CONNECTING MEDICAL INFORMATICS AND BIO-INFORMATICS doc

CONNECTING MEDICAL INFORMATICS AND
BIO-INFORMATICS
Studies in Health Technology and
Informatics
This book series was started in 1990 to promote research conducted under the auspices of the EC
programmes’ Advanced Informatics in Medicine (AIM) and Biomedical and Health Research
(BHR) bioengineering branch. A driving aspect of international health informatics is that
telecommunication technology, rehabilitative technology, intelligent home technology and many
other components are moving together and form one integrated world of information and
communication media. The complete series has been accepted in Medline. Volumes from 2005
onwards are available online.
Series Editors:
Dr. J.P. Christensen, Prof. G. de Moor, Dr. A. Famili, Prof. A. Hasman, Prof. L. Hunter,
Dr. I. Iakovidis, Dr. Z. Kolitsi, Dr. O. Le Dour, Dr. A. Lymberis, Dr. P. Niederer,
Prof. A. Pedotti, Prof. O. Rienhoff, Prof. F.H. Roger France, Dr. N. Rossing,
Prof. N. Saranummi, Dr. E.R. Siegel and Dr. P. Wilson
Volume 116
Recently published in this series
Vol. 115. N. Saranummi, D. Piggott, D.G. Katehakis, M. Tsiknakis and K. Bernstein (Eds.),
Regional Health Economies and ICT Services
Vol. 114. L. Bos, S. Laxminarayan and A. Marsh (Eds.), Medical and Care Compunetics 2
Vol. 113. J.S. Suri, C. Yuan, D.L. Wilson and S. Laxminarayan (Eds.), Plaque Imaging: Pixel to
Molecular Level
Vol. 112. T. Solomonides, R. McClatchey, V. Breton, Y. Legré and S. Nørager (Eds.), From
Grid to Healthgrid
Vol. 111. J.D. Westwood, R.S. Haluck, H.M. Hoffman, G.T. Mogel, R. Phillips, R.A. Robb and
K.G. Vosburgh (Eds.), Medicine Meets Virtual Reality 13
Vol. 110. F.H. Roger France, E. De Clercq, G. De Moor and J. van der Lei (Eds.), Health
Continuum and Data Exchange in Belgium and in the Netherlands – Proceedings of
Medical Informatics Congress (MIC 2004) & 5th Belgian e-Health Conference
Vol. 109. E.J.S. Hovenga and J. Mantas (Eds.), Global Health Informatics Education

Vol. 108. A. Lymberis and D. de Rossi (Eds.), Wearable eHealth Systems for Personalised
Health Management – State of the Art and Future Challenges
Vol. 107. M. Fieschi, E. Coiera and Y C.J. Li (Eds.), MEDINFO 2004 – Proceedings of the
11th World Congress on Medical Informatics
Vol. 106. G. Demiris (Ed.), e-Health: Current Status and Future Trends
Vol. 105. M. Duplaga, K. Zieliński and D. Ingram (Eds.), Transformation of Healthcare with
Information Technologies
Vol. 104. R. Latifi (Ed.), Establishing Telemedicine in Developing Countries: From Inception
to Implementation
ISSN 0926-9630
Connecting Medical Informatics and
Bio-Informatics
Proceedings of MIE2005
The XIXth International Congress of the European Federation for Medical Informatics
Edited by
Rolf Engelbrecht
Institute for Medical Informatics, GSF National Research Centre
for Environment and Health, Munich-Neuherberg, Germany
Antoine Geissbuhler
Service of Medical Informatics, University Hospitals of Geneva, Switzerland
Christian Lovis
Service of Medical Informatics, University Hospitals of Geneva, Switzerland
and
George Mihalas
Department of Biophysics and Medical Informatics, “Victor Babes”
University of Medicine and Pharmacy, Timisoara, Romania
Amsterdam • Berlin • Oxford • Tokyo • Washington, DC
© 2005 EFMI – European Federation for Medical Informatics
All rights reserved. No part of this book may be reproduced, stored in a retrieval system,
or transmitted, in any form or by any means, without prior written permission from the publisher.

ISBN 1-58603-549-5
Library of Congress Control Number: 2005930831
Publisher
IOS Press
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LEGAL NOTICE
The publisher is not responsible for the use which might be made of the following information.
PRINTED IN THE NETHERLANDS
Connecting Medical Informatics and Bio-Informatics v
R. Engelbrecht et al. (Eds.)
IOS Press, 2005
© 2005 EFMI – European Federation for Medical Informatics. All rights reserved.
Preface
After a successful MEDINFO in 1992, the Swiss Society for Medical Informatics hosts
again a major event in medical informatics – the 19
th
Medical Informatics Europe Confer-
ence, under the generic name of MIE2005. The host city, Geneva, is well known for its
commitment in international healthcare, being the residence of several international organi-

sations, including WHO. Geneva is also synonym with other major medical informatics
achievements: the DIOGENE hospital information system and Natural Language Process-
ing, both strongly connected to Geneva and its University Hospital.
The motto of the conference, “Connecting Medical Informatics and Bio-Informatics”
emphasizes the convergence of these disciplines, illustrated by the Swiss Institute of Bioin-
formatics, also founded in Geneva, and home of the SwissProt database. It also reflects the
growing role of the co-operation of different disciplines in healthcare, co-operation which
tends to become integration.
The major challenge of this decade is to develop and extend the use of information
technology for the improvement of patient oriented health care. It has to integrate results
from other areas and scientific disciplines, and interoperability will be the key problem to
be solved. All these trends were already reflected in MIE2005 submissions and addressed a
large palette of topics, including classical topics as standards, terminology, coding, imaging
etc.
The selection process was a difficult task for the Scientific Program Committee. We
kept the scientific quality as the major determinant criterion for selection. There were over
300 submitted papers to be presented orally or as poster. A score was given by 2 and more
reviewers selected from a panel of more than 160 experts. The reviews were accompanied
by suggestions and advice about possible improvements of the submitted paper. The type of
presentation was sometimes modified from oral presentation to a short oral presentation
combined with a poster or just a poster for detailed presentation and deep discussion. In a
second step, when creating the scientific programme, there were a few modifications of the
presentation type, mainly due to the limited time slots available for oral presentations.
The result of SPC activity is reflected by the Conference programme and the Proceed-
ings. The printed version has limited pages and therefore limited numbers of papers of all
types of presentations (oral and poster presentations) which are most qualified. It will be
cited in Medline. The full content was proposed for the CD version of the proceedings; it is
an EFMI publication and contains all accepted papers in the revised version and also the
workshops. This way of publishing enables searching keywords, the title and the full con-
tent.

Workshops were offered to the participants like in previous MIEs, organised or sup-
ported by EFMI working groups. A clearer distinction between presentations in workshops
and presentations in scientific sessions was aimed: while a pure scientific paper presents
results in a classical manner, a workshop paper would rather present and comment unful-
fillments or raise questions. The workshop procedure comprises a brief introduction (usu-
ally invited), followed by several short statements or presentations. The major output is ex-
pected from discussions. The results which might be achieved will be published after
MIE2005 separately. All documents, (material from the workshops) available at publishing
vi
time will be included on the CD proceedings. We plan to make it also available on the
EFMI web site by the moment of this material publication.
We shall also mention that the call for tutorials resulted in a set of high ranked contribu-
tions, included in the “scientific workflow” of each MIE conference. They will provide ba-
sics and deep insight into certain disciplines and topics related to medical informatics. It
may help to develop a better understanding of some presentations and workshops during
MIE2005. In this context tutorials are a substantial part and the material developed should
be available to a broader community.
The proceedings are an integrated part of MIE2005. We would like to thank all those
who have made the printed volume and the CD possible, the authors, the scientific pro-
gramme committee, the reviewers, and the teams in Geneva and Munich, Robert Baud,
Jérôme Billet, Henning Müller, Claudia Hildebrand, Ruslan David, Jutta Balint, Alfred
Breier, Silvia Weinzierl and some more.
Rolf Engelbrecht
Antoine Geissbuhler
Christian Lovis
Gheorghe Mihalas
vii
Reviewers for MIE2005
The following reviewers, listed in alphabetical order, contributed to the selection process of
the papers.

Abidi, Raza
Afrin, Lawrence
Åhleldt, Hans
Albuisson, Eliane
Ammenwerth, Elske
Pitsillides, Andreas
Angelidis, Pantelis
Aronsky, Dominik
Arredondo, María Teresa
Bainbridge, Mike
Barber, Barry
Barton, Amy
Baud, Robert
Bellazzi, Riccardo
Betts, Helen
Beuscart, Régis
Beuscart-Zéphir, Marie-Catherine
Blobel, Bernd
Bodenreider, Olivier
Boire, Jean-Yves
Brender, Jytte
Brigl, Birgit
Bruins Slot, Harm
Brunetaud, Jean Marc
Bruun-Rasmussen, Morten
Bryden, John S.
Bürkle, Thomas
Ceinos, Carmen
Charlet, Jean
Christian, Lovis

Chute, Christopher
Cimino, James
Cinquin, Philippe
Cornet, Ronald
Darmoni, Stefan
David, Ruslan
de Keizer, Nicolette
de Lusignan, Simon
Demichelis, Francesca
Demiris, Thanos
Dudeck, Joachim
Dumitru, Roxana Corina
Effken, Judith
Eich, Hans-Peter
Eils, Roland
Engelmann, Uwe
Frankewitsch, Thomas
Fruman, Amir
García-Rojo, Marcial
Garde, Sebastian
Geissbuhler, Antoine
Gell, Guenther
Gibaud, Bernard
Goetz, Christoph
Goh, Hsien Ming
Grimson, Jane
Grimson, William
Hasman, Arie
Heinzl, Harald
Hildebrand, Claudia

Hippe, Zdzislaw
Hirose, Yasuyuki
Hoelzer, Simon
Horsch, Alexander
Hovenga, Evelyn
Huet, Bernard
Isaacs, Sedick
Jao, Chiang
Jaulent, Marie-Christine
Jávor, András
Jenders, Robert
Joubert, Michel
Juhola, Martti
Jung, Benjamin
Kern, Josipa
Kindler, Hauke
Knaup, Petra
Kokol, Peter
viii
Kondo Oestreicher, Mitsuko
Krauthammer, Michael
Kuma, Hisao
Kverneland, Arne
Kwak, Yun Sik
Laforest, Frederique
Lampe, Kristian
Landais, Paul
Le Beux, Pierre
Le Duff, Franck
Legrand, Louis

Lehmann, Thomas
Lehmann, Christoph
Leiner, Florian
Li, Jack
Liaskos, Joseph
Lippert, Soren
Lorenzi, Nancy
Lungeanu, Diana
Maglaveras, Nicos
Makikawa, Masaaki
Marsh, Andy
Martin-Sanchez, Fernando
Mast, Oliver
Mazzoleni, M.Cristina
Meinzer, Hans-Peter
Mihalas, George
Minato, Kotaro
Moehr, Jochen
Moisil, Ioana
Nishibori, Masahiro
Nordberg, Ragnar
Olivieri, Nora
Oswald, Helmut
Øyri, Karl
Petrovecki, Mladen
Pharow, Peter
Popper, Mikulas
Power, Michael
Punys, Vytenis
Rajkovic, Vladislav

Reichert, Assa
Renard, Jean-Marie
Rigby, Michael
Roberts, Jean
Roger France, Francis
Rossing, Niels
Ruotsalainen, Pekka
Sadan, Batami
Saranummi, Niilo
Sboner, Andrea
Serio, Angelo
Seroussi, Brigitte
Shahsavar, Nosrat
Shifrin, Michael
Simon, Pál
Skiba, Diane
Sousa Pereira, Antonio
Stoicu-Tivadar, Lacramioara
Stroetmann, Karl A.
Surján, György
Suselj, Marjan
Takabayashi, Katsuhiko
Talmon, Jan
Trpisovsky, Tomas
Tschopp, Mathias
van Bemmel, Jan H.
Vellidou, Eleftheria
Vimarlund, Vivian
Vovc, Victor
Wathelet, Bernard

Weber, Patrick
Weltner, János
Yuasa, Tetsuya
Zvárová, Jana
ix
Contents
Preface v
R. Engelbrecht, A. Geissbuhler, C. Lovis and G. Mihalas
Reviewers for MIE2005 vii
Section 1. Bioinformatics and Medical Genomics
Immunogenetics Sequence Annotation: The Strategy of IMGT Based on
IMGT-ONTOLOGY 3
Véronique Giudicelli, Denys Chaume, Joumana Jabado-Michaloud
and Marie-Paule Lefranc
An Integrated Data-Warehouse-Concept for Clinical and Biological Information 9
Dominik Brammen, Christian Katzer, Rainer Röhrig, Katja Weismüller,
Michael Maier, Hamid Hossain, Thilo Menges, Gunter Hempelmann
and Trinad Chakraborty
Time Series Models on Analysing Mortality Rates and Acute Childhood
Lymphoid Leukaemia 15
Maria Kis
Bio-Health Information: A Preliminary Review of On-Line Cystic Fibrosis
Resources 21
Xia Jing, Stephen Kay and Nicholas R. Hardiker
Bioinformatics Meets Clinical Informatics 27
Jeremy Smith and Denis Protti
SITRANS: A Web Information System for Microarray Experiments 33
Frédérique Laforest, Anne Tchounikine, Tarak Chaari, Hubert Charles
and Federica Calevro
Practical Approaches to the Development of Biomedical Informatics: The

INFOBIOMED Network of Excellence 39
Hans-Peter Eich, Guillermo de la Calle, Carlos Diaz, Scott Boyer,
A.S. Peña, Bruno G. Loos, Peter Ghazal and Inge Bernstein
Section 2. Computerized Patient Record
Quality Labelling and Certification of Electronic Health Record Systems 47
Morten Bruun-Rasmussen, Knut Bernstein, Søren Vingtoft, Christian Nøhr
and Stig Kjær Andersen
Computerized Case History – an Effective Tool for Management of Patients
and Clinical Trials 53
Nikita Shklovsky-Kordi, Boris Zingerman, Nikolay Rivkind, Saveli Goldberg,
Scott Davis, Lyuba Varticovski, Marina Krol, A.M. Kremenetzkaia,
Andrei Vorobiev and Ilia Serebriyskiy
Information on Medication History – Basis for Improved Prescribing 59
Martina Zorko and Marjan Sušelj
Users’ Needs and Expectations of Electronic Medical Record Systems in Family
Medicine Residence Settings 65
George Demiris, Karen L. Courtney and Steven E. Waldren
x
Tracking Referents in Electronic Health Records 71
Werner Ceusters and Barry Smith
The French Organ Transplant Data System 77
William Nigel Strang, Philippe Tuppin, Alain Atinault
and Christian Jacquelinet
Avoiding Doubles in Distributed Nominative Medical Databases:
Optimization of the Needleman and Wunsch Algorithm 83
Loïc le Mignot, Claude Mugnier, Mohamed Ben Saïd, Jean-Philippe Jais,
Jean-Baptiste Richard, Christine le Bihan-Benjamin, Pierre Taupin
and Paul Landais
Participatory Work Flow Analysis Prior to Implementation of EPR:
A Method to Discover Needs for Change 89

Pernille Bertelsen, Inge Madsen and Per Hostrup
Use of Computer and Respiratory Inductance Plethysmography for the
Automated Detection of Swallowing in the Elderly 95
Alexandre Moreau-Gaudry, Abdelkebir Sabil, Pierre Baconnier,
Gila Benchetrit and Alain Franco
Representing the Patient’s Therapeutic History in Medical Records and in
Guideline Recommendations for Chronic Diseases Using a Unique Model 101
Vahid Ebrahiminia, Catherine Duclos, Massoud E. Toussi, Christine Riou,
Regis Cohen and Alain Venot
mGen – An Open Source Framework for Generating Clinical Documents 107
Fredrik Lindahl and Olof Torgersson
Comparing Different Approaches to Two-Level Modelling of Electronic
Health Records 113
Line Michelsen, Signe S. Pedersen, Helene B. Tilma and Stig K. Andersen
Introducing the Electronic Health Record in Austria 119
Wolfgang Dorda, Georg Duftschmid, Lukas Gerhold, Walter Gall
and Jürgen Gambal
Medical Record Linkage of Anonymous Registries without Validated Sample
Linkage of the Dutch Perinatal Registries 125
Miranda Tromp, Nora Méray, Anita C.J. Ravelli, Johannes B. Reitsma
and Gouke J. Bonsel
The Core Data Elements of Electronic Health Record in Finland 131
Kristiina Häyrinen and Kaija Saranto
HealthInfoCDA: Case Composition Using Electronic Health Record
Data Sources 137
Grace I. Paterson, Syed Sibte Raza Abidi and Steven D. Soroka
Nursing Documentation in Occupational Health 143
Denise Tolfo Silveira and Heimar de Fátima Marin
Section 3. Decision Support and Clinical Guidelines
Structuring Clinical Guidelines through the Recognition of Deontic

Operators 151
Gersende Georg, Isabelle Colombet and Marie-Christine Jaulent
Prototypical Cases and Adaptation Rules for Diagnosis of Dysmorphic
Syndromes 157
Rainer Schmidt and Tina Waligora
xi
Knowledge Discovery on Functional Disabilities: Clustering Based on Rules
Versus Other Approaches 163
K. Gibert, R. Annicchiarico, U. Cortés and C. Caltagirone
Design of a Multi Dimensional Database for the Archimed DataWarehouse 169
Claudine Bréant, Gérald Thurler, François Borst and Antoine Geissbuhler
Canonical Correlation Analysis for Data Reduction in Data Mining Applied
to Predictive Models for Breast Cancer Recurrence 175
Amir Reza Razavi, Hans Gill, Hans Åhlfeldt and Nosrat Shahsavar
Tools for Statistical Analysis with Missing Data: Application to a Large
Medical Database 181
Cristian Preda, Alain Duhamel, Monique Picavet and Tahar Kechadi
Diagnostic Support for Glaucoma Using Retinal Images: A Hybrid Image
Analysis and Data Mining Approach 187
Jin Yu, Syed Sibte Raza Abidi, Paul Artes, Andy McIntyre
and Malcolm Heywood
SVM Modeling via a Hybrid Genetic Strategy. A Health Care Application 193
Gilles Cohen, Mélanie Hilario, Christian Pellegrini and Antoine Geissbuhler
Improving Pathway Compliance and Clinician Performance by Using
Information Technology 199
R. Blaser, M. Schnabel, O. Heger, E. Opitz, R. Lenz and K.A. Kuhn
Decision Support for Diagnosis of Lyme Disease 205
Ole K. Hejlesen, Kristian G. Olesen, Ram Dessau, Ivan Beltoft
and Michael Trangeled
Towards a Generic Connection of EHR and DSS 211

Helma van der Linden, Sjoerd Diepen, Gerrit Boers, Huibert Tange
and Jan Talmon
Using Blood Glucose Data as an Indicator for Epidemic Disease Outbreaks 217
Eirik Årsand, Ole Anders Walseth, Niklas Andersson, Ruchith Fernando,
Ove Granberg, Johan G. Bellika and Gunnar Hartvigsen
Ontology Driven Construction of a Knowledgebase for Bayesian Decision
Models Based on UMLS 223
Sarmad Sadeghi, Afsaneh Barzi and Jack W. Smith
Estimation of Sex-Age Specific Clinical Reference Ranges by Nonlinear
Optimization Method 229
Takeo Shibata, Yoichi Ogushi, Teppei Ogawa and Takashi Kanno
Comparison Efficiency of the Artificial Intelligence Methods for the
Diagnosis of Acid – Base and Anion Gap Disorders 235
Edward Kacki and Andrzej Małolepszy
Outcome Prediction after Moderate and Severe Head Injury Using an
Artificial Neural Network 241
Min-Huei Hsu, Yu-Chuan Li, Wen-Ta Chiu and Ju-Chuan Yen
Section 4. Educational Technologies and Methodologies
Computer-Based Training in Medicine and Learning Theories 249
Martin Haag, Matthias Bauch, Sebastian Garde, Jörn Heid,
Thorsten Weires and Franz-Josef Leven
Instructional Technology Adoption of Medical Faculty in Teaching 255
Neşe Zayim, Soner Yıldırım and Osman Saka
Postgraduate Studies in Health Informatics in Greece 261
John Mantas
xii
Distance Learning at Biomedical Faculties in Bosnia & Herzegovina 267
Zlatan Masic, Ahmed Novo, Izet Masic, Mensura Kudumovic,
Selim Toromanovic, Admir Rama, Almir Dzananovic, Ilda Bander,
Mirza Basic, Emir Guso and Eldar Balta

Combining Advanced Networked Technology and Pedagogical Methods
to Improve Collaborative Distance Learning 273
Pascal Staccini, Jean-Charles Dufour, Hervé Raps and Marius Fieschi
An Improved Publication Process for the UMVF 279
Jean-Marie Renard, Jean-Marc Brunetaud, Marc Cuggia, Stephan Darmoni,
Pierre Lebeux and Régis Beuscart
A Multimedia Educational System to Teach Epidemiology 284
Marianna Diomidous
Trends in Free WWW-Based E-Learning Modules Seen from the Learning
Resource Server Medicine (LRSMed) 290
Jürgen Stausberg, Martin Geueke and Kevin Bludßat
Testing Repeatability of Forces when Using Neurosurgical Spatulas 296
Lars C. Brix, Claus B. Madsen and Jens Haase
Section 5. Handheld and Wireless Computing
Exploring Electronic Conversion of Behavioral Instruments for Telehealth 305
Karen L. Courtney, George Demiris, Catherine K. Craven,
Debra Parker Oliver and Davina Porock
Pervasive Observation Medicine: The Application of RFID to Improve
Patient Safety in Observation Unit of Hospital Emergency Department 311
Chang-I. Chen, Cheng-Yaw Liu, Yu-Chuan Li, Chia-Cheng Chao,
Chien-Tsai Liu, Chieh-Feng Chen and Ching-Feng Kuan
End-to-End Encryption for SMS Messages in the Health Care Domain 316
Marko Hassinen and Pertti Laitinen
Usability Study on Two Handheld Computers to Retrieve Drug Information 322
Simon Letellier, Klervi Leuraud, Philippe Arnaud and Stefan J. Darmoni
The Digital Pen and Paper Technology: Implementation and Use in an
Existing Clinical Information System 328
Christelle Despont-Gros, Christophe Bœuf, Antoine Geissbuhler
and Christian Lovis
Wireless Transfer of Sensor Data into Electronic Health Records 334

Ole Anders Walseth, Eirik Årsand, Torbjørn Sund and Eva Skipenes
Integration Architecture of a Mobile Virtual Health Record for Shared
Home Care 340
Maria Hägglund, Isabella Scandurra, Dennis Moström and Sabine Koch
Using Mobile Technology to Improve Healthcare Service Quality 352
Chia Chen Chao, Wen Yuan Jen, Yu-Chuan Li, Y.P. Chi, Chang-I. Chen
and Chen Chjeh Feng
Section 6. Healthcare Networks
Developing Online Communities with LAMP (Linux, Apache, MySQL, PHP) –
the IMIA OSNI and CHIRAD Experiences 361
Peter J. Murray and Karl Øyri
xiii
Preparing the Electronic Patient Record for Collaborative Environments
and eHealth 367
Petra Knaup, Sebastian Garde and Reinhold Haux
Understanding Telecardiology Success and Pitfalls by a Systematic Review 373
Stefano Bonacina, Lorenza Draghi, Marco Masseroli and Francesco Pinciroli
Architecture Evaluation for the Implementation of a Regional Integrated
Electronic Health Record 379
Daniel Ferreira Polónia, Carlos Costa and José Luis Oliveira
Semantic Integration in Healthcare Networks 385
Richard Lenz, Mario Beyer and Klaus A. Kuhn
A Model-Driven Approach for the German Health Telematics Architectural
Framework and the Related Security Infrastructure 391
Bernd Blobel and Peter Pharow
Development of Secured Medical Network with TCP2 for Telemedicine 397
Kumiko Ohashi, Yuichiro Gomi, Hiroki Nogawa, Hiroshi Mizushima
and Hiroshi Tanaka
Security Infrastructure Requirements for Electronic Health Cards
Communication 403

Peter Pharow and Bernd Blobel
Security Services for the HemaCAM Project 409
Kjeld Engel, Heiko Kuziela, Bernd Blobel and Peter Pharow
Purposes of Health Identification Cards in Belgium 415
Francis H. Roger France, Etienne de Clercq and Marc Bangels
The Baltic Health Network – Taking Secure, Internet-Based Healthcare
Networks to the Next Level 421
Henning Voss, Vigdis Heimly and Lotta Holm Sjögren
The Israeli Virtual National Health Record: A Robust National Health
Information Infrastructure Based on a Firm Foundation of Trust 427
Esther Saiag
Section 7. Imaging Informatics
Myocardium Tissue Analysis Based on Textures in Ultrasound Images 435
Vytenis Punys, Jurate Puniene, Renaldas Jurkevicius and Jonas Punys
Automatic Measurement of Skin Wheals Provoked by Skin Prick Tests 441
Michael Prinz, Kornelia Vigl and Stefan Wöhrl
Computed Quality Assessment of MPEG4-Compressed DICOM Video Data 447
Thomas Frankewitsch, Sven Söhnlein, Marcel Müller
and Hans-Ulrich Prokosch
Lung CT Analysis and Retrieval as a Diagnostic Aid 453
Henning Müller, Samuel Marquis, Gilles Cohen, Christian Lovis
and Antoine Geissbuhler
A Generic Concept for the Implementation of Medical Image Retrieval
Systems 459
Mark O. Güld, Christian Thies, Benedikt Fischer and Thomas M. Lehmann
Complexity Analysis of the Visual-Motor Cross-Modalities Using the
Correlation Dimension Parameter 465
Monica C. Serban and Dan M. Dobrea
Neural Network Screening of Electromyographic Signals as the First Phase
to Design Novel Human-Computer Interaction 471

Pekka-Henrik Niemenlehto, Martti Juhola and Veikko Surakka
xiv
Object-Oriented Implementation for the Dual Surface Minimisation
Algorithm 477
Jouni Mykkänen, Mikko Itäranta and Jussi Tohka
Analyzing Sub-Classifications of Glaucoma via SOM Based Clustering of
Optic Nerve Images 483
Sanjun Yan, Syed Sibte Raza Abidi and Paul Habib Artes
Section 8. Implementation & Evaluation of Clinical Systems
3LGM²-Modelling to Support Management of Health Information Systems 491
Alfred Winter, Birgit Brigl, Gert Funkat, Anke Häber, Oliver Heller
and Thomas Wendt
Specification of a Reference Model for the Domain Layer of a Hospital
Information System 497
Gudrun Hübner-Bloder, Elske Ammenwerth, Birgit Brigl and Alfred Winter
Analysis and Specification of Telemedical Systems Using Modelling and
Simulation: the MOSAIK-M Approach 503
O.J. Bott, J. Bergmann, I. Hoffmann, T. Vering, E.J. Gomez, M.E. Hernando,
and D.P. Pretschner
Realizing a Realtime Shared Patient Chart Using a Universal Message
Forwarding Architecture 509
Achim Michel-Backofen, Robert Demming, Rainer Röhrig, Matthias Benson,
Kurt Marquardt and Gunter Hempelmann
Designing Web Services in Health Information Systems: From Process to
Application Level 515
Juha Mykkänen, Annamari Riekkinen, Pertti Laitinen, Harri Karhunen,
and Marko Sormunen
MedFlow – Improving Modelling and Assessment of Clinical Processes 521
Samrend Saboor, Elske Ammenwerth, Manfred Wurz
and Joanna Chimiak-Opoka

SOMWeb – Towards an Infrastructure for Knowledge Sharing in Oral
Medicine 527
Göran Falkman, Olof Torgersson, Mats Jontell and Marie Gustafsson
Measuring the Impact of Online Evidence Retrieval Systems Using Critical
Incidents & Journey Mapping 533
Johanna I. Westbrook, Enrico W. Coiera and Jeffrey Braithwaite
Design and Implementation of an ICU Incident Registry 539
Sabine van der Veer, Ronald Cornet and Evert de Jonge
Applicability of Textual Clinical Practice Guidelines: Impact of Physician
Interpretation 545
Jean-Charles Dufour, Roch Giorgi, Jean-Robert Harlé, Dominique Fieschi,
Françoise Volot and Marius Fieschi
Semantic Challenges in Database Federation: Lessons Learned 551
Thomas Ganslandt, Udo Kunzmann, Katharina Diesch, Péter Pálffy
and Hans-Ulrich Prokosch
MobiDis: Toward a Patient Centric Healthcare Information System 557
Fabrizio L. Ricci and Luca D. Serbanati
Obstacles to Implementing an Execution Engine for Clinical Guidelines
Formalized in GLIF 563
Petr Kolesa, Josef Špidlen and Jana Zvárová
xv
Implementing a New ADT Based on the HL-7 Version 3 RIM 569
Stéphane Spahni, Christian Lovis, Richard Mercille, Hervé Verdel,
Michel Cotten and Antoine Geissbühler
Design and Development of a Monitoring System to Assess the Quality
of Hospital Information Systems: Concept and Structure 575
Frauke Ehlers, Elske Ammenwerth and Bernhard Hirsch
Trends in Evaluation Research 1982–2002: A Study on how the Quality
of IT Evaluation Studies Develop 581
Nicolette de Keizer and Elske Ammenwerth

Interfacing Clinical Practice and Error Prevention 587
Carola Hullin, Sioban Nelson, John Dalrymple and Graeme Hart
Using Feedback to Raise the Quality of Primary Care Computer Data:
A Literature Review 593
Simon de Lusignan
Usability Evaluation of a Laboratory Order Entry System: Cognitive
Walkthrough and Think Aloud Combined 599
Linda W.P. Peute and Monique M.W. Jaspers
Operation Management System Evaluation in the Central Finland Health
Care District – End Users’ View of System Implementation 605
Kaisa Lemmetty and Eija Häyrinen
Comparisons of Physicians’ and Nurses’ Attitudes towards Computers 608
Gordana Brumini, Ivor Ković, Dejvid Zombori, Ileana Lulić,
Lidija-Bilic-Zulle and Mladen Petrovečki
Section 9. Terminologies, Ontologies, Standards and Knowledge Engineering
Nursing Outcome Documentation in Nursing Notes of Cardiac-Surgery
Patients 617
Yun Jeong Kim and Hyeoun-Ae Park
ICPCview: Visualizing the International Classification of Primary Care 623
Pierre P. Lévy, Laetitia Duché, Laszlo Darago, Yves Dorléans,
Laurent Toubiana, Jean-François Vibert and Antoine Flahault
Common Nursing Terminology for Clinical Information Systems 629
Yardena Kol, Patricia Zimmerman and Zipora Sadeh
An Ontology for Carcinoma Classification for Clinical Bioinformatics 635
Anand Kumar, Yum Lina Yip, Barry Smith, Dirk Marwede
and Daniel Novotny
Integration of Multiple Ontologies in Breast Cancer Pathology 641
David Ouagne, Christel le Bozec, Eric Zapletal, Maxime Thieu
and Marie-Christine Jaulent
Wüsteria 647

Barry Smith, Werner Ceusters and Rita Temmerman
Desiderata for Representing Anatomical Knowledge 653
Robert H. Baud, Christian Lovis, Paul Fabry and Antoine Geissbuhler
Building Medical Ontologies Based on Terminology Extraction from Texts:
An Experimentation in Pneumology 659
Audrey Baneyx, Jean Charlet and Marie-Christine Jaulent
Towards a Multilingual Version of Terminologia Anatomica 665
Paul Fabry, Robert Baud and Christian Lovis
xvi
Toward a Unified Representation of Findings in Clinical Radiology 671
Valérie Bertaud, Jérémy Lasbleiz, Fleur Mougin, Franck Marin,
Anita Burgun and Régis Duvauferrier
Advanced Information Retrieval Using XML Standards 677
Ralf Schweiger, Simon Hölzer and Joachim Dudeck
Refinement of an Automatic Method for Indexing Medical Literature –
A Preliminary Study 683
Michel Joubert, Anne-Laure Peretti, Joanny Gouvernet and Marius Fieschi
Making Two-Level Standards Work in Legacy Communication Frameworks 689
Istvan Vassanyi, Jozsef Barcza and Tamas Tobak
Issues in the Classification of Disease Instances with Ontologies 695
Anita Burgun, Olivier Bodenreider and Christian Jacquelinet
Terminological System Maintenance: A Procedures Framework and an
Exploration of Current Practice 701
Ferishta Raiez, Danielle Arts and Ronald Cornet
GALEN Based Formal Representation of ICD10 707
Gergely Héja, György Surján, Gergely Lukácsy, Péter Pallinger
and Miklós Gergely
SIGNe: A Geographic Information System on the Web for End-Stage
Renal Disease 713
Jean-Baptiste Richard, Laurent Toubiana, Loïc le Mignot,

Mohamed Ben Said, Claude Mugnier, Christine le Bihan–Benjamin,
Jean Philippe Jaïs and Paul Landais
Which Graphical Approaches should be Used to Represent Medical
Knowledge? 719
Jean-Baptiste Lamy, Catherine Duclos, Vincent Rialle and Alain Venot
mVisualizer: Easily Accessible Data Exploration for Clinicians 725
Nils Erichson and Olof Torgersson
A Knowledge Management Framework to Morph Clinical Cases with
Clinical Practice Guidelines 731
Fehmida Hussain and Syed Sibte Raza Abidi
The Significance of SNODENT 737
Louis J. Goldberg, Werner Ceusters, John Eisner and Barry Smith
Representing Clinical Knowledge in Oral Medicine Using Ontologies 743
Marie Gustafsson and Göran Falkman
The Epistemological-Ontological Divide in Clinical Radiology 749
Dirk Marwede and Matthew Fielding
Representation of Medical Informatics in the Wikipedia and Its Perspectives 755
Udo Altmann
Does HL7 Go towards an Architecture Standard? 761
Frank Oemig and Bernd Blobel
Integrating the Modelling of EN 1828 and Galen CCAM Ontologies with
Protégé: Towards a Knowledge Acquisition Tool for Surgical Procedures 767
J.M. Rodrigues, B. Trombert Paviot, C. Martin and P. Vercherin
Semantic Clarification of the Representation of Procedures and Diseases
in SNOMED
®
CT 773
Stefan Schulz, Udo Hahn and Jeremy Rogers
Method of GLIF Model Construction and Implementation 779
D. Buchtela, J. Peleska, A. Vesely and J. Zvarova

xvii
Section 10. Natural Language, Text Mining and Information Retrieval
Grepator: Accents & Case Mix for Thesaurus 787
Vincent Mary and Pierre le Beux
Predicting Lexical Relations between Biomedical Terms: Towards a
Multilingual Morphosemantics-Based System 793
Fiammetta Namer and Robert Baud
Simplified Representation of Concepts and Relations on Screen 799
Hans Rudolf Straub, Norbert Frei, Hugo Mosimann, Csaba Perger
and Annette Ulrich
Indexing UMLS Semantic Types for Medical Question-Answering 805
Thierry Delbecque, Pierre Jacquemart and Pierre Zweigenbaum
Breaking the Language Barrier: Machine Assisted Diagnosis Using
the Medical Speech Translator 811
Marianne Starlander, Pierrette Bouillon, Manny Rayner,
Nikos Chatzichrisafis, Beth Ann Hockey, Hitoshi Isahara,
Kyoko Kanzaki, Yukie Nakao and Marianne Santaholma
Automatic Annotation of Medical Records 817
Ján Antolík
Evaluation of Medical Problem Extraction from Electronic Clinical
Documents Using MetaMap Transfer (MMTx) 823
Stéphane Meystre and Peter J. Haug
Automatic Lexicon Acquisition for a Medical Cross-Language Information
Retrieval System 829
Kornél Markó, Stefan Schulz and Udo Hahn
Extracting Key Sentences with Latent Argumentative Structuring 835
Patrick Ruch, Robert Baud, Christine Chichester, Antoine Geissbühler,
Frédérique Lisacek, Johann Marty, Dietrich Rebholz-Schuhmann,
Imad Tbahriti and Anne-Lise Veuthey
Section 11. Online Health Information & Patient Empowerment

Physicians’ Use of Clinical Information Systems in the Discharge Process:
An Observational Study 843
Inger Dybdahl Sørby, Øystein Nytrø, Amund Tveit and Eivind Vedvik
Cost-Effective Ambulatory Monitoring 849
Pantelis Angelidis and Markela Psymarnou
Health Information Systems Evaluation: A Focus on Clinical Decision
Supports System 855
Maryati Mohd Yusof, Ray J. Paul and Lampros Stergioulas
User Acceptance of and Satisfaction with a Personal Electronic Health Record 861
A. Ertmer and F. Ückert
Experimenting with Case-Based Reasoning to Present Educative Health
Information on the Internet: The Example of SeniorGezond 867
Nicole P.M. Ezendam, Laurence L. Alpay, Ton A.J.M. Rövekamp
and Pieter J. Toussaint
Log Analysis of a Turkish Web Portal; Febrile Neutropenia 873
Kemal Hakan Gülkesen, Hamdi Akan, Murat Akova and Tamer Çalıkoğlu
Collaborative Approaches to e-Health: Valuable for Users and Non-Users 879
Charles Safran, Grace Pompilio-Weitzner, Kathryn D. Emery
and Lou Hampers
xviii
Health Information on the Internet: Evaluating Greek Health Portals
and Depicting Users’ Attitudes in West Macedonia, Greece 885
Panagiotis Bamidis, Fotis Kerassidis and Kostas Pappas
A Decade Devoted to Improving Online Health Information Quality 891
Celia Boyer and Antoine Geissbuhler
Construction of an Instrument for Measuring Medical Student Satisfaction
with Virtual Campus 897
Ziad EL Balaa, Henri-Jean Philippe, Christelle Volteau, Pierre le Beux
and Jean-Michel Nguyen
Section 12. Organization Change, Information Needs

The Data-Gathering Broker – A User-Based Approach to Viable EPR
Systems 905
Michael Rigby, David Budgen, Pearl Brereton, Keith Bennett,
Michelle Russell, Mark Turner, Ioannis Kotsiopoulos, Paul Layzell,
John Keane and Fujun Zhu
Towards Patient-Related Information Needs 911
Loes Braun, Floris Wiesman, Jaap van den Herik, Arie Hasman
and Erik Korsten
Establishing a Regional Contact & Service Centre for Public Health Care:
The Case in Central Macedonia, Greece 917
Dimitrios Vartzopoulos, Stergiani Spyrou, Eirini Minaoglou,
Viktoria Karolidou and Panagiotis D. Bamidis
Integration of the Cognitive Knowledge of Activity in a Service Oriented
Architecture in the Home Care Context 923
N. Bricon-Souf, E. Dufresne and L. Watbled
Cognitive Analysis of Physicians’ Medication Ordering Activity 929
Sylvia Pelayo, Nicolas Leroy, Sandra Guerlinger, Patrice Degoulet,
Jean-Jacques Meaux and Marie-Catherine Beuscart-Zéphir
The MammoGrid Virtual Organisation – Federating Distributed
Mammograms 935
Florida Estrella, Richard McClatchey and Dmitry Rogulin
Ontological Definition of Population for Public Health Databases 941
György Surján
Section 13. Public Health Informatics, Clinical Trials
Proposal for the Creation of a European Healthcare Identifier 949
Catherine Quantin, François-André Allaert, Béatrice Gouyon
and Olivier Cohen
Linking Primary Care Information Systems and Public Health Information
Networks: Lessons from the Philippines 955
Herman Tolentino, Alvin Marcelo, Portia Marcelo and Inocencio Maramba

An eConsent-Based System Architecture Supporting Cooperation in
Integrated Healthcare Networks 961
Joachim Bergmann, Oliver J. Bott, Ina Hoffmann and Dietrich P. Pretschner
The ISO/IEC 9126-1 as a Supporting Means for the System Development
Process of a Patient Information Web Service 967
Alexander Hörbst, Kerstin Fink and Georg Goebel
xix
Can openEHR Archetypes Empower Multi-Centre Clinical Research? 971
Sebastian Garde, Petra Knaup, Thilo Schuler and Evelyn Hovenga
Brazilian National Standard for Electronic Form Interchange among
Private Health Plan and Healthcare Providers 977
Jussara Macedo Pinho Rửtzsch, Rigoleta Dutra Mediano Dias,
Marcia Franke Piovesan, Maria Angela Scatena,
Josộ Leụncio de Andrade Feitosa, Josộ Ricardo Fragoso Peret Antunes,
and Ceres Albuquerque
Distributed and Mobile Collaboration for Real Time Epidemiological
Surveillance During Forces Deployments 983
Hervộ Chaudet, Jean-Baptiste Meynard, Gaởtan Texier, Olivier Tournebize,
Liliane Pellegrin, Benjamin Queyriaux and Jean-Paul Boutin
MetaSurv: Web-Platform Generator for the Monitoring of Health
Indicators and Interactive Geographical Information System 989
Laurent Toubiana, Stộphane Moreau and Gaộtan Bonnard
A Multi-Source Information System via the Internet for End-Stage Renal
Disease: Scalability and Data Quality 994
Mohamed Ben Saùd, Loic le Mignot, Claude Mugnier, Jean Baptiste Richard,
Christine le Bihan-Benjamin, Jean-Philippe Jais, Didier Guillon, Ana Simonet,
Michel Simonet and Paul Landais
The Necessity of an Electronic SOP Retrieval System 1000
Katja Krockenberger, Petra Knaup, Kornelia Bez and Christoph H. Gleiter
Investigating the Effect of Differences in Entry Criteria on Trial

Populations: A Method with an Application in Severe Sepsis 1004
Linda Peelen, Niels Peek, Nicolette de Keizer and Evert de Jonge
Ensuring the Quality of Aggregated General Practice Data: Lessons from
the Primary Care Data Quality Programme (PCDQ) 1010
Jeremy van Vlymen, Simon de Lusignan, Nigel Hague, Tom Chan
and Billy Dzregah
Central IT-Structures for Integrated Medical Research and Health Care
of Viral Hepatitis Hep-Net 1016
Thomas H. Mỹller
Real Association of Factors with Inappropriate Hospital Days 1021
Bernard Huet and Maxime Cauterman
Author Index 1027
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Section 1
Bioinformatics and Medical Genomics
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Immunogenetics Sequence Annotation: the
Strategy of IMGT based on
IMGT-ONTOLOGY
Véronique Giudicelli
a
, Denys Chaume
a
, Joumana Jabado-Michaloud
a
, Marie-Paule
Lefranc
a, b
a
Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Université Montpellier II, Institut de Génétique

Humaine, Montpellier, France
b
Institut Universitaire de France, 103 Boulevard Saint Michel, 75005 Paris, France
Abstract
IMGT, the international ImMunoGeneTics information system
£
()
created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM),
Université Montpellier II and CNRS, Montpellier, France, is a high quality integrated
information system, specialized in immunoglobulins (IG), T cell receptors (TR),
major histocompatibility complex of human and other vertebrates and related
proteins of the immune system that belong to the IgSF and Mhc superfamilies.
IMGT/LIGM-DB, the first and the largest IMGT database, manages more than
92,000 IG and TR nucleotide sequences from human and 150 other vertebrate species
in May 2005. IMGT/LIGM-DB provides expertly annotated sequences and
standardized knowledge based on IMGT-ONTOLOGY, the first ontology for
immunogenetics and immunoinformatics. The strategy developed by IMGT, for the IG
and TR nucleotide sequence annotation, involves two different approaches that
depend on the nature of the sequences, genomic DNA (gDNA) or complementary
DNA (cDNA).
Keywords:
Immunogenetics; IMGT; Immunoinformatics; Sequence annotation; Database; Immunoglobulin; T cell
receptor; Antibody
1. Introduction
IMGT, the international ImMunoGeneTics information system£ () [1],
created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM), at the
Université Montpellier II and CNRS, Montpellier, France, is a high quality integrated
information system, specialized in immunoglobulins (IG), T cell receptors (TR), major
histocompatibility complex of human and other vertebrates and related proteins of the
immune system that belong to the IgSF and MhcSF superfamilies. IMGT® is the

international reference in immunogenetics and immunoinformatics and consists of several
sequence, genome and structure databases, of Web resources and of interactive tools [2].
IMGT/LIGM-DB is the first and the largest IMGT database in which are managed, analysed
and annotated more than 92,000 IG and TR nucleotide sequences (in May 2005) from human
and 150 other vertebrate species. The expert annotation of these sequences and the added
standardized knowledge are based on IMGT-ONTOLOGY [3], the first ontology developed
Connecting Medical Informatics and Bio-Informatics
R. Engelbrecht et al. (Eds.)
IOS Press, 2005
© 2005 EFMI – European Federation for Medical Informatics. All rights reserved.
3
in the field of immunogenetics and immunoinformatics. IMGT genome annotation has
allowed the IG and TR genes to be entered in the genome database, LocusLink and Entrez
Gene at NCBI [4,5]. This has been a crucial IMGT contribution as these genes were not
identified in the large sequencing project, owing to their unusual structure (non classical
exon/intron structure). In contrast to other loci, where genome annotation means gene
identification usually obtained with automatic procedures, genome annotation of IG and TR
loci can only be performed manually by experts. The IMGT strategy for the sequence
annotation takes into account the complexity of the IG and TR synthesis and genetics [4, 5]
and the need of an automatic procedure due to the acceleration of the sequencing rate of
expressed repertoires.
This strategy involves two different approaches that depend on the nature of the sequences,
genomic DNA (gDNA) or complementary DNA (cDNA): (i) the annotation of gDNA
(germline or rearranged sequences) includes the search of specific IG and TR motifs and
requires a high quality manual curation, by an expert, for the characterization and the
classification of new genes in large sequences. The gene and allele related knowledge, based
on the IMGT-ONTOLOGY CLASSIFICATION concept, is managed, for the human and
mouse, in IMGT/GENE-DB [6], the IMGT gene database, and for the other vertebrates, in
IMGT Repertoire, the IMGT Web resources [7]; (ii) the annotation of cDNA (rearranged
sequences), despite the complexity of the IG and TR synthesis, has been automatised. This

has been possible as the necessary rules for the automatic annotation include the
identification of the sequences, the description of the constitutive motifs and the codon and
amino acid numbering. These rules, described in the IMGT Scientific chart, correspond to the
IMGT-ONTOLOGY IDENTIFICATION, DESCRIPTION and NUMEROTATION
concepts [3], respectively. They have been encoded in IMGT/Automat [8], a Java program
developed by IMGT, which automatically annotates the IG and TR cDNA sequences.
IMGT/Automat implements the IMGT/V-QUEST tool [9] for the gene and allele
identification and classification, and the amino acid numbering, and the
IMGT/JunctionAnalysis tool [10] for the detailed analysis of the V-J or V-D-J junction. More
than 9,000 human and mouse cDNA have already been successfully automatically annotated.
The two different approaches of the IMGT sequence annotation strategy for gDNA and
cDNA, respectively, guarantee, by their complementarity, the validity, the accuracy and the
coherence of the annotations of the nucleotide sequences in IMGT/LIGM-DB. Annotation
accuracy and reliability are the determining factors for the exploitation of the immunogenetic
sequences in sectors as exacting as fundamental research, therapeutical approaches and
medical research, veterinary research and antibody engineering.
2. Material and methods
IMGT/LIGM-DB entries
IMGT/LIGM-DB manages all IG and TR sequences published in the generalist
EMBL/DDBJ/GenBank [11-13]. These sequences mostly belong to the ‘HUM’, ‘MUS’,
‘ROD’, ‘MAM’ and ‘VRT’ divisions. IG and TR sequences include germline (not
rearranged) gDNA sequences, rearranged gDNA sequences that result from V-J or V-D-J
gene recombination in B or T cells, and rearranged cDNA sequences. A prototype of the
molecular organization of the 3 types of IG or TR sequences, with the main IMGT feature
labels, is shown in Figure 1 [4, 5].
Annotation of the gDNA sequences
The annotation of the gDNA sequences consists in the localization of genes, the prediction of
exons, the determination of regulation signals such as promoters and splicing sites, and the
similarity evaluation with other known genes. The programs that usually accomplish these
tasks,

V. Giudicelli et al. / Immunogenetics Sequence Annotation: The Strategy of IMGT4
Figure 1-Prototypes of IG or TR germline genomic DNA (gDNA), rearranged gDNA and
cDNA [4,5]. The IMGT labels (in capital letters) are according to the DESCRIPTION
concept of IMGT-ONTOLOGY [3]. Messenger RNA (mRNA) and cDNA have the same
structure and share the same labels. Note that sequences qualified as mRNA in the databases
are actually cDNA.
are inefficient to find IG and TR genes owing to the particular structure of these genes: as an
example, Figure 1 shows that the second exon of a variable gene in germline configuration
(V-GENE) does not end with a stop codon in 3’, but instead ends with a characteristic IG or
TR recombination signal which is involved in the V-J or V-D-J DNA rearrangement. The
diversity genes (D-GENE) and junction genes (J-GENE) do not begin with an initiation
codon in 5’ [4, 5]. Moreover their coding regions are very short (less than 20 amino acids)
and the classical tools are not able to predict them correctly. IMGT has therefore developed a
program to search for specific IG and TR motifs, LIGMotif, based on the recognition of the
recombination signals, splicing sites and the IMGT standardized numbering of the codons
which allows, in particular, to localize the conserved amino acids (Figure 1). IMGT has
defined a reference sequence for each gene and allele. The sets of these reference sequences
constitute the IMGT reference directory. The coding regions of the new identified genes are
then compared, by BLAST, FASTA and IMGT/V-QUEST, to the sequences of the IMGT
reference directory. The manual curation by an expert is essential and crucial for the gene
identification and classification, the characterization of its alleles, the definition of its
structure and of its functionality. These annotations are based on the IMGT-ONTOLOGY
concepts [3] and on the rules of the IMGT Scientific chart [2, 7].
Annotation of the cDNA sequences
The cDNA represent more than one half of IMGT/LIGM-DB and most of these sequences
are from human and mouse. The IG and TR genomic loci of these species have been studied
in IMGT extensively, and all known genes and alleles from human and mouse [4-6] have
been characterized. The corresponding coding sequences are in the IMGT reference directory
[2]. Since the human and mouse cDNA sequences result from the rearrangement of known
IMGT genes and alleles, these sequences can successfully be analysed by the IMGT

sequence analysis tools, and then automatically annotated by IMGT/Automat [8].
V. Giudicelli et al. / Immunogenetics Sequence Annotation: The Strategy of IMGT 5