproceedings{A.2004, author = {Névéol, A}, title = {Indexation automatique de ressources de santé à l?aide d?un vocabulaire contrôlé}, booktitle = {Rencontre des Etudiants Chercheurs en Informatique pour le Traitement Automatique des Langues (RECITAL)}, address = {Fès, Maroc}, month = {Avril}, year = {2004}, url = {http://aune.lpl.univ-aix.fr/jep-taln04/proceed/actes/recital2004/Neveol.rec04.pdf} }
4 Communication nationale Névéol, A; Douyère, M; Rogozan, A & Darmoni, SJ. Construction de ressources terminologiques en santé pour un système d?indexation automatique.. Journées INTEX/NOOJ, Tours, France, 2004.
BibTeX: @inproceedings{Neveol2004c, author = {Névéol, A and Douyère, M and Rogozan, A and Darmoni, SJ}, title = {Construction de ressources terminologiques en santé pour un système d?indexation automatique.}, booktitle = {Journées INTEX/NOOJ}, address = {Tours, France}, year = {2004} }
4 Communication nationale Névéol, A; Soualmia, L; Rogozan, A; Douyère, M; Thirion, B & Darmoni, SJ. Caractérisation des contenus de l?Internet en santé : l'exemple CISMeF.. Journée ATALA, Paris, France, Janvier, 2004.
BibTeX: @inproceedings{Neveol2004b, author = {Névéol, A and Soualmia, L and Rogozan, A and Douyère, M and Thirion, B and Darmoni, SJ}, title = {Caractérisation des contenus de l?Internet en santé : l'exemple CISMeF.}, booktitle = {Journée ATALA}, address = {Paris, France}, month = {Janvier}, year = {2004}, url = {http://aurelie.neveol.free.fr/NeveolATALA04.pdf} }
4 Communication nationale Sibert, L; Dahamna, B; Darmoni, SJ; Weber, J; Lechevallier, J & Lanson, Y. Evaluation du raisonnement clinique en urologie. Internet et Pédagogie Médicale (IPM), Grenoble, France, Octobre, 2004.
BibTeX: @inproceedings{Louis2004, author = {Sibert, L and Dahamna, B and Darmoni, SJ and Weber, J and Lechevallier, J and Lanson, Y}, title = {Evaluation du raisonnement clinique en urologie}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Grenoble, France}, month = {Octobre}, year = {2004}, url = {http://www.canal-u.fr/index.php/canalu/producteurs/canal_u_medecine/dossier_programmes/urologie/colloque_et_evenement__1/ipm_2004_evaluation_du_raisonnement_clinique_en_urologie} }
4 Communication nationale Soualmia LF.,. Dahamna B, Darmoni SJ.. Représentation du thésaurus MeSH et de la terminologie CISMeF en OWL.. Second Séminaire Web Seménantique Médical, Rouen, France, Mars, 2004.
BibTeX: @inproceedings{Soualmia2004d, author = {Soualmia LF.,. Dahamna B, Darmoni SJ.}, title = {Représentation du thésaurus MeSH et de la terminologie CISMeF en OWL.}, booktitle = {Second Séminaire Web Seménantique Médical}, address = {Rouen, France}, month = {Mars}, year = {2004} }
4 Communication nationale Soualmia, L; Névéol, A; Rogozan, A; Douyère, M; Thirion, B & Darmoni, SJ. Une Terminologie du Domaine Médical : Structure et Exploitation.. Atelier ATALA, Lyon, France, Janvier, 2004.
BibTeX: @inproceedings{Soualmia2004c, author = {Soualmia, L and Névéol, A and Rogozan, A and Douyère, M and Thirion, B and Darmoni, SJ}, title = {Une Terminologie du Domaine Médical : Structure et Exploitation.}, booktitle = {Atelier ATALA}, address = {Lyon, France}, month = {Janvier}, year = {2004} }
5 Résumé Burgun, A; Darmoni, SJ; Le Duff, F & Weber, J. Combining problem-based learning and information technology: an experiment with third-year medical students.. 11th International Ottawa Conference on Medical Education, Barcelona, Spain, July, 2004.
BibTeX: @inproceedings{Burgun2004, author = {Burgun, A and Darmoni, SJ and Le Duff, F and Weber, J}, title = {Combining problem-based learning and information technology: an experiment with third-year medical students.}, booktitle = {11th International Ottawa Conference on Medical Education}, address = {Barcelona, Spain}, month = {July}, year = {2004} }
5 Résumé Dahamna, B; Darmoni, SJ; Roth-Berghofer, TR; Köhler, C; Mayer, MA; Noelle, G & Eysenbach G. Trust heritage in a Quality-Controlled Health Gateway.. Medinfo 2004, Eleventh World Congress on Health and Medical Informatics, San Francisco, USA, September, Pages 1564, 2004.
BibTeX: @inproceedings{Dahamna2004, author = {Dahamna, B and Darmoni, SJ and Roth-Berghofer, TR and Köhler, C and Mayer, MA and Noelle, G and Eysenbach G}, title = {Trust heritage in a Quality-Controlled Health Gateway.}, booktitle = {Medinfo 2004, Eleventh World Congress on Health and Medical Informatics}, address = {San Francisco, USA}, month = {September}, year = {2004}, pages = {1564} }
5 Résumé Darmoni, SJ; Douyère, M; Sibert, L; Hamon, A; Leuraud, K; Benichou, J & Weber, J. Assessment of a quality-controlled health gateway to facilitate access to teaching resources on the Internet: a technological trial.. Ottawa Conference on Medical Education, Barcelona, Spain, July, 2004.
Abstract: Summary: Objective: Measuring the impact of training on student-users of CISMeF (Catalog and Index of Health Resources on the Internet) quality-controlled health gateway. Design: Prospective group-randomised technological trial Participants: Fifty-six third-year medical students of the Rouen Medical School, France on a voluntary basis. One group with training (28); one group untrained (28). Participants were directed to use the CISMeF health information portal (URL: www.chu-rouen.fr or www.cismef.org) to find one teaching document dealing with each of the following objectives: semiology of asthma, main germs of infectious endocarditis, risk factors of colon cancer, and aetiology of hematuria Main outcome measures: Success or failure to find a teaching document in a maximum of 10 minutes, time spent and number of clicks to find it. Results: One-hour training session significantly improved the students? ability to search and access teaching resources: 64% of the students (18 out of 28) found a valid teaching resource for each teaching objective in the untrained group vs. 96% (27 out of 28) in the trained group (p=0.005, Fisher?s exact test). Conclusion: Health information portals may increase access to quality-controlled teaching documents.
BibTeX: @inproceedings{Darmoni2004b, author = {Darmoni, SJ and Douyère, M and Sibert, L and Hamon, A and Leuraud, K and Benichou, J and Weber, J}, title = {Assessment of a quality-controlled health gateway to facilitate access to teaching resources on the Internet: a technological trial.}, booktitle = {Ottawa Conference on Medical Education}, address = {Barcelona, Spain}, month = {July}, year = {2004} }
5 Résumé Darmoni, SJ; Thirion, B; Douyère, M; Dahamna, B & Weber, J. A Quality-Controlled Health Gateway to disseminate French pre-Residency Examination Program teaching resources on the Internet.. Medinfo 2004, Eleventh World Congress on Health and Medical Informatics, San Francisco, USA, September, 2004.
BibTeX: @inproceedings{Darmoni2004a, author = {Darmoni, SJ and Thirion, B and Douyère, M and Dahamna, B and Weber, J}, title = {A Quality-Controlled Health Gateway to disseminate French pre-Residency Examination Program teaching resources on the Internet.}, booktitle = {Medinfo 2004, Eleventh World Congress on Health and Medical Informatics}, address = {San Francisco, USA}, month = {September}, year = {2004} }
5 Résumé Névéol, A; Rogozan, A & Darmoni, SJ. Automatic indexing of health resources in French with a controlled vocabulary for the CISMeF catalogue: a preliminary study.. Medinfo 2004, Eleventh World Congress on Health and Medical Informatics, San Francisco, USA, September, 2004.
BibTeX: @inproceedings{Neveol2004a, author = {Névéol, A and Rogozan, A and Darmoni, SJ}, title = {Automatic indexing of health resources in French with a controlled vocabulary for the CISMeF catalogue: a preliminary study.}, booktitle = {Medinfo 2004, Eleventh World Congress on Health and Medical Informatics}, address = {San Francisco, USA}, month = {September}, year = {2004}, url = {http://aurelie.neveol.free.fr/NeveolMedinfo04.pdf} }
5 Résumé Sibert, L; Dahamna, B; Darmoni, SJ; Weber, J & Lechevallier, J. A Website to validate the Script Concordance test on a large scale: A pilot study in Urology.. 11th International Ottawa Conference on Medical Education, Barcelona, Spain, July, 2004.
BibTeX: @inproceedings{Sibert2004, author = {Sibert, L and Dahamna, B and Darmoni, SJ and Weber, J and Lechevallier, J}, title = {A Website to validate the Script Concordance test on a large scale: A pilot study in Urology.}, booktitle = {11th International Ottawa Conference on Medical Education}, address = {Barcelona, Spain}, month = {July}, year = {2004} }
5 Résumé Wascat, C; Beuscart-Zéphir, MC; Anceaux, F; Alao, O & Darmoni, SJ. Evaluation of the difficulties faced by users of a search engine of a medical web site : the example of Doc?CISMeF. Medinfo 2004, Eleventh World Congress on Health and Medical Informatics, San Francisco, USA, September, 2004.
BibTeX: @inproceedings{Wascat2004, author = {Wascat, C and Beuscart-Zéphir, MC and Anceaux, F and Alao, O and Darmoni, SJ}, title = {Evaluation of the difficulties faced by users of a search engine of a medical web site : the example of Doc?CISMeF}, booktitle = {Medinfo 2004, Eleventh World Congress on Health and Medical Informatics}, address = {San Francisco, USA}, month = {September}, year = {2004}, url = {http://www.univ-lille2.fr/evalab/publisPDF/68%20wascat%20medinfo%202004.pdf} }
2003 1 Publication internationale Crochemore, M; Hancart, C & Lecroq, T. A unifying look at the Apostolico-Giancarlo string matching algorithm. Journal of Discrete Algorithms , Volume 1, Number 1, Pages 37-52, 2003.
BibTeX: @article{Crochemore2003a, author = {Crochemore, M and Hancart, C and Lecroq, T}, title = {A unifying look at the {Apostolico-Giancarlo} string matching algorithm}, journal = {Journal of Discrete Algorithms}, year = {2003}, volume = {1}, number = {1}, pages = {37--52}, url = {http://www-igm.univ-mlv.fr/~lecroq/articles/jda1.pdf}, doi = {10.1016/S1570-8667(03)00005-4} }
1 Publication internationale Crochemore, M; Iliopoulos, CS; Lecroq, T; Pinzon, YJ; Plandowski, W & Rytter, W. Occurrence and Substring Heuristics for $-Matching. Fundamenta Informaticae , Volume 56, Number 1--2, Pages 1-21, 2003.
BibTeX: @article{Crochemore2003, author = {Crochemore, M and Iliopoulos, CS and Lecroq, T and Pinzon, YJ and Plandowski, W and Rytter, W}, title = {Occurrence and Substring Heuristics for $\delta$-Matching}, journal = {Fundamenta Informaticae}, year = {2003}, volume = {56}, number = {1--2}, pages = {1--21}, url = {http://iospress.metapress.com/content/0mc4986ycm8nyutv} }
1 Publication internationale Darmoni, SJ; Amsallem, E; Haugh, M; Lukacs, B; Leroux, V; Thirion, B; Weber, J & Boissel, JP. Level of evidence as a future gold standard for the content quality of health resources on the internet.. Methods Inf Med , Volume 42, Number 3, Pages 220-225, 2003.
Abstract: OBJECTIVE: An assessment of the quality of health information on the Internet is an absolute necessity. In this study 'sensitive' information was defined as information found in documents published on the Internet, which could be used in a medical decision. For sensitive information, the main criterion chosen for the quality of the information was an indication of the level of evidence. A survey was conducted using the CISMeF health catalogue to assess how often a score of the level of evidence is mentioned in the information accessible on the Internet in French-language health resources. METHODS: Since 1999, members of the CISMeF team have systematically been searching for all documents containing 'sensitive' information and verifying whether the level of evidence was explicitly indicated as a score at least once in the document. RESULTS: As of June 2001, 10,190 resources were included in CISMeF; including 2964 textual 'sensitive' resources (29.1. Out of all these resources, only 4.7% (95% confidence interval: 4.0 - 5.5 indicated the level of evidence. A statistically significant difference in the prevalence of indicating the level of evidence according to resource types (e.g., 18.1% for guidelines compared to 0.0% for teaching material), year of publication (almost three times greater in 1997-2001 compared with 1990-1996) and publishers was observed. CONCLUSION: As the number of people accessing the growing amount of information on the Internet is increasing daily, publishers have an ethical obligation to inform their readers about the validity of 'sensitive' information their sites contain. However, the vast majority of the French language Internet resources that were surveyed do not mention a score of the level of evidence for their sensitive information.
BibTeX: @article{Darmoni2003a, author = {Darmoni, SJ and Amsallem, E and Haugh, M and Lukacs, B and Leroux, V and Thirion, B and Weber, J and Boissel, JP}, title = {Level of evidence as a future gold standard for the content quality of health resources on the internet.}, journal = {Methods Inf Med}, year = {2003}, volume = {42}, number = {3}, pages = {220--225}, doi = {10.1267/METH03030220} }
1 Publication internationale Lefebvre, A; Lecroq, T & Alexandre, J. Drastic improvements over repeats found with a factor oracle. Journal of Automata Language and Combinatorics , Volume 8, Number 4, Pages 647-658, 2003.
BibTeX: @article{Lefebvre2003a, author = {Lefebvre, A and Lecroq, T and Alexandre, J}, title = {Drastic improvements over repeats found with a factor oracle}, journal = {Journal of Automata Language and Combinatorics}, year = {2003}, volume = {8}, number = {4}, pages = {647--658} }
1 Publication internationale Lefebvre, A; Lecroq, T; Dauchel, H & Alexandre, J. FORRepeats: detects repeats on entire chromosomes and between genomes. Bioinformatics , Volume 19, Number 3, Pages 319-326, 2003.
BibTeX: @article{Lefebvre2003, author = {Lefebvre, A and Lecroq, T and Dauchel, H and Alexandre, J}, title = {{FORRepeats}: detects repeats on entire chromosomes and between genomes}, journal = {Bioinformatics}, year = {2003}, volume = {19}, number = {3}, pages = {319--326}, doi = {10.1093/bioinformatics/btf843} }
1 Publication internationale Mercier, S; Cellier, D & Charlot, D. An improved approximation for assessing the statistical significance of molecular sequence features. Journal of Applied Probability , Volume 40, Pages 427-441, 2003.
BibTeX: @article{Mercier2003, author = {Mercier, S and Cellier, D and Charlot, D}, title = {An improved approximation for assessing the statistical significance of molecular sequence features}, journal = {Journal of Applied Probability}, year = {2003}, volume = {40}, pages = {427--441}, url = {http://projecteuclid.org/euclid.jap/1053003554}, doi = {10.1239/jap/1053003554} }
2 Publication nationale DARMONI, SJ; THIBAUT, F & WEBER, J. L'universite medicale virtuelle. Confrontations psychiatriques. , Number 44, Pages 147-154, 2003.
Abstract: Les technologies de l'information et de la communication prennent une place de plus en plus importante dans les Facultés de médecine. Il peut s'agir de l'utilisation de polycopiés sur le WEB au lieu des polycopiésclassiques, de l'offre de ressources utilisant le multimédia et l'interactivité, ou encore de l'apprentissage de la pratique médicale à l'aide de patients virtuels. Le projet d'Université médicale virtuelle francophone mis en place en 1999 sera développé dans l'article. Parmi les avantages attendus de ces techniques on peut évoquer l'autonomie d'apprentissage des étudiants, et leur envie de continuer à se former.
BibTeX: @article{DARMONI2003, author = {DARMONI, SJ and THIBAUT, F and WEBER, J}, title = {L'universite medicale virtuelle}, journal = {Confrontations psychiatriques.}, year = {2003}, number = {44}, pages = {147-154}, url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=17304044} }
2 Publication nationale Douyère, M; Thirion, B; Leroy, JP; Dahamna, B & Darmoni, SJ. Doc'CISMEF : un outil de recherche Internet dirigé vers l'enseignement de la médecine.. Document Numérique , Volume 7, Number 1-2, Pages 129-140, 2003. Numéro Spécial "Document et éducation" sous la direction de Christine Vanoirbeek et Omar Abou Khaled.
Abstract: Le nombre de ressources disponibles sur l?internet concernant l?enseignement de la médecine est 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).
BibTeX: @article{Magaly2003, author = {Douyère, M and Thirion, B and Leroy, JP and Dahamna, B and Darmoni, SJ}, title = {Doc'CISMEF : un outil de recherche Internet dirigé vers l'enseignement de la médecine.}, journal = {Document Numérique}, year = {2003}, volume = {7}, number = {1-2}, pages = {129-140}, note = {Numéro Spécial "Document et éducation" sous la direction de Christine Vanoirbeek et Omar Abou Khaled}, url = {http://www.cairn.info/revue-document-numerique-2003-1-p-129.htm} }
2 Publication nationale Lefebvre, A. Une nouvelle heuristique pour la détection de répétitions sur des génomes complets, pour la comparaison de génomes et pour la compression. School: Université de Rouen, France, 2003.
BibTeX: @phdthesis{Lefebvre2003b, author = {Lefebvre, A}, title = {Une nouvelle heuristique pour la d\'etection de r\'ep\'etitions sur des g\'enomes complets, pour la comparaison de g\'enomes et pour la compression}, school = {Universit\'e de Rouen, France}, year = {2003} }
3 Communication internationale A. NEVEOL, LF. SOUALMIA, A. ROGOZAN, M. DOUYERE, Darmoni, SJ.. Utilisation des propriétés sémantiques de la terminologie CISMeF pour la catégorisation de ressources de santé.. JFIM, 2003.
BibTeX: @inproceedings{A.2003, author = {A. NEVEOL, LF. SOUALMIA, A. ROGOZAN, M. DOUYERE, Darmoni, SJ.}, title = {Utilisation des propriétés sémantiques de la terminologie CISMeF pour la catégorisation de ressources de santé.}, booktitle = {JFIM}, year = {2003}, url = {http://aurelie.neveol.free.fr/NeveolJFIM03.pdf} }
3 Communication internationale Beuscart-Zephir, MC; Leroy, N; Watbled, L; Guerlinger, S; Wascat, C & Darmoni, SJ. Evaluation de l?utilisabilité d?un site francophone de resources médicales en ligne : l?exemple de CISMeF. JFIM, 9èmes Journées Francophone d?Informatique Médicale, Québec, Canada, Mai, 2003.
BibTeX: @inproceedings{Beuscart-Zephir2003, author = {Beuscart-Zephir, MC and Leroy, N and Watbled, L and Guerlinger, S and Wascat, C and Darmoni, SJ}, title = {Evaluation de l?utilisabilité d?un site francophone de resources médicales en ligne : l?exemple de CISMeF}, booktitle = {JFIM, 9èmes Journées Francophone d?Informatique Médicale}, address = {Québec, Canada}, month = {Mai}, year = {2003}, url = {http://www.univ-lille2.fr/evalab/publisPDF/31%20mcbz%20JFIM%202002.pdf} }
3 Communication internationale S. J. Darmoni; E. Jarrousse; P. Zweigenbaum; P. Le Beux; F. Namer; R. Baud; M. Joubert; H. Vallée; R. A. Côté; A. Buemi; D. Bourigault; G. Recource; S. Jeanneau & J. M. Rodrigues. VUMeF: extending the French involvement in the UMLS Metathesaurus.. AMIA Annu Symp Proc , Pages 824, 2003.
Abstract: A considerable number of robust vocabularies and thesauri have been developed for the healthcare and biomedical domain. No single vocabulary, however; provides complete coverage of the information needs from a public health perspective. The results of an investigation of vocabulary sources for the development of a comprehensive controlled vocabulary for the public health domain at the Centers for Disease Control and Prevention (CDC) is presented.
BibTeX: @article{Darmoni2003, author = {S. J. Darmoni and E. Jarrousse and P. Zweigenbaum and P. Le Beux and F. Namer and R. Baud and M. Joubert and H. Vallée and R. A. Côté and A. Buemi and D. Bourigault and G. Recource and S. Jeanneau and J. M. Rodrigues}, title = {VUMeF: extending the French involvement in the UMLS Metathesaurus.}, journal = {AMIA Annu Symp Proc}, year = {2003}, pages = {824}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1480335} }
3 Communication internationale Darmoni, SJ. B. THIRION, B. POURCHEZ, J. WEBER.. Use of Information and Communication Technologies to retrieve French pre-Residency Examination Program teaching resources on the Internet.. MIE, 2003.
BibTeX: @inproceedings{SJ.2003, author = {Darmoni, SJ. B. THIRION, B. POURCHEZ, J. WEBER.}, title = {Use of Information and Communication Technologies to retrieve French pre-Residency Examination Program teaching resources on the Internet.}, booktitle = {MIE}, year = {2003}, url = {http://www.med.univ-rennes1.fr/resped/s/mie/CISMeFInternat%20MIE%202003.ppt} }
3 Communication internationale J.-P. Duval; R. Kolpakov; G. Kucherov; T. Lecroq & A. Lefebvre. Linear-Time Computation of Local Periods. Proceedings of the 28th International Symposium on Mathematical Fondations of Computer Science, Bratislava, Slovak Republic, Lecture Notes in Computer Science, Number 2747, Pages 388-397, Springer Verlag Berlin, 2003.
BibTeX: @inproceedings{Duval2003, author = {J.-P. Duval and R. Kolpakov and G. Kucherov and T. Lecroq and A. Lefebvre}, title = {Linear-Time Computation of Local Periods}, booktitle = {Proceedings of the 28th International Symposium on Mathematical Fondations of Computer Science}, address = {Bratislava, Slovak Republic}, publisher = {Springer Verlag Berlin}, year = {2003}, series = {Lecture Notes in Computer Science}, number = {2747}, pages = {388--397}, doi = {10.1007/b11836} }
3 Communication internationale Natalia Grabar; Pierre Zweigenbaum; Lina Soualmia & Stéfan Darmoni. Matching controlled vocabulary words.. Stud Health Technol Inform , Volume 95, Pages 445-450, 2003.
Abstract: This study examines an enabling condition for natural languages access to medical knowledge resources (Medline, CISMeF) indexed with controlled vocabularies (e.g., the MeSH): is the vocabulary of user queries comparable with that of the index terms? The two vocabularies were compared in their original form, then under incrementally normalized forms, using character-based normalizations then linguistic normalizations. Only 16.7% of the user vocabulary, in its original form, is in the MeSH. Progressive normalizations increase this proportion to 65.5 Besides, if the frequencies of occurrence of words are taken into account, 89.3% of user word occurrences can be matched to MeSH words. This shows the interest of taking into account further matching methods between queries and index terms than those presented here.
BibTeX: @article{Grabar2003, author = {Natalia Grabar and Pierre Zweigenbaum and Lina Soualmia and Stéfan Darmoni}, title = {Matching controlled vocabulary words.}, journal = {Stud Health Technol Inform}, year = {2003}, volume = {95}, pages = {445--450} }
3 Communication internationale Groult, R; Léonard, M & Mouchard, L. A linear algorithm for the detection of evolutive tandem repeats. Proceedings of the Prague Stringology Conference (PSC 2003), Prague, République Tchèque, Pages 77-90, 2003.
BibTeX: @inproceedings{Groult2003, author = {Groult, R and Léonard, M and Mouchard, L}, title = {A linear algorithm for the detection of evolutive tandem repeats}, booktitle = {Proceedings of the Prague Stringology Conference (PSC 2003)}, address = {Prague, R\'epublique Tch\`eque}, year = {2003}, pages = {77--90} }
3 Communication internationale LF. SOUALMIA, C. BARRY, Darmoni, SJ.. Knowledge-Based Query Expansion over a Medical Terminology Oriented Ontology.. Artificial Intelligence in Medicine: 9th Conference on Artificial Intelligence in Medicine in Europe, AIME 2003, 2003.
Abstract: This paper deals with the problem of information retrieval on the Web and present the CISMeF project (acronym of Catalogue and Index of French-speaking Medical Sites). Information retrieval in the CISMeF catalogue is done with a terminology that is similar to ontology of medical domain and a set of metadata. This allows us to place the project at an overlap between the present Web, which is informal, and the forthcoming Semantic Web. We also describe an ongoing work, which consists of applying thr ee knowledge-based methods in order to enhance information retrieval.
BibTeX: @inproceedings{LF.2003c, author = {LF. SOUALMIA, C. BARRY, Darmoni, SJ.}, title = {Knowledge-Based Query Expansion over a Medical Terminology Oriented Ontology.}, booktitle = {Artificial Intelligence in Medicine: 9th Conference on Artificial Intelligence in Medicine in Europe, AIME 2003}, year = {2003}, url = {http://www.springerlink.com/content/qlatdrljyd51a8dh} }
3 Communication internationale M. A. Mayer; S. J. Darmoni; M. Fiene; C. Köhler; Thomas R Roth-Berghofer & G. Eysenbach. MedCIRCLE: collaboration for Internet rating, certification, labelling and evaluation of health information on the World-Wide-Web.. Stud Health Technol Inform , Volume 95, Pages 667-672, 2003.
Abstract: We describe MedCIRCLE, an EU-funded semantic web project to implement the first steps towards a global, collaborative rating and guidance system for health information proposed in the MedCERTAIN project. In MedCIRCLE, three European gateway sites for consumer health information will implement the metadata vocabulary HIDDEL (Health Information Disclosure, Description and Evaluation Language). HIDDEL allows portals and gateways to make the results of their evaluations accessible as XML/RDF. The three participating national portals are: AQUMED (Agency for Quality in Medicine) patienten-information, de, COMB (Official Medical College of Barcelona) and CISMeF, a quality-controlled health gateway developed at Rouen University Hospital. Other health subject gateways, accreditation, or rating services are invited to join the collaboration simply by implementing HIDDEL on their gateways. Widespread implementation HIDDEL will allow intelligent agents or client-side software to harvest statements and opinions about the trustworthiness of other websites, assisting users in selecting trustworthy websites. The MedCIRCLE project builds on, expands and continues work on rating health information on the Internet piloted within the MedCERTAIN project. While MedCERTAIN provided the core technologies and software for rating and "trustmarking" health information, MedCIRCLE is built around these technologies and involves a wider medical community to assess health information, demonstrating the power of collaborative and interoperable evaluations in a semantic web environment. MedCIRCLE is a project with the overall objective to develop and promote technologies able to guide consumers to trustworthy health information on the Internet, to establish a global web of trust for networked health information, and to empower consumers to positively select high quality health information on the web. Other aims include refinement and expansion of HIDDEL, to become a standard vocabulary and interchange format for self- and third-party ratings of health information.
BibTeX: @article{Mayer2003, author = {M. A. Mayer and S. J. Darmoni and M. Fiene and C. Köhler and Thomas R Roth-Berghofer and G. Eysenbach}, title = {MedCIRCLE: collaboration for Internet rating, certification, labelling and evaluation of health information on the World-Wide-Web.}, journal = {Stud Health Technol Inform}, year = {2003}, volume = {95}, pages = {667--672} }
3 Communication internationale P. ZWEIGENBAUM; R. BAUD, A. BURGUN, F. NAMER, E. JAROUSSE, N. GRABAR, P. RUCH, F. LE DUFF, B. THIRION, Darmoni, SJ.. UMLF : construction d?un lexique médical francophone unifié.. JFIM, 2003.
BibTeX: @inproceedings{P.2003, author = {P. ZWEIGENBAUM; R. BAUD, A. BURGUN, F. NAMER, E. JAROUSSE, N. GRABAR, P. RUCH, F. LE DUFF, B. THIRION, Darmoni, SJ.}, title = {UMLF : construction d?un lexique médical francophone unifié.}, booktitle = {JFIM}, year = {2003}, url = {http://estime.spim.jussieu.fr/~pz/FTPapiers/Zweigenbaum:JFIM2003.pdf} }
3 Communication internationale J. Pelfrêne; S. Abdeddaim & J. Alexandre. Extracting Approximate Patterns. Proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching (CPM 2003), Morelia, Michocán, Mexique, Lecture Notes in Computer Science, Number 2676, Pages 328-347, Springer Verlag Berlin, 2003.
BibTeX: @inproceedings{Pelfrene2003, author = {J. Pelfr\^ene and S. Abdedda{\"\i}m and J. Alexandre}, title = {Extracting Approximate Patterns}, booktitle = {Proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching (CPM 2003)}, address = {Morelia, Michoc\'an, Mexique}, publisher = {Springer Verlag Berlin}, year = {2003}, series = {Lecture Notes in Computer Science}, number = {2676}, pages = {328--347}, doi = {10.1007/3-540-44888-8_24} }
3 Communication internationale Rogozan, A.; Neveol, A. & Darmoni, S. J.. Text Categorization prior to Indexing for the CISMEF Health Catalogue. Artificial Intelligence in Medicine: 9th Conference on Artificial Intelligence in Medicine in Europe, AIME 2003, Protaras, Cyprus, October, Volume 2780, Pages 81-85, Springer, 2003.
Abstract: This paper is positioned within the development of an automated indexing system for the CISMeF quality controlled health gateway. For disambiguation purposes, we wish to perform text categorization prior to indexing. Hence, a global approach contrasting with the classical analytical methods based on the analysis of keyword counts extracted from the text is necessary. The use of statistical compression models enables us to proceed avoiding keyword extraction at this stage. Preliminary results show that althought this method is not as precise as others in terms of resource categorization, it can significantly benefit indexing.
BibTeX: @inproceedings{Rogozan2003, author = {Rogozan, A. and Neveol, A. and Darmoni, S. J.}, title = {Text Categorization prior to Indexing for the CISMEF Health Catalogue}, booktitle = {Artificial Intelligence in Medicine: 9th Conference on Artificial Intelligence in Medicine in Europe, AIME 2003}, address = {Protaras, Cyprus}, month = {October}, publisher = {Springer}, year = {2003}, volume = {2780}, pages = {81-85}, url = {http://aurelie.neveol.free.fr/RogozanAIME03.pdf}, doi = {10.1007/b12009} }
3 Communication internationale SOUALMIA, L & DARMONI, SJ. Etude du web sémantique : vers une recherche d?information intelligente en santé.. JFIM, 2003.
BibTeX: @inproceedings{SOUALMIA2003, author = {SOUALMIA, L and DARMONI, SJ}, title = {Etude du web sémantique : vers une recherche d?information intelligente en santé.}, booktitle = {JFIM}, year = {2003} }
3 Communication internationale Lina F Soualmia; Stéfan J Darmoni; Magaly Douyère & Benoît Thirion. Modelisation of consumer health information in a quality-controlled gateway.. Stud Health Technol Inform , Volume 95, Pages 701-706, 2003.
Abstract: 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 CISMeF-patients. It is a sub-part of CISMeF, a structured quality-controlled subject gateway. CISMeF-patients has been designed for the patients, their families and the general public who are often unfamiliar with the medical domain and the medical vocabulary. The resources included in CISMeF-patients are described using the Dublin Core metadata format. To index them, CISMeF-patients and CISMeF share the same terminology, which 'encapsulates' the MeSH thesaurus with a layer of synonyms. Unlike Medline-plus and Medline, sharing the same terminology allows to a CISMeF-patients end-user the possibility to extend his query to the CISMeF catalogue (e.g. for searching teaching resources or clinical guidelines).
BibTeX: @article{Soualmia2003, author = {Lina F Soualmia and Stéfan J Darmoni and Magaly Douyère and Benoît Thirion}, title = {Modelisation of consumer health information in a quality-controlled gateway.}, journal = {Stud Health Technol Inform}, year = {2003}, volume = {95}, pages = {701--706} }
3 Communication internationale Benoit Thirion; Gaelle Loosli; Magaly Douyère & Stéfan J Darmoni. Metadata element set in a quality-controlled subject gateway: a step to a health semantic Web.. Stud Health Technol Inform , Volume 95, Pages 707-712, 2003.
Abstract: BACKGROUND: Quality-controlled subject gateways are Internet services which apply a selected set of targeted measures to support systematic resource discovery. Considerable manual effort is used to process a selection of resources which meet quality criteria and to display a extensive description and indexing of these resources with standards-based metadata. OBJECTIVE: Several metadata element sets are proposed to describe, index and quality health resources to be included in a French quality-controlled health gateway called CISMeF. The main objectives were to enhance Internet health document retrieval and navigation, and to allow interoperability with other Internet services. RESULTS: The Dublin Core metadata element set is used to describe and index all Internet health resources included in CISMeF. For teaching resources, some elements from IEEE1484 Learning Object Metadata are also used. For evidenced-base medicine resources, specific metadata are employed which assess the health content quality. The HIDDEL metadata set is used to enhance transparency, trust and quality of health information on the Internet. CONCLUSION: Comprehensive metadata element sets can be extremely useful to describe, index and assess health resources on the Internet in a quality-controlled subject gateway. Machine-readable metadata creates an Semantic Web which is more efficient for end-users as compared to the current Web.
BibTeX: @article{Thirion2003, author = {Benoit Thirion and Gaelle Loosli and Magaly Douyère and Stéfan J Darmoni}, title = {Metadata element set in a quality-controlled subject gateway: a step to a health semantic Web.}, journal = {Stud Health Technol Inform}, year = {2003}, volume = {95}, pages = {707--712} }
3 Communication internationale Pierre Zweigenbaum; Robert Baud; Anita Burgun; Fiammetta Namer; Eric Jarrousse; Natalia Grabar; Patrick Ruch; Franck Le Duff; Benoît Thirion & Stéfan Darmoni. UMLF: a Unified Medical Lexicon for French.. AMIA Annu Symp Proc , Pages 1062, 2003.
Abstract: Lexical resources for medical language, such as lists of words with inflectional and derivational information, are publicly available for the English lantuate with the UMLS Specialist Lexicon. The goal of the UMLF project is to pool and unify existing resources and to add extensively to them by exploiting medical terminologies and corpora, resulting in a Unified Medical Lexicon for French. We present here the current status of the project.
BibTeX: @article{Zweigenbaum2003, author = {Pierre Zweigenbaum and Robert Baud and Anita Burgun and Fiammetta Namer and Eric Jarrousse and Natalia Grabar and Patrick Ruch and Franck Le Duff and Benoît Thirion and Stéfan Darmoni}, title = {UMLF: a Unified Medical Lexicon for French.}, journal = {AMIA Annu Symp Proc}, year = {2003}, pages = {1062}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1480196} }
3 Communication internationale Pierre Zweigenbaum; Robert Baud; Anita Burgun; Fiammetta Namer; Eric Jarrousse; Natalia Grabar; Patrick Ruch; Franck Le Duff; Benoît Thirion & Stéfan Darmoni. Towards a unified medical lexicon for French.. Stud Health Technol Inform , Volume 95, Pages 415-420, 2003.
Abstract: Medical Informatics has a constant need for basic Medical Language Processing tasks, e.g., for coding into controlled vocabularies, free text indexing and information retrieval. Most of these tasks involve term matching and rely on lexical resources: lists of words with attached information, including inflected forms and derived words, etc. Such resources are publicly available for the English language with the UMLS Specialist Lexicon, but not in other languages. For the French language, several teams have worked on the subject and built local lexical resources. The goal of the present work is to pool and unify these resources and to add extensively to them by exploiting medical terminologies and corpora, resulting in a unified medical lexicon for French (UMLF). This paper exposes the issues raised by such an objective, describes the methods on which the project relies and illustrates them with experimental results.
BibTeX: @article{Zweigenbaum2003a, author = {Pierre Zweigenbaum and Robert Baud and Anita Burgun and Fiammetta Namer and Eric Jarrousse and Natalia Grabar and Patrick Ruch and Franck Le Duff and Benoît Thirion and Stéfan Darmoni}, title = {Towards a unified medical lexicon for French.}, journal = {Stud Health Technol Inform}, year = {2003}, volume = {95}, pages = {415--420} }
4 Communication nationale C. WASCAT, N. LEROY, MC. BEUSCART-ZEPHIR, F. ANCEAUX, Darmoni, SJ.. Evaluation du niveau de difficulté rencontrée par les utilisateurs face à un moteur de recherche médical : l?exemple de Doc?CISMeF.. Internet et Pédagogie Médicale (IPM), Marseille, France, 2003.
BibTeX: @inproceedings{C.2003, author = {C. WASCAT, N. LEROY, MC. BEUSCART-ZEPHIR, F. ANCEAUX, Darmoni, SJ.}, title = {Evaluation du niveau de difficulté rencontrée par les utilisateurs face à un moteur de recherche médical : l?exemple de Doc?CISMeF.}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Marseille, France}, year = {2003} }
4 Communication nationale J. Ladner, M. Douyère , MP. Tavolacci, SJ. Darmoni, X. Coutour, P. Czernichow.. La formation en santé publique à portée d'un clic : un essai à transformer ?. Internet et Pédagogie Médicale (IPM), Marseille, France, 2003.
BibTeX: @inproceedings{J.2003, author = {J. Ladner, M. Douyère , MP. Tavolacci, SJ. Darmoni, X. Coutour, P. Czernichow.}, title = {La formation en santé publique à portée d'un clic : un essai à transformer ?}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Marseille, France}, year = {2003} }
4 Communication nationale LF. SOUALMIA, A. Néveol, B. DAHAMNA, M. DOUYERE, JL. LEROY, B. THIRION, Darmoni, SJ.. CISMeF dans l'infrastructure du Web Sémantique.. Premier Séminaire du Web Sémantique Médical, Rennes, France, 2003.
BibTeX: @inproceedings{LF.2003, author = {LF. SOUALMIA, A. Néveol, B. DAHAMNA, M. DOUYERE, JL. LEROY, B. THIRION, Darmoni, SJ.}, title = {CISMeF dans l'infrastructure du Web Sémantique.}, booktitle = {Premier Séminaire du Web Sémantique Médical}, address = {Rennes, France}, year = {2003}, url = {http://aurelie.neveol.free.fr/SoualmiaWSM03.pdf} }
4 Communication nationale LF. SOUALMIA, Darmoni, SJ.. Une Terminologie Orientée Ontologie pour la Recherche d'Information sur la Toile.. JFT, Pages 185-194, 2003.
Abstract: L?information accessible sur la Toile (ou Web) est disponible en quantité importante et elle ne cesse de croître. La recherche d?information demeure problématique malgré l?existence de nombreux moteurs de recherche et de sites catalogues en ligne. Le Web doit faire face aux problèmes d?exhaustivité et de précision en recherche d?information. Le projet CISMeF (Catalogue et Index de Sites Médicaux Francophones) a été développé afin de faciliter l?accès à l?information de santé disponible sur l?Internet. La problématique d?aujourd?hui se veut aussi être une recherche d?information intelligente dans l?infrastructure du Web Sémantique, une extension du web actuel qui permettrait de rendre interprétable le contenu des ressources par les hommes mais aussi par les machines, grâce à des ontologies et des méta-données. La recherche d?information dans CISMeF se fait à l?aide d?une terminologie semblable à une ontologie et un ensemble de méta-données qui nous permettent de placer le projet à cheval entre le Web actuel qui est informel, et le Web Sémantique de demain.
BibTeX: @inproceedings{LF.2003a, author = {LF. SOUALMIA, Darmoni, SJ.}, title = {Une Terminologie Orientée Ontologie pour la Recherche d'Information sur la Toile.}, booktitle = {JFT}, year = {2003}, pages = {185-194}, url = {http://www.antsearch.univ-tours.fr/jft2003/file/ActesJFT2003.pdf} }
4 Communication nationale LF. SOUALMIA, Darmoni, SJ.. Projection de Requêtes pour une Recherche d'Information Intelligente sur le Web.. RJCIA (Rencontres Jeunes Chercheurs en Intelligence Artificielle), Laval, France, Juillet, 2003.
BibTeX: @inproceedings{LF.2003b, author = {LF. SOUALMIA, Darmoni, SJ.}, title = {Projection de Requêtes pour une Recherche d'Information Intelligente sur le Web.}, booktitle = {RJCIA (Rencontres Jeunes Chercheurs en Intelligence Artificielle)}, address = {Laval, France}, month = {Juillet}, year = {2003}, url = {http://afia.lri.fr/plateforme-2003/Articles/RJCIA/rjcia-05-Soualmia.pdf} }
4 Communication nationale P. ZWEIGENBAUM, Darmoni, SJ, A. CRACIUN, P. JACQUEMART, LF. SOUALMIA.. Questions réponses dans le domaine médical.. Journées d'Étude de l'Association pour le Traitement Automatique des LAngues (ATALA), Paris, France, mai, 2003.
BibTeX: @inproceedings{P.2003a, author = {P. ZWEIGENBAUM, Darmoni, SJ, A. CRACIUN, P. JACQUEMART, LF. SOUALMIA.}, title = {Questions réponses dans le domaine médical.}, booktitle = {Journées d'Étude de l'Association pour le Traitement Automatique des LAngues (ATALA)}, address = {Paris, France}, month = {mai}, year = {2003} }
4 Communication nationale É. Rivals; G. Kucherov & T. Lecroq editors. Actes de la réunion des Actions Spécifiques og Algorithmes et Séquences fg et og Indexation de texte et découverte de motifs fg. , 2003. Montpellier, 20 et 21 novembre 2003 .
BibTeX: @misc{Rivals, author = {\'E. Rivals and G. Kucherov and T. Lecroq editors}, title = {Actes de la r\'eunion des Actions Sp\'ecifiques \og Algorithmes et S\'equences \fg\ et \og Indexation de texte et d\'ecouverte de motifs \fg}, year = {2003}, note = {Montpellier, 20 et 21 novembre 2003 } }
4 Communication nationale SJ. Darmoni, M. Douyère , A. Hamon, J. Benichou, J. Weber.. Evaluation d'un catalogue de santé pour diffuser des ressources pédagogiques sur l'Internet : une étude randomisée.. Internet et Pédagogie Médicale (IPM), Marseille, France, 2003.
BibTeX: @inproceedings{SJ.2003a, author = {SJ. Darmoni, M. Douyère , A. Hamon, J. Benichou, J. Weber.}, title = {Evaluation d'un catalogue de santé pour diffuser des ressources pédagogiques sur l'Internet : une étude randomisée.}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Marseille, France}, year = {2003} }
4 Communication nationale TD Tran, F. Mougin, SJ. Darmoni, P. Le Beux.. Indexation semi-automatique conceptuelle des cours de médecine de l'Université Médicale Virtuelle Francophone (UMVF).. Internet et Pédagogie Médicale (IPM), Marseille, France, 2003.
BibTeX: @inproceedings{TD2003, author = {TD Tran, F. Mougin, SJ. Darmoni, P. Le Beux.}, title = {Indexation semi-automatique conceptuelle des cours de médecine de l'Université Médicale Virtuelle Francophone (UMVF).}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Marseille, France}, year = {2003} }
2002 1 Publication internationale J. M. Brunetaud; S. Darmoni; N. Souf; E. Dufresne & R. Beuscart. A resource server for medical training.. Methods Inf Med , Volume 41, Number 2, Pages 177-182, 2002.
Abstract: OBJECTIVES: We have developed a RESOURCE SERVER to collect and store various elements used by a professor during his lecture. METHODS: The server manages four types of objects: ELEMENTS, RESOURCES (set of elements referring to a given topic), INDEXES (to organize the resources for further search and use), and USERS (to identify providers, users, and access rights). If an ELEMENT s modified, the RESOURCE is automatically updated. RESULTS: An example (preparation of an anatomy lecture) explains how the RESOURCE SERVER works in three steps: organization of the training material, indexing, and retrieval. CONCLUSIONS: The RESOURCE SERVER will help instructors develop, update and share pedagogic resources for supporting their training courses, lessons and conferences. Moreover, these techniques, based on Internet technologies for easy handling of and access to these resources, allow local and distant access. Within the general framework of the French-speaking Virtual Medical University, the RESOURCE SERVER will represent an important link between data collection and its use in intelligent pedagogic training.
BibTeX: @article{Brunetaud2002, author = {J. M. Brunetaud and S. Darmoni and N. Souf and E. Dufresne and R. Beuscart}, title = {A resource server for medical training.}, journal = {Methods Inf Med}, year = {2002}, volume = {41}, number = {2}, pages = {177--182} }
1 Publication internationale Stéfan Darmoni; Benoit Thirion; Sylvie Platel; Magsly Douyère; Philippe Mourouga & Jean-Philippe Leroy. CISMeF-patient: a French counterpart to MEDLINEplus.. J Med Libr Assoc , Apr, Volume 90, Number 2, Pages 248-253, 2002.
BibTeX: @article{Darmoni2002, author = {Stéfan Darmoni and Benoit Thirion and Sylvie Platel and Magsly Douyère and Philippe Mourouga and Jean-Philippe Leroy}, title = {CISMeF-patient: a French counterpart to MEDLINEplus.}, month = {Apr}, journal = {J Med Libr Assoc}, year = {2002}, volume = {90}, number = {2}, pages = {248--253}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=100773} }
1 Publication internationale Stefan J Darmoni; Francis Roussel; Jacques Benichou; Benoit Thirion & Nicole Pinhas. Reading factor: a new bibliometric criterion for managing digital libraries.. J Med Libr Assoc , Jul, Volume 90, Number 3, Pages 323-327, 2002.
BibTeX: @article{Darmoni2002b, author = {Stefan J Darmoni and Francis Roussel and Jacques Benichou and Benoit Thirion and Nicole Pinhas}, title = {Reading factor: a new bibliometric criterion for managing digital libraries.}, month = {Jul}, journal = {J Med Libr Assoc}, year = {2002}, volume = {90}, number = {3}, pages = {323--327}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=116406} }
1 Publication internationale Thirion B, Robu I.. Too many discussion lists for health sciences librarians?. EAHIL Newsletter to European Health Librarians , Volume 58, Pages 10-11, 2002.
BibTeX: @article{Thirion2002a, author = {Thirion B, Robu I.}, title = {Too many discussion lists for health sciences librarians?}, journal = {EAHIL Newsletter to European Health Librarians}, year = {2002}, volume = {58}, pages = {10-11}, url = {http://www.eahil.net/newsletter/58/feb2002.pdf} }
2 Publication nationale Darmoni, SJ, MA. Mayer, C. Thomeczek,, G. Eysenbach.. Qualité de l?information : le projet MedCIRCLE.. Revue du Praticien - Médecine Générale , Mai, Volume 16, Number 576, Pages 851-852, 2002.
BibTeX: @article{SJ.2002, author = {Darmoni, SJ, MA. Mayer, C. Thomeczek,, G. Eysenbach.}, title = {Qualité de l?information : le projet MedCIRCLE.}, month = {Mai}, journal = {Revue du Praticien - Médecine Générale}, year = {2002}, volume = {16}, number = {576}, pages = {851-852} }
2 Publication nationale Gehanno, JF. L'Internet, facteur de changement des pratiques en santé au travail ?. Archives des Maladies Professionnelles , Volume 63, Number 3-4, Pages 261-267, 2002.
BibTeX: @article{Gehanno2002b, author = {Gehanno, JF}, title = {L'Internet, facteur de changement des pratiques en santé au travail ?}, journal = {Archives des Maladies Professionnelles}, year = {2002}, volume = {63}, number = {3-4}, pages = {261-267}, url = {http://www.em-consulte.com/article/72546} }
2 Publication nationale MA. Mayer, SJ. Darmoni, M. Fiene, G. Eysenbach, R. Sarrias, C. Köhler, Thomas R. Roth-Berghofer, M. Gelabert.. Información de Calidad en Internet: proyecto MedCIRCLE.. Informed 2002 IX Congreso Nacional de Informática Médica, Valencia, Nov, 2002.
BibTeX: @inproceedings{MA.2002, author = {MA. Mayer, SJ. Darmoni, M. Fiene, G. Eysenbach, R. Sarrias, C. Köhler, Thomas R. Roth-Berghofer, M. Gelabert.}, title = {Información de Calidad en Internet: proyecto MedCIRCLE.}, booktitle = {Informed 2002 IX Congreso Nacional de Informática Médica}, address = {Valencia}, month = {Nov}, year = {2002}, url = {http://wma.comb.es/Upload/Documents/MedCIRCLE_Informed2002.pdf} }
2 Publication nationale Nicolas, D; Boulard, P; Boitel, L; Muller, F & Gehanno, JF. Internet et services médicaux interentreprises : bilan d'une enquête sur 287 Services interentreprises de Médecine du travail.. Archives des Maladies Professionnelles , Volume 63, Number 3-4, Pages 261-267, 2002.
BibTeX: @article{Nicolas2002a, author = {Nicolas, D and Boulard, P and Boitel, L and Muller, F and Gehanno, JF}, title = {Internet et services médicaux interentreprises : bilan d'une enquête sur 287 Services interentreprises de Médecine du travail.}, journal = {Archives des Maladies Professionnelles}, year = {2002}, volume = {63}, number = {3-4}, pages = {261-267}, url = {http://www.em-consulte.com/article/72548} }
3 Communication internationale BEUSCART MC, LEROY N, WASCAT C, DARMONI SJ. Usability Study of a Medical Resources Web Site. Methods for User's Behaviour Monitoring.. Human Factors & the Web : Designing and Evaluating for the Web., Nice, France, March, 2002.
Abstract: We present here the usability assessment study of a medical web site dedicated to the Cataloguing and Indexing of French speaking Medical web Sites (http://www.cismef.org). We performed a usability inspection using heuristic evaluation and an empirical usability test using a portable lab. From these results, we draw up a set of recommendations for the re-engineering of the Human Computer Interface (HCI). We conclude on the necessity to integrate usability engineering early enough in the projects lifecycle.
BibTeX: @inproceedings{BEUSCART2002, author = {BEUSCART MC, LEROY N, WASCAT C, DARMONI SJ}, title = {Usability Study of a Medical Resources Web Site}, booktitle = {Methods for User's Behaviour Monitoring.. Human Factors \& the Web : Designing and Evaluating for the Web.}, address = {Nice, France}, month = {March}, year = {2002}, url = {http://psimail.insa-rouen.fr/MnemosNet/psipubli.nsf/cc186bfe393798efc1256cc70057d255/2a695bd953199c66c1256b7a0031f123/$FILE/mcbeuscartzephir%20HFand%20the%20web2002%20.doc} }
3 Communication internationale Marie-Catherine Beuscart-Zéphir; Nicolas Leroy; Omolade Alao & Stefan Darmoni. Usability assessment study of a web site displaying medical resources on line: the CISMeF.. Stud Health Technol Inform , Volume 90, Pages 133-137, 2002.
Abstract: We present here the usability assessment study of a medical web site dedicated to the Cataloguing and Indexing of French speaking Medical web Sites (CISMeF). We performed a usability inspection using heuristic evaluation and an empirical usability test using a portable lab. The results of the heuristic evaluation show usability flaws along guidance, prompting and legibility ergonomic criteria. The usability test confirms this result and gives some more hints about the severity rating of the problems. From these results, we draw up a set of recommendations for the re-engineering of the Human Computer Interface (HCI). We conclude on the necessity to integrate usability engineering early enough in the projects lifecycle.
BibTeX: @article{Beuscart-Zephir2002, author = {Marie-Catherine Beuscart-Zéphir and Nicolas Leroy and Omolade Alao and Stefan Darmoni}, title = {Usability assessment study of a web site displaying medical resources on line: the CISMeF.}, journal = {Stud Health Technol Inform}, year = {2002}, volume = {90}, pages = {133--137} }
3 Communication internationale C. Köhler, SJ. Darmoni, MA. Mayer, TR. Roth-Berghofer, M. Fiene, G. Eysenbach.. MedCIRCLE - The Collaboration for Internet Rating, Certification, Labelling, and Evaluation of Health Information.. Mednet 2002, World Congress of the Internet in Medicine, Amsterdam, The Netherlands, december, 2002.
BibTeX: @inproceedings{C.2002, author = {C. Köhler, SJ. Darmoni, MA. Mayer, TR. Roth-Berghofer, M. Fiene, G. Eysenbach.}, title = {MedCIRCLE - The Collaboration for Internet Rating, Certification, Labelling, and Evaluation of Health Information.}, booktitle = {Mednet 2002, World Congress of the Internet in Medicine}, address = {Amsterdam, The Netherlands}, month = {december}, year = {2002}, url = {http://www.mednet2002.org/abstracts/display.cfm?id=104184401} }
3 Communication internationale S. J. Darmoni; F. Le Duff; M. Joubert; P. Le Beux; M. Fieschi; J. Weber & J. Benichou. A preliminary study to assess a French code of ethics for health teaching resources on the Internet.. Stud Health Technol Inform , Volume 90, Pages 621-626, 2002.
Abstract: BACKGROUND: Constant assessment of the quality of health information on the Internet is an absolute necessity as peer review is often lacking in this media. OBJECTIVE: To develop a simple and easy French Code of Ethics, which will enable medical students to judge quality of health information in teaching material available on the Internet. DESIGN: Three medical informaticians selected ten criteria from previously established codes of ethics from Europe and the USA. This instrument was tested on a sample of 30 health Internet teaching resources. RESULTS: For the panel of experts, chance corrected inter-observer agreement (kappa) for quality rating ranged from k = -0.19 and k = 0.33, demonstrating poor agreement among the raters. CONCLUSION: If negative results of this preliminary study are confirmed by further research, this finding may detrimentally affect projects in Europe to accredit or certify Internet health resources.
BibTeX: @article{Darmoni2002a, author = {S. J. Darmoni and F. Le Duff and M. Joubert and P. Le Beux and M. Fieschi and J. Weber and J. Benichou}, title = {A preliminary study to assess a French code of ethics for health teaching resources on the Internet.}, journal = {Stud Health Technol Inform}, year = {2002}, volume = {90}, pages = {621--626} }
3 Communication internationale S. J. Darmoni; F. Le Duff; M. Joubert; P. Le Beux; M. Fieschi; J. Weber & J. Benichou. Assessment of a French code of ethics for health teaching resources on the Internet. (Poster). Proc. AMIA Symp., Pages 1017, 2002.
Abstract: BACKGROUND: Constant assessment of the quality of health information on the Internet is an absolute necessity as peer review is often lacking in this media. OBJECTIVE: To develop a simple and easy French Code of Ethics, which will enable medical students to judge quality of health information in teaching material available on the Internet. DESIGN: Three medical informaticians selected ten criteria from previously established codes of ethics from Europe and the USA. This instrument was tested on a sample of 30 health Internet teaching resources. RESULTS: For the panel of experts, chance corrected inter-observer agreement (kappa) for quality rating ranged from k = -0.19 and k = 0.33, demonstrating poor agreement among the raters. CONCLUSION: If negative results of this preliminary study are confirmed by further research, this finding may detrimentally affect projects in Europe to accredit or certify Internet health resources.
BibTeX: @inproceedings{Darmoni2002c, author = {S. J. Darmoni and F. Le Duff and M. Joubert and P. Le Beux and M. Fieschi and J. Weber and J. Benichou}, title = {Assessment of a French code of ethics for health teaching resources on the Internet. (Poster)}, booktitle = {Proc. AMIA Symp.}, year = {2002}, pages = {1017} }
3 Communication internationale Darmoni, SJ, E. AMSALLEM, MC. HAUGH, M. DOUYERE, B. THIRION, J. WEBER, JP. BOISSEL.. Indication du niveau preuve : critère de qualité du contenu de l?information de santé sur l?Internet.. JFIM, Québec, Canada, Pages 245-254, 2002.
BibTeX: @inproceedings{SJ.2002a, author = {Darmoni, SJ, E. AMSALLEM, MC. HAUGH, M. DOUYERE, B. THIRION, J. WEBER, JP. BOISSEL.}, title = {Indication du niveau preuve : critère de qualité du contenu de l?information de santé sur l?Internet.}, booktitle = {JFIM}, address = {Québec, Canada}, year = {2002}, pages = {245-254} }
3 Communication internationale Gehanno, JF.. Use of Internet Among Occupational Health Practitioners in France.. 6th International Conference of the Scientific Committee on Education and Training in Occupational Health, ICOH, Baltimore, USA, October, 2002.
BibTeX: @inproceedings{Gehanno2002a, author = {Gehanno, JF.}, title = {Use of Internet Among Occupational Health Practitioners in France.}, booktitle = {6th International Conference of the Scientific Committee on Education and Training in Occupational Health, ICOH}, address = {Baltimore, USA}, month = {October}, year = {2002} }
3 Communication internationale GRABAR N., ZWEIGENBAUM P., SOUALMIA LF., Darmoni SJ.. A Study of the Adequacy of User and Indexing Vocabularies in Natural Language Queries to a MeSH-Indexed Health Gateway.. Proc AMIA Symp., Pages 1029, 2002.
BibTeX: @inproceedings{GRABAR2002a, author = {GRABAR N., ZWEIGENBAUM P., SOUALMIA LF., Darmoni SJ.}, title = {A Study of the Adequacy of User and Indexing Vocabularies in Natural Language Queries to a MeSH-Indexed Health Gateway.}, booktitle = {Proc AMIA Symp.}, year = {2002}, pages = {1029}, url = {http://estime.spim.jussieu.fr/~pz/FTPapiers/Grabar:AMIA2002.pdf} }
3 Communication internationale Grabar, N.; Zweigenbaum, P.; Soualmia, L. & Darmoni, S. J.. Les utilisateurs de Doc'CISMeF peuventils trouver ce qu'ils cherchent? Une étude de l'adéquation du vocabulaire des requêtes des utilisateurs au MeSH. JFIM, Québec Canada, Mai, Pages 158-169, JFIM, 2002.
BibTeX: @inproceedings{Grabar2002, author = {Grabar, N. and Zweigenbaum, P. and Soualmia, L. and Darmoni, S. J.}, title = {Les utilisateurs de Doc'CISMeF peuventils trouver ce qu'ils cherchent? Une étude de l'adéquation du vocabulaire des requêtes des utilisateurs au MeSH}, booktitle = {JFIM}, address = {Québec Canada}, month = {Mai}, publisher = {JFIM}, year = {2002}, pages = {158-169} }
3 Communication internationale J. WEBER, Darmoni, SJ.. French Medical Virtual University.. The 10th Ottawa Conference on Medical Education, Ottawa, Canada, July, 2002.
BibTeX: @inproceedings{J.2002, author = {J. WEBER, Darmoni, SJ.}, title = {French Medical Virtual University.}, booktitle = {The 10th Ottawa Conference on Medical Education}, address = {Ottawa, Canada}, month = {July}, year = {2002} }
3 Communication internationale SOUALMIA LF; DARMONI SJ; DOUYERE M; LE DUFF F; THELWALL M. Web Impact Factor: un outil bibliométrique appliqué aux sites Web des facultés de médecine et des CHU français. JFIM, Québec, Canada, Mai, Pages 496, 2002.
BibTeX: @inproceedings{M2002, author = {SOUALMIA LF; DARMONI SJ; DOUYERE M; LE DUFF F; THELWALL M}, title = {Web Impact Factor: un outil bibliométrique appliqué aux sites Web des facultés de médecine et des CHU français}, booktitle = {JFIM}, address = {Québec, Canada}, month = {Mai}, year = {2002}, pages = {496} }
3 Communication internationale Mary V., Pouliquen B., Le Duff F, Darmoni SJ., Segui A., Le Beux P.. Indexation automatique conceptuelle de thèses pharmaceutiques françaises.. JFIM, Québec, Canada, Mai, 2002.
BibTeX: @inproceedings{Mary2002a, author = {Mary V., Pouliquen B., Le Duff F, Darmoni SJ., Segui A., Le Beux P.}, title = {Indexation automatique conceptuelle de thèses pharmaceutiques françaises.}, booktitle = {JFIM}, address = {Québec, Canada}, month = {Mai}, year = {2002} }
3 Communication internationale Vincent Mary; Bruno Pouliquen; Franck Le Duff; Stefan J Darmoni; Alain Segui & Pierre Le Beux. Automatic conceptual indexing of French pharmaceutical theses.. Stud Health Technol Inform , Volume 90, Pages 388-392, 2002.
Abstract: French pharmaceutical theses are rarely quoted. If the main obstacles originate from language or access barriers, proper indexation could also be blamed. Manually extracted key-words don't necessary come from a structured thesaurus. In the following work, this manual indexing method is compared to an automated one, "Nomindex", based on UMLS. The automated method is improved by the addition of a relevance scoring system. The first indexing step consists of downloading, adapting and indexing theses in electronic format. Results will then be analyzed and sorted by relevance, through the comparison of classic statistical indices (noise, silence and relevance). It was assumed that the manually obtained key-words were always relevant. The silence of manual indexing is nevertheless high: seven new key-words are proposed by Nomindex, which results are mixed (10% of silence, but 50% of noise). These results are promising on the first experiment on pharmaceutical document without lexicon improvement. The indexing, if it is currently insufficient for a real life use, could easily be improved by specific updates of the lexicon.
BibTeX: @article{Mary2002, author = {Vincent Mary and Bruno Pouliquen and Franck Le Duff and Stefan J Darmoni and Alain Segui and Pierre Le Beux}, title = {Automatic conceptual indexing of French pharmaceutical theses.}, journal = {Stud Health Technol Inform}, year = {2002}, volume = {90}, pages = {388--392}, url = {http://langtech.jrc.it/Documents/MIE-02_Vincent.pdf} }
3 Communication internationale Lina Fatima Soualmia; Stéfan Jacques Darmoni; Franck Le Duff; Magaly Douyere & Maurice Thelwall. Web impact factor: a bibliometric criterion applied to medical informatics societies' web sites.. Stud Health Technol Inform , Volume 90, Pages 178-183, 2002.
Abstract: Several methods are available to evaluate and compare medical journals. The most popular is the journal Impact Factor, derived from averaging counts of citations to articles. Ingwersen adapted this method to assess the attractiveness of Web sites, defining the external Web Impact Factor (WIF) to be the number of external pages containing a link to a given Web site. This paper applies the WIF to 43 medical informatics societies' Web sites using advanced search engine queries to obtain the necessary link counts. The WIF was compared to the number of publications available in the Medline bibliographic database in medical informatics in these 43 countries. Between these two metrics, the observed Pearson correlation was 0.952 (p < 0.01) and the Spearman rank correlation was 0.548 (p < 0.01) showing in both cases a positive and strong significant correlation. The WIF of medicalm informatics society's Web site is statistically related to national productivity and discrepancies can be used to indicate countries where there are either weak medical informatics associations, or ones that do not make optimal use of the Web.
BibTeX: @article{Soualmia2002, author = {Lina Fatima Soualmia and Stéfan Jacques Darmoni and Franck Le Duff and Magaly Douyere and Maurice Thelwall}, title = {Web impact factor: a bibliometric criterion applied to medical informatics societies' web sites.}, journal = {Stud Health Technol Inform}, year = {2002}, volume = {90}, pages = {178--183} }
3 Communication internationale Benoit Thirion; Stéfan Jacques Darmoni; Magaly Douyere & Jean-Philippe Leroy. Webmastering in academic institutions: a new job opportunity.. Stud Health Technol Inform , Volume 90, Pages 832-837, 2002.
Abstract: In cyberspace, the health webmaster could be regarded as a virtual editor-in-chief, in charge of content and design. In this circumstance, he/she must follow quality criteria when building any resource. At the Rouen University Hospital (RUH), we have chosen "Net Scoring" as an effective tool to aid the design of a quality Web site. "Net Scoring" contains a list of 49 criteria which fall into eight categories: credibility, content, links, design, interactivity, quantitative aspects, ethics, and accessibility. The webmaster is the key element of the editorial board process. He/she must regularly monitor the Web site in order to retrieve information about whether the site is used and by whom: the method most commonly used is log analysis. At the RUH, an average of 9,000 unique machines visit our Web site each working day. Webmaster is a new job opportunity in academic institutions, in particular for medical informaticians and medical librarians both whom are information science professionals.
BibTeX: @article{Thirion2002, author = {Benoit Thirion and Stéfan Jacques Darmoni and Magaly Douyere and Jean-Philippe Leroy}, title = {Webmastering in academic institutions: a new job opportunity.}, journal = {Stud Health Technol Inform}, year = {2002}, volume = {90}, pages = {832--837} }
3 Communication internationale P. Zweigenbaum; S. J. Darmoni; N. Grabar; M. Douyère & J. Benichou. An assessment of the visibility of MeSH-indexed medical web catalogs through search engines.. Proc AMIA Symp , Pages 954-958, 2002.
Abstract: Manually indexed Internet health catalogs such as CliniWeb or CISMeF provide resources for retrieving high-quality health information. Users of these quality-controlled subject gateways are most often referred to them by general search engines such as Google, AltaVista, etc. This raises several questions, among which the following: what is the relative visibility of medical Internet catalogs through search engines? This study addresses this issue by measuring and comparing the visibility of six major, MeSH-indexed health catalogs through four different search engines (AltaVista, Google, Lycos, Northern Light) in two languages (English and French). Over half a million queries were sent to the search engines; for most of these search engines, according to our measures at the time the queries were sent, the most visible catalog for English MeSH terms was CliniWeb and the most visible one for French MeSH terms was CISMeF.
BibTeX: @article{Zweigenbaum2002, author = {P. Zweigenbaum and S. J. Darmoni and N. Grabar and M. Douyère and J. Benichou}, title = {An assessment of the visibility of MeSH-indexed medical web catalogs through search engines.}, journal = {Proc AMIA Symp}, year = {2002}, pages = {954--958} }
4 Communication nationale A. Hamon, SJ. Darmoni, F. Le Duff, JC. Dufour, M. Joubert, P. Le Beux, M. Fieschi, J. Weber, J. Bénichou.. Evaluation d'une grille de critères de qualité de ressources pédagogiques disponibles sur l?Internet.. Internet et Pédagogie Médicale (IPM), Lille, France, 2002.
BibTeX: @inproceedings{A.2002, author = {A. Hamon, SJ. Darmoni, F. Le Duff, JC. Dufour, M. Joubert, P. Le Beux, M. Fieschi, J. Weber, J. Bénichou.}, title = {Evaluation d'une grille de critères de qualité de ressources pédagogiques disponibles sur l?Internet.}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Lille, France}, year = {2002}, url = {http://w3med.univ-lille2.fr/ipm2002/programme/resumes.pdf} }
4 Communication nationale B. Dahamna, LF. Soualmia, B. Pourchez, E. Pichon, B. Thirion, J. Weber, SJ. Darmoni.. Codage MESH des questions d?internat : intérêt pour Doc?CISMeF, catalogue de ressources pédagogiques. Internet et Pédagogie Médicale (IPM), Lille, France, 2002.
BibTeX: @inproceedings{B.2002, author = {B. Dahamna, LF. Soualmia, B. Pourchez, E. Pichon, B. Thirion, J. Weber, SJ. Darmoni.}, title = {Codage MESH des questions d?internat : intérêt pour Doc?CISMeF, catalogue de ressources pédagogiques}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Lille, France}, year = {2002}, url = {http://w3med.univ-lille2.fr/ipm2002/programme/resumes.pdf} }
4 Communication nationale DARMONI SJ, LE DUFF F, JOUBERT M, LE BEUX P, FIESCHI M, WEBER J, BENICHOU J. Evaluation d'un code d'éthique pour l'étudiant en médecine sur l'Internet. Formation médicale et Technologies de l'Information et de la Communication, Informatique et Santé Internet et Pédagogie Médicale (IPM) 2001, Volume 14, Pages 63-72, 2002.
Abstract: Background: An assessment of the quality of health information on the Internet is an absolute necessity because peer review is often lacking in this media. Objective: To develop a simple and easy French code of ethics, which will enable medical students to judge quality of health information in teaching material available on the Internet. Design: Three medical informaticians generated ten criteria from previous codes of ethics from Europe and the USA. This instrument was tested on a sample of 30 health Internet teaching resources. Results: Chance corrected inter-observer agreement (kappa) for the quality rating ranged from k=-0.19 to k=0.33 amongst the expert panel, showing poor agreement among the raters. Conclusion: If the negative results of this study are confirmed by further research, they will affect detrimentally projects in Europe to accredit or certify Internet health resources.
BibTeX: @inproceedings{DARMONI2002z, author = {DARMONI SJ, LE DUFF F, JOUBERT M, LE BEUX P, FIESCHI M, WEBER J, BENICHOU J}, title = {Evaluation d'un code d'éthique pour l'étudiant en médecine sur l'Internet}, booktitle = {Internet et Pédagogie Médicale (IPM) 2001}, journal = {Formation médicale et Technologies de l'Information et de la Communication, Informatique et Santé}, year = {2002}, volume = {14}, pages = {63-72}, url = {http://litismail.insa-rouen.fr/MnemosNet/psipubli.nsf/ce6c2c540f564a2dc125680200361b7c/6fbb0ea481fe4ad9c1256b6c003269ef/$FILE/robustesseFR.doc} }
4 Communication nationale Gehanno, JF.. L'Internet, facteur de changement des pratiques en santé au travail ?. 27eme Congrès National de Médecine et Santé au Travail, Grenoble, France, Juin, 2002.
BibTeX: @inproceedings{Gehanno2002, author = {Gehanno, JF.}, title = {L'Internet, facteur de changement des pratiques en santé au travail ?}, booktitle = {27eme Congrès National de Médecine et Santé au Travail}, address = {Grenoble, France}, month = {Juin}, year = {2002}, url = {http://www.federationsantetravail.org/publications/m23Internet.html} }
4 Communication nationale Gehanno, JF. L'Internet, facteur de changement des pratiques en santé au travail ?. 27eme Congrès National de Médecine et Santé au Travail, Grenoble, France, Juin, 2002.
BibTeX: @inproceedings{Gehanno2002c, author = {Gehanno, JF}, title = {L'Internet, facteur de changement des pratiques en santé au travail ?}, booktitle = {27eme Congrès National de Médecine et Santé au Travail}, address = {Grenoble, France}, month = {Juin}, year = {2002} }
4 Communication nationale J. Weber, SJ. Darmoni, F. Charles, R. Bourru.. Quelle est l'apport des Techniques de l?Information et de la Communication (TIC) à la pédagogie médicale ?. Internet et Pédagogie Médicale (IPM), Lille, France, 2002.
BibTeX: @inproceedings{J.2002a, author = {J. Weber, SJ. Darmoni, F. Charles, R. Bourru.}, title = {Quelle est l'apport des Techniques de l?Information et de la Communication (TIC) à la pédagogie médicale ?}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Lille, France}, year = {2002}, url = {http://w3med.univ-lille2.fr/ipm2002/programme/resumes.pdf} }
4 Communication nationale JM. Brunetaud, SJ. Darmoni, RENARD JM, F. Le Duff, P. Le Beux, T. FERRE, R. Beuscart.. Le rôle d?une plate-forme de télé-enseignement au sein de l?Université Médicale Virtuelle Francophone.. ormation médicale et Technologies de l'Information et de la Communication, Informatique et Santé Internet et Pédagogie Médicale (IPM) 2001, Volume 14, Pages 13-20, 2002.
BibTeX: @inproceedings{JM.2002, author = {JM. Brunetaud, SJ. Darmoni, RENARD JM, F. Le Duff, P. Le Beux, T. FERRE, R. Beuscart.}, title = {Le rôle d?une plate-forme de télé-enseignement au sein de l?Université Médicale Virtuelle Francophone.}, booktitle = {Internet et Pédagogie Médicale (IPM) 2001}, journal = {ormation médicale et Technologies de l'Information et de la Communication, Informatique et Santé}, year = {2002}, volume = {14}, pages = {13-20} }
4 Communication nationale LF. SOUALMIA, C. BARRY-GREBOVAL, H. ABDULRAB, Darmoni, SJ.. Modélisation et représentation des connaissances dans un catalogue de santé.. Treizièmes Journées Francophones d?Ingénierie des Connaissances, Rouen, France, mai, 2002.
BibTeX: @inproceedings{LF.2002, author = {LF. SOUALMIA, C. BARRY-GREBOVAL, H. ABDULRAB, Darmoni, SJ.}, title = {Modélisation et représentation des connaissances dans un catalogue de santé.}, booktitle = {Treizièmes Journées Francophones d?Ingénierie des Connaissances}, address = {Rouen, France}, month = {mai}, year = {2002} }
4 Communication nationale LF. SOUALMIA, M. DOUYERE, JP. LEROY, B. THIRION, Darmoni, SJ.. Modélisation de l'information dans un catalogue de santé sur l'Internet.. Journée "Ingénierie des connaissances et santé", Paris, France, 28 janvier, 2002.
BibTeX: @inproceedings{LF.2002a, author = {LF. SOUALMIA, M. DOUYERE, JP. LEROY, B. THIRION, Darmoni, SJ.}, title = {Modélisation de l'information dans un catalogue de santé sur l'Internet.}, booktitle = {Journée "Ingénierie des connaissances et santé"}, address = {Paris, France}, month = {28 janvier}, year = {2002} }
4 Communication nationale M. Cuggia, G. Soula, SJ. Darmoni, F. Mougin, P. Le Beux.. Indexation audiovisuelle de l?UMVF : vers une approche web sémantique.. Internet et Pédagogie Médicale (IPM), Lille, France, 2002.
BibTeX: @inproceedings{M.2002, author = {M. Cuggia, G. Soula, SJ. Darmoni, F. Mougin, P. Le Beux.}, title = {Indexation audiovisuelle de l?UMVF : vers une approche web sémantique.}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Lille, France}, year = {2002}, url = {http://w3med.univ-lille2.fr/ipm2002/programme/resumes.pdf} }
4 Communication nationale MASSARI P, DARMONI SJ, FUSS J, STREIFF J, ROUSSEL F.. Communication du dossier électronique du patient entre établissements.. Télémédecine et e-santé, Informatique et Santé Journée AIM 2001, Volume 13, Pages 11-16, Springer-Verlag France, 2002.
Abstract: The communication of electronic patient records through telecommunication networks to healthcare professionals between different hospitals and also between hospitals and family physicians is one of the main challenges for this decade. In the year 2000, this approach proved to be successful for communication between three hospitals in Rouen (France) when used for 966 electronic patient records which contained, on average, 23 reports in psychiatry, 48 in gastroenterology, and 83 in pneumology. We used a three layer architecture, and security and confidentiality obligations were fulfilled. This first experience will be extended to communication between hospitals and family physicians in the second semester of 2001. A national health patient identification would facilitate and accelerate the communication of electronic patient records in France.
BibTeX: @inproceedings{MASSARI2002, author = {MASSARI P, DARMONI SJ, FUSS J, STREIFF J, ROUSSEL F.}, title = {Communication du dossier électronique du patient entre établissements.}, booktitle = {Journée AIM 2001}, journal = {Télémédecine et e-santé, Informatique et Santé}, publisher = {Springer-Verlag France}, year = {2002}, volume = {13}, pages = {11-16}, url = {http://litismail.insa-rouen.fr/MnemosNet/psipubli.nsf/6584347b5ce03e72c1256b0f007003f0/76659e02f6f8fe86c1256a8b0049864b/$FILE/Article%20AIM_2001_vf.doc} }
4 Communication nationale Nicolas D, Boulard P, Boitel L, Muller F, Gehanno JF. Internet et services médicaux interentreprises : bilan d'une enquête sur 287 Services interentreprises de Médecine du travail.. 27eme Congrès National de Médecine et Santé au Travail, Grenoble, France, Juin, 2002.
BibTeX: @inproceedings{Nicolas2002, author = {Nicolas D, Boulard P, Boitel L, Muller F, Gehanno JF}, title = {Internet et services médicaux interentreprises : bilan d'une enquête sur 287 Services interentreprises de Médecine du travail.}, booktitle = {27eme Congrès National de Médecine et Santé au Travail}, address = {Grenoble, France}, month = {Juin}, year = {2002}, url = {http://www.federationsantetravail.org/publications/m23Internet.html} }
4 Communication nationale P. Le Beux, B. Kamendje, JM. Brunetaud, AC. Benhamou, SJ. Darmoni, P. Gillois, D. Pagonis, G. Soula, M. Spector, J. Weber.. L?Université médicale virtuelle francophone : les réalisations.. Internet et Pédagogie Médicale (IPM), Lille, France, 2002.
BibTeX: @inproceedings{P.2002, author = {P. Le Beux, B. Kamendje, JM. Brunetaud, AC. Benhamou, SJ. Darmoni, P. Gillois, D. Pagonis, G. Soula, M. Spector, J. Weber.}, title = {L?Université médicale virtuelle francophone : les réalisations.}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Lille, France}, year = {2002}, url = {http://w3med.univ-lille2.fr/ipm2002/programme/resumes.pdf} }
4 Communication nationale P. Le Beux, F. Le Duff, G. Soula,, JM. Brunetaud, SJ. Darmoni, P. Gillois, D. Pagonis, M. Spector, M. Fieschi, R. Beuscart, P. Degoulet, AC. Benhamou, A. Bonnin, J. Weber. Définition des spécifications du projet de l'Université Médicale Virtuelle Française. Télémédecine et e-santé, Informatique et Santé Journée AIM 2001, Paris, France, Volume 13, Pages 105-112, 2002.
BibTeX: @inproceedings{P.2002b, author = {P. Le Beux, F. Le Duff, G. Soula,, JM. Brunetaud, SJ. Darmoni, P. Gillois, D. Pagonis, M. Spector, M. Fieschi, R. Beuscart, P. Degoulet, AC. Benhamou, A. Bonnin, J. Weber}, title = {Définition des spécifications du projet de l'Université Médicale Virtuelle Française}, booktitle = {Journée AIM 2001}, address = {Paris, France}, journal = {Télémédecine et e-santé, Informatique et Santé}, year = {2002}, volume = {13}, pages = {105-112} }
4 Communication nationale P. Le Beux, F. Le Duff, J. Weber, SJ. Darmoni, AC. Benhamou.. Intégration des Nouvelles Technologies Educatives dans l?Université Médicale Virtuelle Francophone.. Formation médicale et Technologies de l'Information et de la Communication, Informatique et Santé Internet et Pédagogie Médicale (IPM) 2001, Volume 14, Pages 3-12, Springer-Verlag France, 2002.
BibTeX: @inproceedings{P.2002c, author = {P. Le Beux, F. Le Duff, J. Weber, SJ. Darmoni, AC. Benhamou.}, title = {Intégration des Nouvelles Technologies Educatives dans l?Université Médicale Virtuelle Francophone.}, booktitle = {Internet et Pédagogie Médicale (IPM) 2001}, journal = {Formation médicale et Technologies de l'Information et de la Communication, Informatique et Santé}, publisher = {Springer-Verlag France}, year = {2002}, volume = {14}, pages = {3-12} }
4 Communication nationale P. ZWEIGENBAUM, N. GRABAR, Darmoni, SJ.. Projection de requêtes en langue naturelle sur les termes du MeSH : l?apport de connaissances.. Formation médicale et Technologies de l'Information et de la Communication, Informatique et Santé Internet et Pédagogie Médicale (IPM) 2001, Volume 14, Pages 55-62, 2002.
BibTeX: @inproceedings{P.2002d, author = {P. ZWEIGENBAUM, N. GRABAR, Darmoni, SJ.}, title = {Projection de requêtes en langue naturelle sur les termes du MeSH : l?apport de connaissances.}, booktitle = {Internet et Pédagogie Médicale (IPM) 2001}, journal = {Formation médicale et Technologies de l'Information et de la Communication, Informatique et Santé}, year = {2002}, volume = {14}, pages = {55-62} }
4 Communication nationale P. Zweigenbaum, SJ. Darmoni, N. Grabar, M. Douyère, J. Bénichou.. Visibilité relative de catalogues web médicaux à travers des moteurs de recherche.. Internet et Pédagogie Médicale (IPM), Lille, France, 2002.
BibTeX: @inproceedings{P.2002a, author = {P. Zweigenbaum, SJ. Darmoni, N. Grabar, M. Douyère, J. Bénichou.}, title = {Visibilité relative de catalogues web médicaux à travers des moteurs de recherche.}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Lille, France}, year = {2002}, url = {http://w3med.univ-lille2.fr/ipm2002/programme/resumes.pdf} }
4 Communication nationale SJ. Darmoni SJ., MA. Mayer, C. Thomeczek, G. Eysenbach.. MEDCIRCLE : un projet européen pour évaluer la qualité de l?information de santé. Internet et Pédagogie Médicale (IPM), Lille, France, 2002.
BibTeX: @inproceedings{SJ.2002b, author = {SJ. Darmoni SJ., MA. Mayer, C. Thomeczek, G. Eysenbach.}, title = {MEDCIRCLE : un projet européen pour évaluer la qualité de l?information de santé}, booktitle = {Internet et Pédagogie Médicale (IPM)}, address = {Lille, France}, year = {2002}, url = {http://w3med.univ-lille2.fr/ipm2002/programme/resumes.pdf} }
4 Communication nationale SJ. Darmoni, F. Le Duff, JM. Brunetaud, L. SIBERT, A. BURGUN, D. Pagonis, s. ALLORGE, P. Le Beux, R. Beuscart, J. Weber.. Apprentissage par problème assisté par ordinateur : étude de faisabilité.. Formation médicale et Technologies de l'Information et de la Communication, Informatique et Santé Internet et Pédagogie Médicale (IPM) 2001, Volume 14, Pages 45-54, Springer-Verlag France, 2002.
BibTeX: @inproceedings{SJ.2002c, author = {SJ. Darmoni, F. Le Duff, JM. Brunetaud, L. SIBERT, A. BURGUN, D. Pagonis, s. ALLORGE, P. Le Beux, R. Beuscart, J. Weber.}, title = {Apprentissage par problème assisté par ordinateur : étude de faisabilité.}, booktitle = {Internet et Pédagogie Médicale (IPM) 2001}, journal = {Formation médicale et Technologies de l'Information et de la Communication, Informatique et Santé}, publisher = {Springer-Verlag France}, year = {2002}, volume = {14}, pages = {45-54} }
2001 1 Publication internationale B.THIRION, JP. LEROY, F. BAUDIC, M. DOUYERE, J. PIOT, Darmoni, SJ.. SDI selecting, describing and indexing: did you mean automatically?. Knowledge Organization. , Volume 28, 2001.
BibTeX: @article{B.THIRION2001, author = {B.THIRION, JP. LEROY, F. BAUDIC, M. DOUYERE, J. PIOT, Darmoni, SJ.}, title = {SDI selecting, describing and indexing: did you mean automatically?}, journal = {Knowledge Organization.}, year = {2001}, volume = {28} }
1 Publication internationale S. J. Darmoni; M. C. Haugh; B. Lukacs & J. P. Boissel. Quality of health information about depression on internet. Level of evidence should be gold standard.. BMJ , Jun, Volume 322, Number 7298, Pages 1367, 2001.
BibTeX: @article{Darmoni2001d, author = {S. J. Darmoni and M. C. Haugh and B. Lukacs and J. P. Boissel}, title = {Quality of health information about depression on internet. Level of evidence should be gold standard.}, month = {Jun}, journal = {BMJ}, year = {2001}, volume = {322}, number = {7298}, pages = {1367}, url = {http://www.bmj.com/cgi/content/full/322/7298/1366#resp1} }
1 Publication internationale S. J. Darmoni; B. Thirion; J. P. Leroy & M. Douyère. The use of Dublin Core metadata in a structured health resource guide on the internet.. Bull Med Libr Assoc , Jul, Volume 89, Number 3, Pages 297-301, 2001.
BibTeX: @article{Darmoni2001c, author = {S. J. Darmoni and B. Thirion and J. P. Leroy and M. Douyère}, title = {The use of Dublin Core metadata in a structured health resource guide on the internet.}, month = {Jul}, journal = {Bull Med Libr Assoc}, year = {2001}, volume = {89}, number = {3}, pages = {297--301}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=34564} }
1 Publication internationale S. J. Darmoni; B. Thirion; J. P. Leroyt; M. Douyère; B. Lacoste; C. Godard; I. Rigolle; M. Brisou; S. Videau; E. Goupyt; J. Piott; M. Quéré; S. Ouazir & H. Abdulrab. A search tool based on 'encapsulated' MeSH thesaurus to retrieve quality health resources on the internet.. Med Inform Internet Med , Volume 26, Number 3, Pages 165-178, 2001.
Abstract: In the year 2001, the Internet has become a major source of health information for the health professional and the Netizen. The objective of Doc' CISMeF (D'C) was to create a powerful generic search tool based on a structured information model which 'encapsulates' the MeSH thesaurus to index and retrieve quality health resources on the Internet. To index resources, D'C uses four sections in its information model: 'meta-term', keyword, subheading, and resource type. Two search options are available: simple and advanced. The simple search requires the end-user to input a single term or expression. If this term belongs to the D'C information structure model, it will be exploded. If not, a full-text search is performed. In the advanced search, complex searches are possible combining Boolean operators with meta-terms, keywords, subheadings and resource types. D'C uses two standard tools for organising information: the MeSH thesaurus and the Dublin Core metadata format. Resources included in D'C are described according to the following elements: title, author or creator, subject and keywords, description, publishers, date, resource type, format, identifier, and language.
BibTeX: @article{Darmoni2001, author = {S. J. Darmoni and B. Thirion and J. P. Leroyt and M. Douyère and B. Lacoste and C. Godard and I. Rigolle and M. Brisou and S. Videau and E. Goupyt and J. Piott and M. Quéré and S. Ouazir and H. Abdulrab}, title = {A search tool based on 'encapsulated' MeSH thesaurus to retrieve quality health resources on the internet.}, journal = {Med Inform Internet Med}, year = {2001}, volume = {26}, number = {3}, pages = {165--178} }
1 Publication internationale F. Roussel; S. J. Darmoni & B. Thirion. Cost effectiveness of a medical digital library.. Med Inform Internet Med , Volume 26, Number 4, Pages 325-330, 2001.
Abstract: The rapid increase in the price of electronic journals has made the optimization of collection management an urgent task. As there is currently no standard procedure for the evaluation of this problem, we applied the Reading Factor (RF), an electronically computed indicator used for consultation of individual articles. The aim of our study was to assess the cost effective impact of modifications in our digital library (i.e. change of access from the Intranet to the Internet or change in editorial policy). The digital OVID library at Rouen University Hospital continues to be cost-effective in comparison with the interlibrary loan costs. Moreover, when electronic versions are offered alongside a limited amount of interlibrary loans, a reduction in library costs was observed.
BibTeX: @article{Roussel2001, author = {F. Roussel and S. J. Darmoni and B. Thirion}, title = {Cost effectiveness of a medical digital library.}, journal = {Med Inform Internet Med}, year = {2001}, volume = {26}, number = {4}, pages = {325--330}, url = {http://litismail.insa-rouen.fr/MnemosNet/psipubli.nsf/ce6c2c540f564a2dc125680200361b7c/bd3e3f5dbb12efb0c1256b6c0030d248/$FILE/CAVLMEDINF.doc} }
2 Publication nationale B. Thirion, JP. LEROY, F. BAUDIC, M. DOUYERE, J. PIOT, Darmoni, SJ.. Sélection, description, indexation : vous avez dit automatique ?. L'indexation à l'ère d'Internet., Lyon, France, Pages 37-32, ISKO-France, 2001.
BibTeX: @inproceedings{B.2001a, author = {B. Thirion, JP. LEROY, F. BAUDIC, M. DOUYERE, J. PIOT, Darmoni, SJ.}, title = {Sélection, description, indexation : vous avez dit automatique ?}, booktitle = {L'indexation à l'ère d'Internet.}, address = {Lyon, France}, publisher = {ISKO-France}, year = {2001}, pages = {37-32} }
2 Publication nationale B. Thirion, S. Platel, M. Douyère, P. Mourouga, S. Ouazir, J. Piot, S. Darmoni.. CISMeF et la Ligue Nationale contre le Cancer : ensemble pour les patients.. Revue du Praticien - Médecine Générale , Septembre, Volume 15, Number 544, Pages 1455-6, 2001.
BibTeX: @article{B.2001, author = {B. Thirion, S. Platel, M. Douyère, P. Mourouga, S. Ouazir, J. Piot, S. Darmoni.}, title = {CISMeF et la Ligue Nationale contre le Cancer : ensemble pour les patients.}, month = {Septembre}, journal = {Revue du Praticien - Médecine Générale}, year = {2001}, volume = {15}, number = {544}, pages = {1455-6} }
2 Publication nationale Gehanno, JF; Thirion, B & Caillard, JF. Approche bibliométrique de la veille documentaire en médecine du travail. Archives des Maladies Professionnelles , Volume 62, 2001.
BibTeX: @article{Gehanno2001, author = {Gehanno, JF and Thirion, B and Caillard, JF}, title = {Approche bibliométrique de la veille documentaire en médecine du travail}, journal = {Archives des Maladies Professionnelles}, year = {2001}, volume = {62} }
2 Publication nationale J. DARMONI, B. Lacoste, S. Videau, JP. LEROY, M. DOUYERE, J. PIOT, H. Abdulrab H, B. THIRION.. Doc' CISMeF : Un "Medline" francophone pour les ressources Internet : Un outil de recherche fonde sur le MeSH.. Médecine d'urgence , Volume 23, Number HS, Pages 279-283, 2001.
Abstract: Les ressources disponibles sur l'Internet concernant l'enseignement et la formation dans le domaine de la médecine sont en croissance exponentielle. L'objectif de Doc'CISMeF est de créer un outil de recherche générique fondé sur un modèle d'information qui encapsule le thésaurus MeSH. Pour indexer les ressources de qualité, Doc'CISMeF utilise 4 niveaux hiérarchiques : métaterme, mot-clé, qualificatif et type de ressources. Deux recherches sont possibles dans Doc'CISMeF :- la recherche simple qui permet à l'utilisateur de saisir un terme ou une expression ; si ce terme appartient à notre modèle d'information, il sera explosé, c'est-à-dire que Doc'CESMeF affichera toutes les ressources indexées avec des termes hiérarichiquement inférieurs ; - la recherche avancée permet des requêtes plus complexes, combinant avec des opérateurs booléens, méta-termes, mots-clés , qualificatifs et types de ressources, mais aussi tous les champs de Doc'CISMeF, comme par exemple la cible d'une ressource éducative, notamment le cycle d'études. Doc'CISMeF utilise deux outils standards pour organiser l'information le thésaurus MeSH et le format de données et de méta-données Dublin Core. Les champs de Doc'CISMeF sont: titre, auteur, desciption, site éditeur, date, identifiant, format, langue, mots-clés et type de ressources, institution, ville départemen ou province ou état, pays public concerné, coût, parrainage. Doc'CISMeF est un des outils de recherche qui sera utilisé au sein de la future Université Médicale Virtuelle Francophone.
BibTeX: @article{J.2001, author = {J. DARMONI, B. Lacoste, S. Videau, JP. LEROY, M. DOUYERE, J. PIOT, H. Abdulrab H, B. THIRION.}, title = {Doc' CISMeF : Un "Medline" francophone pour les ressources Internet : Un outil de recherche fonde sur le MeSH.}, journal = {Médecine d'urgence}, year = {2001}, volume = {23}, number = {HS}, pages = {279-283} }
2 Publication nationale SJ Darmoni, M. Haugh, B. Lukacs, JP Boissel.. Un nouveau critère de qualité du contenu de santé : le niveau de preuve .. Revue du Praticien - Médecine Générale , Number 529, Pages 479-80, 2001.
BibTeX: @article{SJ2001, author = {SJ Darmoni, M. Haugh, B. Lukacs, JP Boissel.}, title = {Un nouveau critère de qualité du contenu de santé : le niveau de preuve .}, journal = {Revue du Praticien - Médecine Générale}, year = {2001}, number = {529}, pages = {479-80} }
2 Publication nationale Stéfan Jacques DARMONI, Jean-Philippe LEROY, Magaly DOUYÈRE, Josette PIOT, Saïda OUAZIR, Benoît LACOSTE, Christophe GODARD, Isabelle RIGOLLE, Martial BRISOU, Stéphane VIDEAU, Myriam QUÉRÉ, Eric GOUPY, Habib ABDULRAB, Benoît THIRION. Doc'CISMeF : un outil de recherche Internet orienté vers l'enseignement et la formation à distance en médecine.. Pédagogie médicale , Août, Volume 2, Number 3, Pages 170-178, 2001.
BibTeX: @article{Stefan2001, author = {Stéfan Jacques DARMONI, Jean-Philippe LEROY, Magaly DOUYÈRE, Josette PIOT, Saïda OUAZIR, Benoît LACOSTE, Christophe GODARD, Isabelle RIGOLLE, Martial BRISOU, Stéphane VIDEAU, Myriam QUÉRÉ, Eric GOUPY, Habib ABDULRAB, Benoît THIRION}, title = {Doc'CISMeF : un outil de recherche Internet orienté vers l'enseignement et la formation à distance en médecine.}, month = {Août}, journal = {Pédagogie médicale}, year = {2001}, volume = {2}, number = {3}, pages = {170-178}, url = {http://www.pedagogie-medicale.org/2-3-darmoni.pdf} }
3 Communication internationale S. J. Darmoni; B. Thirion; J. P. Leroy; M. Douyère; B. Lacoste; C. Godard; I. Rigolle; M. Brisou; S. Videau; E. Goupy; J. Piot; M. Quéré; S. Ouazir & H. Abdulrab. Doc'CISMEF: a search tool based on "encapsulated" MeSH thesaurus.. Medinfo , Volume 10, Number Pt 1, Pages 314-318, 2001.
Abstract: In the year 2000, the Internet became a major source of health information for the health professional and the Netizen. The objective of Doc'CISMeF (D'C) was to create a powerful generic search tool based on an structured information model which â encapsulates' the MeSH thesaurus to index and retrieve quality health resources on the Internet. To index resources, D'C uses four sections in its information model: 'meta-term', keyword, subheading, and resource type. Two search options are available: simple and advanced. The simple search requires the end-user to input a single term or expression. If this term belongs to the D'C information structure model, it will be exploded. If not, a full-text search is performed. In the advanced search, complex searches are possible combining Boolean operators with meta-terms, keywords, subheadings and resource types. D'C uses two standard tools for organising information: the MeSH thesaurus and the Dublin Core metadata format. Resources included in D'C are described according to the following elements: title, author or creator, subject and keywords, description, publisher, date, resource type, format, identifier, and language.
BibTeX: @article{Darmoni2001b, author = {S. J. Darmoni and B. Thirion and J. P. Leroy and M. Douyère and B. Lacoste and C. Godard and I. Rigolle and M. Brisou and S. Videau and E. Goupy and J. Piot and M. Quéré and S. Ouazir and H. Abdulrab}, title = {Doc'CISMEF: a search tool based on "encapsulated" MeSH thesaurus.}, journal = {Medinfo}, year = {2001}, volume = {10}, number = {Pt 1}, pages = {314--318} }
3 Communication internationale P. Le Beux, AC. Benhamou, R. Beuscart, A. Bonnin, JM. Brunetaud, SJ. Darmoni, J. DEMONGEOT, M. Fieschi, P. GILLOIS, F. KOHLER, F. Le Duff, V. MORICE, D. Pagonis, M. Spector, G. Soula,, J. Weber.. A common platform for French Virtual Medical Universities.. Challenges of Primary Care-Oriented Health Systems : Innovations by Educational institutions, Health Professions, and Health Services, Londrina, Brazil, October, 2001.
BibTeX: @inproceedings{P.2001, author = {P. Le Beux, AC. Benhamou, R. Beuscart, A. Bonnin, JM. Brunetaud, SJ. Darmoni, J. DEMONGEOT, M. Fieschi, P. GILLOIS, F. KOHLER, F. Le Duff, V. MORICE, D. Pagonis, M. Spector, G. Soula,, J. Weber.}, title = {A common platform for French Virtual Medical Universities.}, booktitle = {Challenges of Primary Care-Oriented Health Systems : Innovations by Educational institutions, Health Professions, and Health Services}, address = {Londrina, Brazil}, month = {October}, year = {2001} }
3 Communication internationale B. Thirion; S. J. Darmoni & J. Benichou. Reading factor: a bibliometric tool to manage a virtual library.. Medinfo , Volume 10, Number Pt 1, Pages 385-389, 2001.
Abstract: Among the many bibliometric criteria used to evaluate biomedical journals, the impact factor is the most commonly used. Despite its limitations, it quantifies the influence of a journal on secondary publications. It does not however evaluate the practical usefulness of primary documents. Usefulness is field-related and varies greatly among specialities. We introduce a new bibliographic criterion, the "reading factor", and define it as the ratio between the number of electronic consultations of a particular journal (i.e., number of clicks on a hyper-link) and the mean number of electronic consultations of all the journals studied (itself calculated by dividing the total number of electronic accesses by the number of journals in the database). We describe its observed distribution, relative to that of the impact factor, based on electronic consultation records from our University Hospital medical digital library, where full-text electronic versions of 45 major biomedical journals have been available since December 1997. From this analysis we found no correlation between the 1999 reading factor and the 1998 impact factor of these 45 journals, and we observed a dramatic change in the hierarchy of journals upon using the reading factor as the yardstick rather than the impact factor. Moreover, we describe how using the reading factor has helped in managing the collection of our University Hospital's virtual library. The selection of journals to be discarded from the virtual library for the year 2001 was based on journals' RF values and this process will repeated over the coming years. The reading factor also permits a cost-analysis of a virtual library. CONCLUSION: The measurement of the reading factor is highly automated, practical and efficient. It appears as a new tool for electronic collection management by librarians, well fitting with economical data.
BibTeX: @article{Thirion2001, author = {B. Thirion and S. J. Darmoni and J. Benichou}, title = {Reading factor: a bibliometric tool to manage a virtual library.}, journal = {Medinfo}, year = {2001}, volume = {10}, number = {Pt 1}, pages = {385--389} }
3 Communication internationale P. Zweigenbaum; S. J. Darmoni & N. Grabar. The contribution of morphological knowledge to French MeSH mapping for information retrieval.. Proc AMIA Symp , Pages 796-800, 2001.
Abstract: MeSH-indexed Internet health directories must provide a mapping from natural language queries to MeSH terms so that both health professionals and the general public can query their contents. We describe here the design of lexical knowledge bases for mapping French expressions to MeSH terms, and the initial evaluation of their contribution to Doc'CISMeF, the search tool of a MeSH-indexed directory of French-language medical Internet resources. The observed trend is in favor of the use of morphological knowledge as a moderate (approximately 5 but effective factor for improving query to term mapping capabilities.
BibTeX: @article{Zweigenbaum2001, author = {P. Zweigenbaum and S. J. Darmoni and N. Grabar}, title = {The contribution of morphological knowledge to French MeSH mapping for information retrieval.}, journal = {Proc AMIA Symp}, year = {2001}, pages = {796--800}, url = {http://litismail.insa-rouen.fr/MnemosNet/psipubli.nsf/ce6c2c540f564a2dc125680200361b7c/3b9e8673a13b74c8c1256a8b00485551/$FILE/amia2001cismeflex.pdf} }
4 Communication nationale Darmoni, SJ. Intérêt de l'Internet dans un service médical. 12ème Journée de la Fédération des Cercles d'Etudes des Gynécologues-Obstétriciens des Hopitaux Généraux Français, Deauville, France, septembre, 2001.
BibTeX: @inproceedings{SJ.2001, author = {Darmoni, SJ}, title = {Intérêt de l'Internet dans un service médical}, booktitle = {12ème Journée de la Fédération des Cercles d'Etudes des Gynécologues-Obstétriciens des Hopitaux Généraux Français}, address = {Deauville, France}, month = {septembre}, year = {2001} }
5 Résumé Darmoni, SJ, MC. HAUGH, B. LUKACS, JP. BOISSEL.. Level of evidence to assess health content quality on the internet.. 9th International Cochrane Colloquium, Lyon, France, October, 2001.
BibTeX: @inproceedings{SJ.2001a, author = {Darmoni, SJ, MC. HAUGH, B. LUKACS, JP. BOISSEL.}, title = {Level of evidence to assess health content quality on the internet.}, booktitle = {9th International Cochrane Colloquium}, address = {Lyon, France}, month = {October}, year = {2001}, url = {http://www.biomedcentral.com/abstracts/cochrane/1/pb076/} }
5 Résumé ZWEIGENBAUM P., GRABAR N., DARMONI SJ.. L'apport de connaissances morphologiques pour la projection de requêtes sur une terminologie normalisée.. TALN (Traitement automatique des langues naturelles), Tours, France, Juillet, Pages 397-402, 2001.
BibTeX: @inproceedings{ZWEIGENBAUM2001a, author = {ZWEIGENBAUM P., GRABAR N., DARMONI SJ.}, title = {L'apport de connaissances morphologiques pour la projection de requêtes sur une terminologie normalisée.}, booktitle = {TALN (Traitement automatique des langues naturelles)}, address = {Tours, France}, month = {Juillet}, year = {2001}, pages = {397-402}, url = {http://www.tln.li.univ-tours.fr/Tln_Colloques/TALN2001-RECITAL2001/Actes/tome1_PDF/partie3_p323_402/art13_p397_402.pdf} }

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