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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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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.}
}

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}
}

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}
}

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.}
}

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.}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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.}
}

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}
}

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}
}

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}
}

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}
}

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.}
}

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}
}

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}
}

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}
}

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


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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

BibTeX:
@incollection{Crochemore2015,
  author = {Maxime Crochemore and Thierry Lecroq},
  title = {Multiple String Matching},
  booktitle = {Encyclopedia of Algorithms},
  publisher = {Springer},
  year = {2015}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

BibTeX:
@inproceedings{Schuers2015,
  author = {Schuers, M},
  title = {Interroger Medline en français : c'est possible !},
  booktitle = {CMGF Paris},
  year = {2015},
  note = {Accepté}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

BibTeX:
@incollection{DBLP:reference/algo/CrochemoreL15b,
  author = {Maxime Crochemore and Thierry Lecroq},
  title = {String Matching},
  booktitle = {Encyclopedia of Algorithms},
  publisher = {Springer},
  year = {2015}
}

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}
}

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}
}

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}
}

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


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 Θ ( m β ) -time algorithm to solve it, where m is the length of the shortest sequence to be extended, and β 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 Θ ( m β ) -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 ℓ-gaps in time Θ ( m β ℓ ) . 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}
}

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}
}

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}
}

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}
}

Abstract: Constantinescu and Ilie [S. Constantinescu, L. Ilie. Fine and Wilf’s theorem for abelian periods, Bulletin of the European Association for Theoretical Computer Science 89 (2006) 167–170] introduced the notion of an Abelian period of a word. A word of length n over an alphabet of size σ can have Θ ( n 2 ) distinct Abelian periods. The Brute-Force algorithm computes all the Abelian periods of a word in time O ( n 2 × σ ) using O ( n × σ ) 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, Élise},
  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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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 &amp; 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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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


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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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/m≥5√km/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 − 1 + 1) − 2 if j is even or F j ( F j + 1 + F j − 1 ) − 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 ≥ 3, the Fibonacci word f j has abelian period equal to F n , where n=⌊j/2⌋n = textbackslashlfloorj/2textbackslashrfloor if j=0,1,2mod4j = 0, 1, 2textbackslashmod4 , or n=1+⌊j/2⌋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, Élise},
  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}
}

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}
}

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}
}

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}
}

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 ρ of similar strings, the SAA for ρ is a lexicographically sorted list of all the alignment-suffixes of ρ. 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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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


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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

BibTeX:
@inproceedings{Gehanno2012c,
  author = {Gehanno, J.-F.},
  title = {Grossesse et travail},
  booktitle = {Salon de Gynécologie Obstétrique Pratique},
  address = {Paris},
  month = {March},
  year = {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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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/}
}

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 &amp; 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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

BibTeX:
@inproceedings{Coutant2012b,
  author = {Coutant, S},
  title = {Exome Variations Analyzer},
  booktitle = {journées du Canceropôle Nord-Ouest},
  address = {Rouen, France},
  year = {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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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-}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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


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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

BibTeX:
@inproceedings{Coutant2011b,
  author = {Coutant, S},
  title = {Exome Variations Analyzer},
  booktitle = {Bioinformatics and High Throughput Sequencing},
  address = {Institut Pasteur, Paris, France},
  year = {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}
}

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}
}

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/}
}

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}
}

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}
}

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}
}

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}
}

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/}
}

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/}
}

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}
}

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}
}

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}
}

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.}
}

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/}
}

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}
}

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}
}

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}
}

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}
}

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


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}
}

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}
}

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}
}

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}
}

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}
}

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/}
}

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}
}

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}
}

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/}
}

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/}
}

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}
}

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}
}

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}
}

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/}
}

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}
}

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/}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

BibTeX:
@inproceedings{Merabti2010a,
  author = {Merabti, T and Darmoni SJ},
  title = {ATC to PubMed: a bibliographic tool for drugs},
  booktitle = {AMIA},
  year = {2010},
  pages = {1174}
}

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/}
}

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/}
}

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/}
}

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}
}

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}
}

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}
}

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


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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

BibTeX:
@phdthesis{Salson2009b,
  author = {Salson, M},
  title = {Structures d'indexation compressées et dynamiques pour le texte},
  school = {Université de Rouen, France},
  year = {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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

BibTeX:
@inproceedings{Faro2009,
  author = {Faro, S and Lecroq, T},
  title = {Efficient Pattern Matching on Binary Strings},
  booktitle = {SOFSEM},
  year = {2009}
}

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}
}

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}
}

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}
}

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


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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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/}
}

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}
}

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}
}

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}
}

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}
}

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}
}

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}
}