Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Termkonferens 2003 Network of Excellence: Semantic Interoperability and Data Mining in Biomedicine [SemanticMining] Hans Åhlfeldt - Linköpings universitet – Co-ordinator Gunnar Klein - Karolinska institutet

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining EUs sjätte ramprogram FP6 Integrated Project - IP –storskaliga forsknings- och utvecklingsprojekt –industrinära, applikationsnära, produktutveckling Network of Excellence - NoE –nätverk, motverka fragmentisering, främja samverkan –europeisk forskning världsledande –long term - “self-sustainable network” ”Traditionella” projekt och utbytesprogram –FP1 - FP5 –forsknings- och utvecklingsprojekt –utbytesprogram för forskare och studenter

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining FP6 - tematiska områden biomedicin informationsteknologi …... hållbar tillväxt rymdforskning livsmedel, jordbruk …...

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining IST - Information Society Technologies eHealth Semantic-based Knowledge Systems

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining SemanticMining Semantic Interoperability and Data Mining in Biomedicine 25 partners från 11 länder 100 forskare, 34 doktorander

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining...Research Areas Health Care Bioinformatics Health Statistics  Knowledge engineering  Ontology engineering  Coding, indexing and information retrieval  Data mining, knowledge extraction and representation  Natural Language Processing  The Semantic Web  …to support application areas  Information and decision support  Infrastructure for health care information systems Application Areas...

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining NoE SemanticMining Network is not about harmonising software devices or delivering common services Network is about harmonising knowledge representation strategies and ontologies –Ontology and knowledge queries pervade all levels of semantic web architecture (not just middleware) –Can’t take result of one query, and use it as argument in next query to a different service, if KR strategies and ontologies are inconsistent, or not compatible Domain Ontologies Information Models Decision Support Models NLP Ontologies Applications

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Ongoing projects  Ongoing, nationally or EU-funded research projects –Swedish/Nordic evaluation of SNOMED CT –Machine translation based on parallel corpus –The German Specialist Lexicon –MEDTAG - text tagging and retrieval, Swiss-Prot –MedO - domain ontology for medicine –CLEF, OntoWeb, OpenGALEN –EBI - Gene Ontology, ORIEL, BioBabel –Electronic Health Record –ECHI - European Community Health Indicators –HDP - Hospital Data project (comparing hospital activity across EU)

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Research areas Ontology engineering Multilingual medical dictionary SNOMED CT Health care statistics Data mining and information retrieval Concept systems for laboratory medicine The electronic health record

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Integration activities Sharing of knowledge and research tools –workshops –common web site Mobility program –researchers, PhD students Summer school 2004 Educational material Contribution to standards

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Contribution to Standards CEN / ISO –Gunnar Klein (TC 251 Chairman ) –Anders Thurin (Vocabulary for Terminological Systems Project leader ) –Magnus Fågelberg (European Terminology Group Convenor ) –Dipak Kalra (TC 251) IUPAC –Urban Forsum (C-NPU, IFCC-IUPAC Chair) HL7 –Dipak Kalra - Electronic Health Records –Jeremy Rogers, Alan Rector – vocabulary, terminology W3C / Semantic Web / OWL –Robert Stevens, Jeremy Rogers SWISS-PROT, Gene Ontology de facto standards –EBI, Midori Harris OMG Life Sciences Research Domain Task Force –EBI

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining REFTERM - SNOMED CT Several separate nationally funded evaluations Interest from Nordic National Boards of Health to co-operate across Europe in evaluating SNOMED NoE will support and coordinate... Methods for machine translation based on parallel corpora Development of multi-lingual medical dictionary Translation and evaluation of SNOMED CT

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Förädling av medicintexter till detaljerade termbanker NLPLAB, Institutionen för datavetenskap, LiU Lars Ahrenberg, Magnus Merkel, Michael Petterstedt i samarbete med Medicinsk informatik, LiU Mikael Nyström, Hans Åhlfeldt i samarbete med Karolinska institutet, KI Gunnar Klein, Gunnar Nilsson, Rong Chen

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Ordlänkning (word alignment) Parallellställa textsegment på ord- och frasnivå –Input: parallella dokument (dvs. original och motsvarande översättning) –Output: 1) tvåspråkig termbank på ord- och termnivå, 2) detaljerad lingvistisk information om översättningskorrespondenser.

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Parallell corpus - källterminologier på svenska och engelska ICD10, KSH97, KSH97P ICF NCSP MeSH

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Källterminologier

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Exempel Bryta ned till kortare, mer specifika termer –sv: psykiska språkfunktioner eng: mental functions of language  –sv: psykiska eng: mental –sv:språkfunktioner eng: functions of language –sv: Andra specificerade anemier orsakade av enzymrubbningar eng: Other anaemias due to enzyme disorders  –sv: andra eng: other –sv:specificerade eng: NULL –sv:anemier eng: anaemias –sv: orsakade av eng: due to –sv: enzymrubbningar eng: enzyme disorders

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining I*Link – interaktiv träning

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining I*Trix - Automatisk länkning

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Partners in SemanticMining Academia Dept Biomedical Engineering/Medical Informatics, Linköping University, Sweden Dept of Computer Science, Linköping University, Sweden Karolinska Institutet, Stockholm, Sweden Sahlgrenska University Hospital, Göteborg, Sweden Dept of Medical Informatics, Computational Linguistics, Freiburg University, Germany Dept of Computer Science, Freiburg University, Germany Institute of Formal Ontology and medical Information Science (IFOMIS), Leipzig, Germany Institute of Informatics and Applied Mathematics, University of Kiel, Germany Division of Medical Informatics, Geneve University Hospital, Switzerland Dept of Computer Science, University of Manchester, UK Centre for Health Informatics and Multiprofessional Education, University College London, UK The Information Technology Research Institute, University of Brighton, UK Public Health and Medical Informatics Laboratory, Broussais University Hospital, Paris, France Institute of Cognitive Science (CNR – ISTC), Laboratory for Applied Ontology, Roma, Italy Institutes, Health and Welfare Organisations European Bioinformatics Institute (EBI), Hinxton, UK National Institute and Library for Health Information, Budapest, Hungary The Nordic Terminology Network (Public Health and Welfare Organisations in the Nordic Countries) WHO Collaborating Centre for Classification of Diseases in the Nordic countries Committee Nomenclature, Properties and Units in Laboratory Medicine (C-NPU) Enterprises Merrall-Ross International Ltd, Cheshire, UK European Dynamics, Greece

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining NoE SemanticMining Ontology engineering Multilingual medical dictionary SNOMED CT Health care statistics Data mining and information retrieval Concept systems for laboratory medicine The electronic health record

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining

Termkonferens 5-6 nov 2003 Network of Excellence SemanticMining Management Decision making –The Assembly (all members) –The Board (elected annually by assembly) Flexible steering –Committees, Work packages, Annual budgeting Communication –web service, group-ware Management Office –Co-ordinator’s Office (Hans Åhlfeldt, Hans Gill) –International Office Director (Johan Åkerman, Ann-Christine Comstock) –Legal Advisor (Göran Hessling) –Management Advisory Group (Magnus Holmström)