Information Technology in Bio- and Medical Informatics, ITBAM 2010: First International Conference, Bilbao, Spain, September 1-2, 2010. Proceedings PDF
Preview Information Technology in Bio- and Medical Informatics, ITBAM 2010: First International Conference, Bilbao, Spain, September 1-2, 2010. Proceedings
Lecture Notes in Computer Science 6266 CommencedPublicationin1973 FoundingandFormerSeriesEditors: GerhardGoos,JurisHartmanis,andJanvanLeeuwen EditorialBoard DavidHutchison LancasterUniversity,UK TakeoKanade CarnegieMellonUniversity,Pittsburgh,PA,USA JosefKittler UniversityofSurrey,Guildford,UK JonM.Kleinberg CornellUniversity,Ithaca,NY,USA AlfredKobsa UniversityofCalifornia,Irvine,CA,USA FriedemannMattern ETHZurich,Switzerland JohnC.Mitchell StanfordUniversity,CA,USA MoniNaor WeizmannInstituteofScience,Rehovot,Israel OscarNierstrasz UniversityofBern,Switzerland C.PanduRangan IndianInstituteofTechnology,Madras,India BernhardSteffen TUDortmundUniversity,Germany MadhuSudan MicrosoftResearch,Cambridge,MA,USA DemetriTerzopoulos UniversityofCalifornia,LosAngeles,CA,USA DougTygar UniversityofCalifornia,Berkeley,CA,USA GerhardWeikum Max-PlanckInstituteofComputerScience,Saarbruecken,Germany Sami Khuri Lenka Lhotská Nadia Pisanti (Eds.) Information Technology in Bio- and Medical Informatics, ITBAM 2010 First International Conference Bilbao, Spain, September 1-2, 2010 Proceedings 1 3 VolumeEditors SamiKhuri SanJoséStateUniversity DepartmentofComputerScience OneWashingtonSquare SanJosé,CA95192-0249,USA. E-mail:[email protected] LenkaLhotská CzechTechnicalUniversity FacultyofElectricalEngineering DepartmentofCybernetics,Technicka2 16627Prague6,CzechRepublic E-mail:[email protected] NadiaPisanti UniversityofPisa DipartimentodiInformatica LargoPontecorvo3 56127Pisa,Italy E-mail:[email protected] LibraryofCongressControlNumber:2010931841 CRSubjectClassification(1998):H.3,H.5.2,I.4,H.4,H.5,J.1 LNCSSublibrary:SL3–InformationSystemsandApplication,incl.Internet/Web andHCI ISSN 0302-9743 ISBN-10 3-642-15019-5SpringerBerlinHeidelbergNewYork ISBN-13 978-3-642-15019-7SpringerBerlinHeidelbergNewYork Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,re-useofillustrations,recitation,broadcasting, reproductiononmicrofilmsorinanyotherway,andstorageindatabanks.Duplicationofthispublication orpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyrightLawofSeptember9,1965, initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Violationsareliable toprosecutionundertheGermanCopyrightLaw. springer.com ©Springer-VerlagBerlinHeidelberg2010 PrintedinGermany Typesetting:Camera-readybyauthor,dataconversionbyScientificPublishingServices,Chennai,India Printedonacid-freepaper 06/3180 Preface Biomedical engineering and medical informatics are challenging and rapidly growing areas. Applications of information technology in these areas are of paramount impor- tance. The aim of the first ITBAM conference was to bring together scientists, re- searchers and practitioners from different disciplines (mathematics, bioinformatics, biology, medicine, biomedical engineering and computer science) having such com- mon interests. We hope that ITBAM conferences will provide opportunities for fruit- ful discussions between all attendees and provide a platform where participants can exchange their most recent results, identify future directions and challenges, initiate possible collaborative research and system development, and develop common lan- guages for solving problems in the realm of biomedical engineering, bioinformatics and medical informatics. The importance of computer-aided diagnosis and therapy has drawn more and more attention worldwide and laid the foundation for modern medicine with excellent potential for promising applications such as telemedicine, Web-based healthcare and analysis of genetic information. For this conference, after a peer-review process, we finally selected 13 long papers and 8 short papers that are now published in this volume. They are divided in to the following groups: workflow management and database; decision support and data management in biomedicine; medical data modelling and information retrieval; data mining in bioinformatics; knowledge representation and data management in bioin- formatics; biological data and signal processing. The papers show how broad the spectrum of topics in applications of information technology to biomedical engineer- ing and medical informatics is. The editors would like to thank all the participants for their high-quality contribu- tions and Springer for publishing the proceedings of this conference. Our special thanks go to Gabriela Wagner for her hard work on various aspects of this event. June 2010 Lenka Lhotska Nadia Pisanti Sami Khuri Organization Honorary Chair Rudolf Freund Technical University Vienna, Austria Marie-France Sagot INRIA, France Anna Tramontano University of Rome „La Sapienza”, Italy General Chair Roland R. Wagner University of Linz, Austria Conference Program Chair Sami Khuri San José State University, USA Lenka Lhotska Czech Technical University Prague, Czech Republic Nadia Pisanti University of Pisa, Italy Poster Session Chair Vaclav Chudacek Czech Technical University in Prague, Czech Republic Roland Wagner University of Linz, Austria Program Committee Werner Aigner FAW, Austria Fuat Akal Functional Genomics Center Zurich, Switzerland Tatsuya Akutsu Kyoto University, Japan Andreas Albrecht Queen's University Belfast, UK Lijo Anto University of Kerala, India Rubén Armañanzas Arnedillo University of the Basque Country, Spain Peter Baumann Jacobs University Bremen, Germany Balaram Bhattacharyya Visva-Bharati University, India Christian Blaschke Bioalma Madrid, Spain Veselka Boeva Technical University of Plovdiv, Bulgaria Gianluca Bontempi Université Libre de Bruxelles, Belgium Roberta Bosotti Nerviano Medical Science s.r.l., Italy Rita Casadio University of Bologna, Italy VIII Organization Sònia Casillas Universitat Autonoma de Barcelona, Spain Silvana Castano Universita' degli Studi di Milano, Italy Carlo Cattani Difarma, Università di Salerno, Italy Kun-Mao Chao National Taiwan University, Taiwan Vaclav Chudacek Czech Technical University in Prague, Czech Republic Bin Cui Peking University, China Coral del Val Muñoz University of Granada, Spain Qiwen Dong Harbin Institute of Technology, China Béatrice Duval University of Angers, France Hans-Dieter Ehrich Technical University of Braunschweig, Germany Mourad Elloumi University of Tunis, Tunisia Maria Federico University of Modena and Reggio Emilia, Italy Pedro Fernandes Inst.Gulbenkian de Ciência, Portugal Rudolf Freund European Molecular Computing Consortium, Austria Christoph M. Friedrich Fraunhofer SCAI, Germany Xiangchao Gan University of Oxford, UK Alejandro Giorgetti University of Verona, Italy Alireza Hadj Khodabakhshi Simon Fraser University, Canada Volker Heun Ludwig-Maximilians-Universität München, Germany Chun-Hsi Huang University of Connecticut, USA Lars Kaderali University of Heidelberg, Germany Alastair Kerr University of Edinburgh, UK Sami Khuri San Jose State University, USA Erich Peter Klement University of Linz, Austria Michal Krátký Technical University of Ostrava, Czech Republic Josef Küng University of Linz, Austria Gorka Lasso-Cabrera CICbioGUNE, Spain Reinhard Laubenbacher Virginia Tech, USA Marc F. Lensink SCMBB, Belgium Lenka Lhotska Czech Technical University, Czech Republic Roger Marshall Plymouth Ystate University, USA Elio Masciari ICAR-CNR, Università della Calabria, Italy Henning Mersch RWTH Aachen University, Germany Silvia Miksch Danube University Krems, Austria Aleksandar Milosavljevic Baylor College of Medicine, USA Jean-Christophe Nebel Kingston University, UK See Kiong Ng Institute for Infocomm Research, Singapore Vit Novacek National University of Ireland, Galway, Ireland Philipp Pagel Technische Universität München, Germany Francisco Pinto ITQB, University of Lisbon, Portugal Nadia Pisanti University of Pisa, Italy Cinzia Pizzi Universita' degli Studi di Padova, Italy Clara Pizzuti ICA-CNR, Italy Meikel Poess Oracle Corporation, USA Nicole Radde Universität Stuttgart, Germany Organization IX Dietrich Rebholz-Schuhmann European Bioinformatics Institute, UK Cristina Rubio-Escudero University of Seville, Spain Victor Sabbia Universidad de la República, Uruguay Hershel Safer Weizmann Institute of Science, Israel Nick Sahinidis Carnegie Mellon University, USA Francisca Sánchez Jiménez University of Málaga, Spain Roberto Santana University of the Basque Country, Spain Kenji Satou Kanazawa University, Japan Kristan Schneider University of Vienna, Austria Kathleen Steinhofel King's College London, UK Ralf Tautenhahn The Scripps Research Institute, USA A. Min Tjoa Vienna University of Technology, Austria Thodoros Topaloglou University of Toronto, Canada Paul van der Vet University of Twente, The Netherlands Jano van Hemert University of Edinburgh, UK Roland R. Wagner University of Linz, Austria Viacheslav Wolfengagen JurInfoR-MSU Institute for Contemporary Education, Russia Borys Wrobel Polish Academy of Sciences, Poland Filip Zavoral Charles University in Prague, Czech Republic Filip Zelezny Czech Technical University, Czech Republic Songmao Zhang Chinese Academy of Sciences, China Qiang Zhu The University of Michigan, USA Frank Gerrit Zoellner University of Heidelberg, Germany External Reviewers Francisco Martínez-Álvarez Ben Liu Olivier Caelen Yi Guo Abhilash Miranda Zhe Xu Qian Gang Rung-Ren Lin Chao Zhu Leonidas Kapsokalivas Manish Singh Abu Z. Dayem Ullah Shen Xu Table of Contents Workflow Management and Database e-BioFlow: Improving Practical Use of Workflow Systems in Bioinformatics................................................... 1 Ingo Wassink, Matthijs Ooms, Pieter Neerincx, Gerrit van der Veer, Han Rauwerda, Jack A.M. Leunissen, Timo M. Breit, Anton Nijholt, and Paul van der Vet MEDCollector: Multisource Epidemic Data Collector ................. 16 Jo˜ao Zamite, Fabr´ıcio A.B. Silva, Francisco Couto, and Ma´rio J. Silva Epidemic Marketplace: An Information Management System for Epidemiological Data............................................. 31 Luis F. Lopes, Fabr´ıcio A.B. Silva, Francisco Couto, Jo˜ao Zamite, Hugo Ferreira, Carla Sousa, and Ma´rio J. Silva Decision Support and Data Management in Biomedicine DCM Data Management Framework: A Data Warehousing Approach... 45 Shehla Khalid, Claire Surr, and Daniel Neagu Automatic Classification of Intrapartal Fetal Heart-Rate Recordings – Can It Compete with Experts? ........................ 57 V´aclav Chud´aˇcek, Jiˇr´ı Spilka, Michal Huptych, George Georgoulas, Petr Jank˚u, Michal Kouck´y, Chrysostomos Stylios, and Lenka Lhotsk´a Clinical Informatics to Diagnose Cardiac Diseases Based on Data Mining ......................................................... 67 Sung Ho Ha and Zhen Yu Zhang Decision Support in Biomedicine (Short Papers) The Case-BasedSoftware System for Physician’s Decision Support ..... 78 Leonid Karpov and Valery Yudin SASAgent: An Agent Based Architecture for Search, Retrieval and Composition of e-Science Models and Tools ......................... 86 Luiz Felipe Mendes, Regina Braga, and Fernanda Campos XII Table of Contents Clustering of Protein Substructures for Discovery of a Novel Class of Sequence-Structure Fragments..................................... 94 Ivana Rudolfova, Jaroslav Zendulka, and Matej Lexa A Comorbidity Network Approach to Predict Disease Risk ............ 102 Francesco Folino, Clara Pizzuti, and Maria Ventura Mining and Post-Processingof Association Rules in the Atherosclerosis Risk Domain .................................................... 110 Petr Berka and Jan Rauch Medical Data Modeling and Information Retrieval Optimized Column-Oriented Model: A Storage and Search Efficient Representation of Medical Data.................................... 118 Razan Paul and Abu Sayed Md. Latiful Hoque A Semantic Query Interface for the OGO Platform................... 128 Jos´e Antonio Min˜arro-Gim´enez, Mikel Egan˜a Aranguren, Francisco Garc´ıa-Sa´nchez, and Jesualdo Toma´s Ferna´ndez-Breis BioMedical Information Retrieval: The BioTracer Approach ........... 143 Heri Ramampiaro Data Mining in Bioinformatics A Self-Organizing State Space Approach to Inferring Time-Varying Causalities between Regulatory Proteins ............................ 158 Osamu Hirose and Kentaro Shimizu Knowledge Representation and Data Management in Bioinformatics Retrieving Samples from Biobanks ................................. 172 Claus Dabringer and Johann Eder Logical Knowledge Representation of Regulatory Relations in Biomedical Pathways............................................. 186 Sine Zambach and Jens Ulrik Hansen Smooth Introduction of Semantic Tagging in Genotyping Procedures ... 201 Alessio Bechini, Jacopo Viotto, and Riccardo Giannini Biological Data and Signal Processing Laboratory Kit for Oscillometry Measurement of Blood Pressure....... 215 Jan Dvoˇra´k and Jan Havl´ık Table of Contents XIII Initial Analysis of the EEG Signal Processing Methods for Studying Correlations between Muscle and Brain Activity ..................... 220 Helena Valentov´a and Jan Havl´ık Highlighting the Current Issues with Pride Suggestions for Improving the Performance of Real Time Cardiac Health Monitoring............. 226 Mohamed Ezzeldin A. Bashir, Dong Gyu Lee, Makki Akasha, Gyeong Min Yi, Eun-jong Cha, Jang-whan Bae, Myeong Chan Cho, and Keun Ho Ryu Author Index.................................................. 235
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