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About the Contributors
Violaine Prince is full professor at the University Montpellier 2 (Montpellier, France). She obtained her PhD in 1986 at the University of Paris VII, and her ‘habilitation’ (post-PhD degree) at the Univer- sity of Paris XI (Orsay). Previous head of Computer Science department at the Faculty of Sciences in Montpellier, previous head of the National University Council for Computer Science (grouping 3,000 professors and assistant professors in Computer Science in France), she now leads the NLP research team at LIRMM (Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, a CNRS research unit). Her research interests are in natural language processing (NLP) and cognitive science. She has published more than 70 reviewed papers in books, journals and conferences, authored 10 research and education books, founded and chaired several conferences and belonged to program committees as well as journals reading committees. She is member of the board of the IEEE Computer Society French Chapter.
Mathieu Roche is assistant professor at the University Montpellier 2, France. He received a PhD in computer science at the University Paris XI (Orsay) in 2004. With Jérôme Azé, he created in 2005 the DEFT challenge (‘DEfi Francophone de Fouille de Textes’ meaning ‘Text Mining Challenge’) which is a francophone equivalent of the TREC Conferences. His current main research interests at LIRMM (Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, a CNRS research unit) are text mining, information retrieval, terminology, and natural language processing for schema mapping.
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Sophia Ananiadou is director of The National Centre for Text Mining (NaCTeM)providing text mining services with particular focus on biomedicine. She is also reader in text mining in the School of Computer Science University of Manchester. She has authored over 150 publications in journals and conferences including the first edited book on text mining for biomedicine. She has received twice the IBM UIMA innovation award for her work on interoperability of text mining tools and the DAIWA award for her research in biotext mining.
Frederic Andres has been an associate professor at National Institute of Informatics (NII) since 2000 and at The Graduate University for Advanced Studies since 2002. He received is his PhD from University of PARIS VI and his Doctor Habilitate (specialization: information engine) from University of Nantes, in 1993 and 2000 respectively. He was scientist at Bull (France) from 1989 to 1993, informa-
Copyright © 2009, IGI Global, distributing in print or electronic forms without written permission of IGI Global is prohibited. About the Contributors
tion system architect at Ifatec/Euriware (France) between 1996 and 2000. He is project leader of the Geomedia project and Myscoper project in the Digital Content and Media Sciences Research Division. Research interests include, but are not limited to, distributed semantic information management sys- tems for Geomedia and multimedia applications. He has been serving at The World Organization for Digital Equality (WODE), as general secretary since January 2006. He is member of IEEE, ACM, and of many other societies.
Rolf Apweiler studied biology in Heidelberg and Bath. He worked three years in drug discovery in the pharmaceutical industry and is involved in bioinformatics since 1987. Apweiler started his bioinfor- matics career working on Swiss-Prot at EMBL in Heidelberg, moved in 1994 to the EMBL Outstation EBI in Hinxton, UK, and is now Joint Head of the Protein and Nucleotide Data (PANDA) Group at EBI (http://www.ebi.ac.uk/panda/). This group coordinates the UniProt activities, InterPro, GOA, Reactome, PRIDE, IntAct, Ensembl, EMBL nucleotide sequence database, and some other projects at the EBI.
Pooyan Asari graduated in software engineering from Tehran Azad University in 2005 and comple- ted a Masters of Information Technology from Macquarie University in 2007. He is currently studying for a PhD at the University of Sydney in the field of natural language processing applied to clinical settings. Since 1999, he has been involved in the IT industry as a software engineer and system deve- loper in different industrial and commercial projects in Iran and Australia. His professional experience includes working with MIS design and implementation, embedded system development and portable transaction solutions.
Evelyn Camon, PhD, studied cellular and molecular immunology at the Institute for Animal Health (Berkshire, UK) in collaboration with University College Dublin (UCD) (Ireland). In 1998 she joined the EBI as an EMBL-Bank Scientific Curator responsible for assessment and preparation of nucleotide sequence and alignment data for inclusion in EMBL-Bank and EMBL-align databases. In October 2000 she took on a more senior role as the EBIs first Gene Ontology Annotation Project Co-ordinator project, a post funded by the NIH. Essentially this role involved training a team of curators to extract biological knowledge from the scientific literature in a standardized way (using Gene Ontology) and ensuring this data was linked to the relevant UniProtKB proteins and regularly disseminated. Camon has also been involved in evaluating data submitted to text mining competitions (BioCreative) and in reviewing bioinformatic articles. Furthermore in collaboration with EBI, MGI and UCL she has been involved in a new proposal to improve the annotation and ontology content for immunology and the immune system (http://www.geneontology.org/GO.immunology.shtml). She is currently affiliated with UCD, School of Biological Sciences.
Vincent Claveau is a researcher for the French National Center for Scientific Research (CNRS). His research area includes natural language processing, machine learning and multimedia information retrieval. Vincent Claveau was first trained as an engineer. He obtained his PhD in computer science from University of Rennes 1, France, in 2003. During his doctoral thesis he developed methods of symbolic machine learning applied to lexical information extraction. After obtaining his PhD degree, he held a post-doctoral position in the Observatoire de linguistique Sens-Texte (OLST) research group of the University of Montreal, QC, Canada, where he worked in the linguistic and terminological fields.
415 About the Contributors
Besides his research activities, Vincent Claveau also teaches graduate students natural language pro- cessing and machine learning.
Francisco M. Couto has a Master (2001) in informatics and computer engineering from the Insti- tuto Superior Técnico. He obtained a PhD (2006) in Informatics, specialization Bioinformatics, from the Universidade de Lisboa. He is currently an assistant professor with the Informatics Department at Faculdade de Ciências da Universidade de Lisboa. He teaches courses in Information Systems and coordinates the Master in Biomedical Informatics. He is currently a member of the LASIGE research group, co-coordinating the Biomedical Informatics research line.
Manuel C. Díaz-Galiano is assistant professor in the Department of Computer Science at Jaén University (Spain). He received MS degree in computer science from the University of Granada. His current main research interest is intelligent search, including search engines, search assistants, natural language processing tools for text mining and retrieval and human computer interaction. Relevant topics include multilingual-multimodal information access, ontologies (wordnets, MeSH, UMLS), Web search engines. Mr. Díaz is member of the Research Group of Intelligent Systems of Information Access in the University of Jaén and member of SEPLN. He has participated in several research projects and several contracts with companies in technology transfer.
Emily Dimmer, PhD, studied plant genetics (University of Cambridge). In 2003, she joined the EBI as a scientific database curator. She is presently the coordinator of the GOA group at the EBI (http:// www.ebi.ac.uk
Laura Dioşan currently works as PhD student in the Computer Science Department ofBabes-Bolyai University, Cluj-Napoca, Romania and in Laboratoire d’Informatique, de Traitement de l’Information et des Systèmes, Institut National des Sciences Appliquées, Rouen, France. Her main research area is in Evolutionary Computation. Laura Dioşan is authored/co-authored of several papers in peer reviewed international journals and proceedings of the international conferences. She proposed some evolutionary techniques for optimization of algorithm’s architecture, a genetic programming technique for solving symbolic regression and classification problems, an evolutionary framework for evolving kernel func- tions for support vector machines. She is member of the IEEE (CS), IEEE (NN) and ACM.
Anastasios D. Doulamis received the Diploma degree in electrical and computer engineering from the National Technical University of Athens (NTUA) in 1995 with the highest honor. In 2000, he has received the PhD degree in electrical and computer engineering from the NTUA. From 1996-2000, he was with the Image, Video and Multimedia Lab of the NTUA as research assistant. In 2002, he join the NTUA as senior researcher. He is now assistant professor at the Technical University of Crete. His PhD thesis was supported by the Bodosakis Foundation Scholarship. Dr. Doulamis has received several awards and prizes during his studies, including the Best Greek Student in the field of engineering in national level in 1995, the Best Graduate Thesis Award in the area of electrical engineering with A.
416 About the Contributors
Doulamis in 1996 and several prizes from the National Technical University of Athens, the National Scholarship Foundation and the Technical Chamber of Greece. In 1997, he was given the NTUA Medal as Best Young Engineer. In 2000, he received the best PhD thesis award by the Thomaidion Foundation in conjunction with N. Doulamis. He has also served as program committee in several international conferences and workshops, like EUSIPCO, ICPR. He is author of more than 100 papers in the above areas, in leading international journals and conferences.
Nikolaos D. Doulamis received a Diploma in Electrical and Computer Engineering from the National Technical University of Athens (NTUA) in 1995 with the highest honor and the PhD degree from the same department in 2000. His PhD thesis was supported by the Bodosakis Foundation. Since 2002, he is a senior researcher at NTUA and at the Research Academic Computer Technology Institute. Dr. Doulamis received the Best Greek Student award in the field of engineering at national level by the Technical chamber of Greece in 1995. He is a recipient of the Best Graduate Thesis Award in the area of electrical engineering, with A. Doulamis, and of NTUA‘s Best Young Engineer Medal. He has served as Chairman or member of the program committee of several international conferences. He is author of more than 30 journals papers in the field of video transmission, content-based image retrieval, and grid computing, and of more than 120 conference papers. Among them 14 journals papers have been published in the IEEE transactions.
Laura Inés Furlong received her PhD in biological sciences from the University of Buenos Aires, Argentina in 2002, and the MSc in bioinformatics for Health from the University Pompeu Fabra (UPF) and University of Barcelona, Spain in 2007. She is a post-doctoral researcher at the Research Unit on Biomedical Informatics (GRIB) of UPF and IMIM-Hospital del Mar, Spain, and assistant professor at the UPF. She has several publications in the field of molecular biology of human fertilization, and in biomedical text mining. Her current research focus is on the development of text mining applications for the study of genotype–phenotype relationships and the mechanisms of adverse drug reactions.
Jean-Gabriel Ganascia first studied mathematics and physics to be an engineer. Then he got his graduation in physics (Orsay University), a DEA in acoustics (Paris VI University). In parallel he studied philosophy and computer science. He obtained a grant to prepare a doctorate on knowledge-based system applied to geology. He got his “Doctorat d’ingénieur” in 1983. After that, he pursued his research on machine learning from both a theoretical view and a practical one until he obtained his “Thèse d’état” in 1987. Jean-Gabriel Ganascia was successively named assistant professor at Orsay University (Paris XI) (1982), “Maître de conférences” at Orsay University (1987), and professor at Paris VI University (1988). He was also program leader in the CNRS executive from November 1988 to April 1992 before moving to direct the Cognitive Science Coordinated Research Program and head the Cognition Sciences Scientific Interest Group since January 1993 until 2000. Jean-Gabriel Ganascia is presently first class professor of computer science at Paris VI University and ACASA team group leader in the LIP6 labora- tory. His main scientific interests cover different areas of artificial intelligence: Knowledge acquisition, symbolic machine learning, data mining, data fusion, scientific discovery, cognitive modeling, digital humanities, and investigation of creativity.
Jörg Hakenberg received his Diploma in computer science from Ulm University, Germany. He started his Phd in 2003 at Humboldt-Universität zu Berlin in the Knowledge Management in Bioinformatics
417 About the Contributors
group. From 2006-2007, he worked for the Bioinformatics group at Technische UniversitŠt Dresden. He currently is a research associate with the BioAI lab at Arizona State University. Jšrg’s main research interests are text mining in the life sciences and bioinformatics.
Graeme Hirst’s present research includes the problem of near-synonymy in lexical choice in language generation; computer assistance for collaborative writing; and applications of lexical chaining as an indi- cator of semantic distance in texts. He was a member of the Waterloo-Toronto HealthDoc project, which aimed at building intelligent systems for the creation and customization of healthcare documents, and of the EpoCare project on answering clinical questions for physicians from clinical-evidence publications. Hirst is the author of two monographs: Anaphora in Natural Language Understanding (Springer-Verlag, 1981) and Semantic Interpretation and the Resolution of Ambiguity (Cambridge University Press, 1987). He was elected chair of the North American Chapter of the Association for Computational Linguistics for 2004-05 and treasurer of the Association for 2008-2012.
Zhang-Zhi Hu received his BS/MD in medicine from Wannan Medical College, China in 1984, and his MS in physiology from Beijing University Health Science Center in 1989. He received the National Institutes of Health (NIH) Intramural Research Training Award during 1993-1998 and received the NIH Fellows Award for Research Excellence in 1996. He continued his research at the NIH until 2001 and then joined the Protein Information Resource (PIR) at the Georgetown University, Washington DC. He is currently a research associate professor at the Department of Biochemistry and Molecular & Cellular Biology, Georgetown University. His primary research focuses on the understanding of biological path- ways and networks from large-scale omics data. He is also interested in text mining tool development that supports the systems biology and ontology research. He is a member of ISCB, USHUPO and the Endocrine Society. He has over 45 journal publications and book chapters.
Antonio Jimeno-Yepes received a Master Degree in computer science (Universitat Jaume I, Cas- tellon, Spain) and a Master Degree in intelligent systems (Universitat Jaume I). He worked at CERN (European Organization for Nuclear Research) on the LHC layout database and in several projects within the EDMS document management systems. In 2006 he joined the text mining group at the European Bioinformatics Institute. He is a PhD candidate at the Universitat Jaume I.
Christophe Jouis received his PhD degree in 1993. He worked at CR2A/IBM and CAMS (Centre d’Analyse et de Mathématiques Sociales, UMR CNRS, EHESS, Université Paris Sorbonne) in knowledge modeling and expertise transfert. Currently, his research interests focus on (1) contextual exploration, a new computational method to extract semantic values and information from texts in order to build ontologies and (2) the logic of relationships between concepts in thesauri and ontologies.
Asanee Kawtrakul received the Bachelor Degree (honor) and Master Degree in electrical engineering from Kasetsart University, Bangkok, Thailand, and Doctoral Degree in information engineering from Nagoya University, Japan. Currently, she is an associate professor of Computer Engineering Department at Kasetsart University and the Deputy Director of National Electronics and Computer Technology Center, the member of National Science and Technology Development Agency. Her research interests are in natural language processing, information engineering and knowledge engineering.
418 About the Contributors
Harald Kirsch is a computer scientist by training. From 2000 to 2003 he developed commercial software for biomedical text mining before joining the the Rebholz Group (Text Mining) at the EMBL- EBI in 2003. EMBL-EBI is using his IT infrastructure based on Finite State Automata for information extraction. Since 2006, he is now developing information retrieval solutions as member of the Raytion GmbH, Duesseldorf.
Dimitrios Kokkinakis received his PhD in computational linguistics from the University of Gothen- burg in December 2001. He is currently a postdoctoral fellow at the Department of Swedish Language, University of Gothenburg, Sweden. His research interests include computational lexical Semantics (particularly word-sense disambiguation, automatic lexical acquisition and relation extraction), Medi- cal and clinical informatics, corpus linguistics (particularly standardization of resources and shallow syntactic/semantic analysis) and text mining (particularly information extraction, machine learning and visualization of linguistic and multidimensional data).
Dimosthenis Kyriazis received the diploma from the Dept. of Electrical and computer engineering of the National Technical University of Athens, Athens, Greece in 2001, the MS degree in techno- economic systems (MBA) co-organized by the Electrical and Computer Engineering Dept - NTUA, Economic Sciences Dept - National Kapodistrian University of Athens, Industrial Management Dept - University of Piraeus and his PhD from the Electrical and Computer Engineering Department of the National Technical University of Athens in 2007. He is currently a researcher in the Telecommunication Laboratory of the Institute of Communication and Computer Systems (ICCS). Before joining the ICCS he has worked in the private sector as Telecom Software Engineer. He has participated in numerous EU / National funded projects (such as IRMOS, NextGRID, Akogrimo, BEinGRID, HPC-Europa, GRIA, Memphis, CHALLENGERS, FIDIS, etc). His research interests include grid computing, scheduling, quality of service provision and workflow management in heterogeneous systems and service oriented architectures.
Vivian Lee works as curator in the Rebholz Group (Text Mining) at the EMBL-EBI. She received her PhD in genetics from the University of Nottingham in 2002. She then joined the EMBL-EBI as a scientific curator in the gene ontology annotation project and the protein-protein interaction database IntAct. Following this she took up a postdoc fellowship in cancer genetic research at the Sanger Institute, UK. Vivian’s expertise lies in the domain of bioinformatics (ontological design, data/text mining, data- base curation) and laboratory investigation (cancer research, molecular biology and protein chemistry). She has publications in all these domains.
Ulf Leser holds a Diploma in computer science from the Technical University in München and a PhD in distributed query optimization from the Technical University Berlin. After spending some years as a project manager in industry, he was appointed a professor for Knowledge Management in Bioinformatis at Humboldt-Universität Berlin in 2003. His main research interests are information integration, text mining, and modelling and scalability of complex databases, all applied in a Life Science context.
Nadine Lucas is a researcher at the French National Center for Scientific Research CNRS. She works at Université de Caen Basse-Normandie in the GREYC laboratory (Groupe de Rercherche en Informa- tique, Image, Automatique et Electronique de Caen). Her research in text comparative linguistics and
419 About the Contributors
rhetoric started with academic writing. It later included NLP and encompassed news and web-based discussions. Her main interests are scale management in discourse parsing and multilingual NLP with scarce lexical resources. She currently is a member of the French Bingo2 project relating genomics and inductive data mining, where she focuses on textual data mining.
Maria Teresa Martín-Valdivia is lecturer in the Department of Computer Science at Jaén Univer- sity (Spain). She received MS degree in computer science from the University of Granada, and PhD in computer science from Software Engineering Department of Málaga. Her current research interest in- cludes natural language processing, tools for text mining, neural networks, machine learning algorithms, text categorization, multilingual and multimodal information retrieval. In addition, she is treasurer of SEPLN (Spanish Society of Natural Language Processing) Committee from 2007. She is member of Intelligent Systems of Information Access Research Group. She is author or co-author of more than 50 scientific publications, technical reviewer in several journals and in the program committee of some major conferences.
Arturo Montejo-Ráez is assistant professor in the Department of Computer Science at Jaén Uni- versity (Spain). He received a MS degree in computer science at the University of Jaén in 1999, and a PhD in computer science at Software Engineering Department of Granada University in 2006. His current research includes information retrieval, text categorization and management systems of natural language processing, and spoken language dialogue systems.
Meenakshi Narayanswamy is a co-founder of Serene Innovations, a company with business focus on text analytics. She completed both her Bachelor’s and Master’s degree in biotechnology and is close to completing her PhD program in in computational biology. She is University Top Rank holder in her Master’s degree. She is a recipient of a research fellowship from University Grants Commission, Govt. of India for her doctoral programme. Her PhD dissertation included the design of some parts of the RLIMS-P system.
Yun Niu is a post-doctoral researcher at the Ontario Cancer Institute, University Health Network since January 2007. Niu received her PhD in computer science from the University of Toronto in 2007. Her research focuses on question answering, information extraction, probabilistic classification in natu- ral language processing and their applications in the biomedical domain. One of such applications is to extract important relations between biological entities, such as protein protein interactions. She was a member of the EPoCare project which aimed at providing accurate answers to questions posed by clini- cians in patient treatment. Her role in the project was applying computational linguistics technologies to refine the results obtained by information retrieval. In her previous work, Niu investigated cause-effect relations in medical text, and developed automatic approaches to extract causal relations.
Jon Patrick graduated with his PhD in computer science from Monash University in 1978 after completing degrees at RMIT and Trinity College, Dublin. He has subsequently completed two degrees in psychology and he is a registered psychologist. He has held the chairs of Information Systems at Massey University and Sydney University. More recently he has moved to the chair of Language Technology to give more attention to his research in language processing. His early work in this field concentrated on processing systems for second language learners (English-Basque) and more recently he developed
420 About the Contributors
the widely reported Scamseek system for the Australian Securities and Investment Commission (ASIC) for which he was awarded the Eureka Science prize in 2005. Since then he has worked on applying language technology to medical contexts. He has built a number of technologies with his collaborators and introduced the first real-time language processing system for ward rounds with his collaborators at the Intensive Care Service of the Royal Prince Alfred Hospital, Sydney. He is also working with the Sydney West Area Health Service to introduce a range of IT research technologies into the AHS.
Chaveevan Pechsiri achieved a Bachelor’s Degree in food science and technology from Kasetsart University, Thailand. She achieved both the Masters Degree in food sciences, the Masters Degree computer sciences from Mississippi State University, USA. She also achieved a Doctoral degree in computer engineering from Kasetsart University. Currently, she is an assistant professor at Dhurakij Pundij University and is currently researching on NLP.
Jean Pierre Pecuchet currently works as a full professor in Laboratoire d’Informatique, de Traitement de l’Information et des Systèmes, Institut National des Sciences Appliquées, Rouen, France, since 1988. His main research area regards the modelling and simulation of complex systems and the interactions between the users and the information systems. He is also interested in ontology modelling and multi- agent systems. His main research results are: the creation of an education simulator (projects ANTIC2 and Métascène), the modelling and the analysis of computerized medical records (project DOPAMINE), the methods and tools for evaluating the learner on the Web (project MARWAN) and contribution of ontology for finding information on the Web (projects ATONANT et VODEL).
José M. Perea-Ortega is a research member of the Intelligent Systems of Information Access Research Group in the University of Jaén (Spain). He received a MS degree in computer science at the University of Jaén and a PhD in computer science at Software Engineering Department of Granada University. His current research includes information retrieval, text categorization and management systems of natural language processing.
Piotr Pęzik received a PhD in computational linguistics from the University of Łódź, Poland. He is currently a member of the text mining group at the European Bioinformatics Institute in Cambridge, UK. He has contributed to the development of a number of Information Extraction and Information Retrieval tools and resources as part of both UK and European research projects, including the MedEvi search engine and the BioLexicon.
Sachit Rajbhandari, received a Master degree in information and communication technologies from Asian Institute of Technology (AIT), Thailand in 2006. He received his Bachelor degree in electronics engineering and Master degree in business studies from Tribhuvan University, Nepal in 2001 and 2003 respectively. He is working as an information management consultant at Food and Agriculture Organi- zation of the United Nations (FAO). He had been involved in many software development projects since 2001 working at different software companies and institutions. His research interests are in Semantic Web, search engine, database management system, and information management.
K. E. Ravikumar is a co-founder of Serene Innovations, a company with prime focus on text analyt- ics. As a CSIR senior research fellow in Anna University, he has completed all formalities for his PhD
421 About the Contributors
programme (Anna University) and is awaiting his defence. His PhD dissertation included the design of some parts of the RLIMS-P system. He received a BTech diploma in pharmaceutical technology, and a Masters in biotechnology. During his masters program, he was recipient of Junior research Fellowship from Directorate of Biotechnology, Govt. of India and received the University Gold medal award.
Dietrich Rebholz-Schuhmann, MD, PhD, studied medicine (University of Düsseldorf) and computer science (University of Passau). He worked in medical informatics research and at LION bioscience AG, Heidelberg, Germany, where he headed a research group in text mining and led the EUREKA research project „Bio-Path?. In 2003 he joined the EBI and thereafter served as area chair in text mining for the ISMB (2004, 2005 and 2007) and co-organized the Symposium for Semantic Mining in Biomedicine (2005 and 2008). He was member of the Network of Excellence “SemanticMining” (NoE 507505) and is team leader in the FP6-IST project “BOOTStrep” (contract FP-6 028099, www.bootstrep.eu). Fur- thermore, he has contributed major parts to the project plan of UKPMC that is currently instantiated at Manchester Information & Associated Services (MIMAS) and co-chairs the work package in bio- logical information infrastructures of the ELIXIR project (part of the European initiative in scientific infrastructures ESFRI).
Alexandrin Rogozan currently works as associate professor in Laboratoire d’Informatique, de Traite- ment de l’Information et des Systèmes, Institut National des Sciences Appliquées, Rouen, France, since 2000. Her main research area regards the models for text indexation (using techniques for automatic language processing based on a controlled vocabulary and on terminologies), the models for image indexation (in order to create a digital and symbolic signature for image searching by keywords and/or content), the hybrid models for generation of kernel function for support vector machine (with applica- tions in the problem of concept alignment based on definitions), the fusion models for ruttier obstacle classification and the models for compression for text clusterization.
Magali Roux-Rouquie (Roux-Dosseto) received a MS degree in biochemistry and cell biology and a PhD (“Doctorat de 3e cycle”, 1979 and “Thèse d’état”, 1984) at the University of Aix-Marseille II, France. Magali Roux-Rouquie was successively named assistant professor (Timone Hospital, Marseille, 1979-1981), research fellow CNRS (Immunology Center, Inserm-CNRS of Marseille, 1981-1983), full- time post-doc (Harvard University, Department of Molecular Biology Cambridge, USA, 1981-1983), director of research (Centre Hospitalo-Universitaire URA CNRS 1175, Marseille, 1984-1995), repre- sentative - “chargé de mission” - Ministry of Research, Paris, 1995-2000), director of research CNRS (GENATLAS Necker-University of Paris V Hospital, Paris 1998-2000), «Biosystems Engineering Modeling» team/group leader (Institut Pasteur, Paris, 2000-2004), director of research CNRS (Computer Science Laboratory of Paris VI UMR CNRS 7606, Paris, 2004). The main scientific interests of Magali Roux-Rouquie are knowledge organisation and standards in systems biology, molecular mechanisms of regulation in breast cancer, and regulation of human major histocompatibility complex class II genes and cytotoxic genes.
Ferran Sanz is professor of Biostatistics and Biomedical Informatics at the University Pompeu Fabra (UPF), Director of the IMIM-UPF joint Research Unit on Biomedical Informatics (GRIB, www. imim.es/grib), and currently vice-rector for scientific policy of the UPF. Author of about 100 articles in SCI indexed journals. Mentor of 17 PhD thesis. Coordinator of several EC-funded initiatives, as well
422 About the Contributors
as a STOA report for the European Parliament. President of the European Federation for Medicinal Chemistry from 2003 to 2005. Involved as invited expert in the genesis of the Innovative Medicines Initiative (www.imi-europe.org) and currently academic coordinator of the Spanish Platform Medi- camentos Innovadores. Coordinator of the node of Biomedical Informatics of the Spanish Institute of Bioinformatics (INB).
Torsten Schiemann received his Diploma in computer science from Humboldt-Humboldt-Univer- sität zu Berlin in 2006. He wrote his Master’s thesis on word sense disambiguation at the Knowledge Management in Bioinformatics group. He currently works as a software engineer in industry.
Burr Settles is a graduate student in computer sciences at the University of Wisconsin, Madison. His research interests center on machine learning and its applications to text and data mining, includ- ing information extraction, information retrieval, and modeling social and biological networks. Burr is currently finishing his PhD thesis on active learning and multiple-instance learning algorithms for the rapid development of information management systems. He has released several open-source software projects related to his research, including ABNER (A Biomedical Named Entity Recognizer), which is described in this book.
Vijay Shanker is a professor in Computer Science at the University of Delaware. His primary research focus has been in the area of natural language processing and parsing. His current interests include information extraction, text mining and machine learning. He received his PhD in computer science from the University of Pennsylvania. He has served in program committees of over 40 confer- ences and has served a program committee co-chair of ACL and TAG+ conferences. He has served on editorial boards of computational linguistics and grammars journals. He has published close to 100 peer-reviewed papers.
Mário J. Silva received his undergraduate and Master degrees from the Instituto Superior Técnico, Lisboa, Portugal, and PhD degrees from the University of California, Berkeley, USA (1994). He joined the University of Lisbon (Faculty of Sciences) in 1996, where he is now associate professor (with Habili- tation) in the Department of Informatics. He has published over 70 refereed technical papers and book chapters. He has advised 20 Master dissertations and 5 PhD theses, and leads a research team of 15 faculty, graduate students and technical staff (XLDB Group, http://xldb.fc.ul.pt). His current research interests are on information integration, information retrieval and text mining systems, with applications in biomedical informatics and geographic information systems. Prior research interests have included mobile computing systems, VLSI CAD and microelectronics.
L. Alfonso Ureña-López is senior lecturer in the Department of Computer Science at Jaén Univer- sity (Spain). He received MS degree in computer science from the University of Granada, and PhD in computer science from Software Engineering Department of Granada. His PhD thesis was the winner of the 2001 Awards of the Spanish Society for Natural Language Processing. His current main research interest is intelligent search, including search engines, search assistants, natural language processing tools for text mining and retrieval and human computer interaction. Relevant topics include multilingual- multimodal information access, information synthesis and summarization, Semantic networks (wordnets, lexical acquisition, Web as corpus, word sense disambiguation), Web search engines (clustering and
423 About the Contributors
visualization of search results, portal search engines). Dr. Ureña was head of the Computer Science Department at University of Jaén (1997-2004). Currently he is deputy director of the Polytechnic School at Jaén. He is head and founder of Intelligent Systems of Information Access Research Group. Also, he is President of SEPLN since 2007 and editor of Procesamiento de Lenguaje Natural Journal. He has directed several research projects and several contracts with companies in technology transfer, as well as several Ph. D. in Computer Science and research works. He is author or co-author of more than 100 scientific publications, a technical reviewer in several journals and in the Program Committee of some major conferences.
Theodora A. Varvarigou received the BTech degree from the National Technical University of Athens, Athens, Greece in 1988, the MS degrees in electrical engineering (1989) and in computer sci- ence (1991) from Stanford University, Stanford, California in 1989 and the PhD degree from Stanford University as well in 1991. She worked at AT&T Bell Labs, Holmdel, New Jersey between 1991 and 1995. Between 1995 and 1997 she worked as an assistant professor at the Technical University of Crete, Chania, Greece. Since 1997 she was elected as an assistant professor while since 2007 she is a professor at the National Technical University of Athens, and Director of the Postgraduate Course “Engineering Economics Systems”. Prof. Varvarigou has great experience in the area of Semantic Web technologies, scheduling over distributed platforms, embedded systems and grid computing. In this area, she has pub- lished more than 150 papers in leading journals and conferences. She has participated and coordinated several EU funded projects such as IRMOS, SCOVIS, POLYMNIA, Akogrimo, NextGRID, BEinGRID, Memphis, MKBEEM, MARIDES, CHALLENGERS, FIDIS, and other.
Cathy H. Wu is professor of Biochemistry and Molecular Biology and director of the Protein In- formation Resource (PIR). With background and experience in both biology and computer science, she has conducted bioinformatics and computational biology research for 20 years. Since 1999 she has led the development of PIR as a major public bioinformatics resource that supports genomic, proteomic and systems biology research. Dr. Wu has served on several advisory boards, including the HUPO Board of Directors, the PDB Scientific Advisory Board, the NIGMS Protein Structure Initiative Advi- sory Committee, and the NSF TeraGrid User Advisory Committee. She has also served on numerous program committees for international bioinformatics and proteomics conferences and workshops. She has published about over peer-reviewed papers and three books, and given more than 100 invited lectures. Her research interests include protein evolution-structure-function relationships, proteomics informatics and computational systems biology, biomedical text mining and ontology, and bioinformat- ics cyberinfrastructure.
Yitao Zhang is a PhD student in Health Information Technologies Research Laboratory (HITRL), School of Information Technologies, The University of Sydney. He holds a Bachelor degree of engi- neering from Tsinghua University, China, in 1998, and a Master degree of information technology from The University of Sydney, Australia, in 2004. His current research focuses on using natural language processing techniques to extract domain-specific knowledge from medical case studies which are re- ported in openly-available journal articles. His other research interests include textual paraphrasing and entailment, and assigning meaningful medical concepts, such as ICD-9-CM codes, to free-text clinical notes through a text categorization approach.
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