International Symposium on Biomedical Informatics in Europe - Topic E

Standards and Ontologies in Biomedical Informatics.

Chairperson: Hans Ahlfeldt
Linköping University
Linköping, Sweden

Gunnar Klein
Karolinska Institute
Stockholm, Sweden
"Standards and Ontologies in Biomedical Informatics"
There is today well established agreement that standards and agreed terms are essential to achieve interoperability of health information systems and the European Commission and the European member states have included standards actions as part of the strategy for eHealth. Much of the achievements from Europe and global efforts for informatics standards is not widely known and not used as the important enabler it could be for eHealth and Biomedical Research. The presentation will give an overview of some of the available standards to consider for electronic messages, service architecture, point of care medical devices, electronic health records, security protection and terminology and knowledge representation. Furthermore the important interaction between the R&D projects, the Network of Excellence and formal standards bodies will be described and exemplified with the work on the ontology.

Dipak Kalra
University College London
London, United Kingdom
"Advancing the Realisation of EHR Interoperability"
The goal of communicating electronic health record information seamlessly between diverse and distributed clinical systems includes many challenges. Research has made significant inroads over the past 15 years, and informatics standards offer a basis for progressively more rich interoperability. This presentation will outline those challenges and research outputs, including the work of the openEHR Foundation, EHR Archetypes the EN13606 EHR Communications standard and EN13940 (System of Concepts for Continuity of Care). The presentation will focus on the contemporary issues to be addressed towards the communication of clinical meaning (semantic interoperability). It will provide an overview of the research results of the SemanticMining Network of Excellence in this field, and also some of the early findings of the SementicHEALTH roadmap that relate to EHRs.

Susanna-Assunta Sansone
The European Bioinformatics Institute
Cambridge, United Kingdom
"Reporting Standards for Omics Data – An Overview"
The marriage of conventional biomedical research with transcriptomic, proteomic and metabolomic technologies has created not only opportunities, but also new informatics challenges for biologists and bioinformaticians. New approaches for the description, storage and exchange of the voluminous data generated by such investigations are urgently required, to support the effective analysis, comparison and integration of those data sets. Standards for data content (minimal information checklists), syntax (file formats), and semantics (ontology) are being developed jointly across communities. In my presentation I will (1) introduce the topic of “reporting standards”, (2) describe the international omics-specific standardisation initiatives (MGED, PSI and MSI) and (3) present cross-domains synergistic projects (MIBBI, FuGE and OBI). Links can be found at the project website: www.ebi.ac.uk/net-project.

Arne Kverneland
National Board of Health
Denmark
"SNOMED CT – New International Governance – New Possibilities?"
SNOMED CT is considered to be the most comprehensive, multilingual clinical healthcare terminology available in the world. When implemented in software applications, SNOMED CT represents clinically relevant information as an integral part of producing electronic health records. The work is a result of extensive collaboration between: SNOMED® International, a division of the College of American Pathologists (CAP), and the United Kingdom’s National Health Service (NHS). The International Health Terminology Development Organisation (IHTSDO) (established in Denmark, with 5 European and 4 international member countries) has the purpose of making the development and access to SNOMED-CT an open process. Prospective charter members including Australia, Canada, Denmark, Lithuania, The Netherlands, New Zealand, Sweden, the United Kingdom and the United States have decided to form this IHTSDO (International Health Terminology Standard Development Organisation). The non-for-profit organisation will be presented, as the terms for license and the process for developing and research an innovation.

Victor Maojo
Universidad Politécnica de Madrid
Madrid, Spain
"Using Ontologies in Clinico-Genomic Applications. The INFOBIOMED and ACGT Experiences"
In Biomedical Informatics researchers try to normalize and reuse vocabularies, data models and knowledge conceptualizations for ontological development. Ontologies facilitate the semantics needed to bridge current differences and gaps between heterogeneous data sources and a formal language for information search, access and retrieval. Within medicine, vocabulary and coding systems such as the ICD, SNOMED, LOINC, UMLS, and others are being used for ontological engineering. They are not “true” ontologies from a formal computing perspective, but they can be used in some Biomedical Informatics applications. In genetics, Gene Ontology (GO) has led ontological efforts in the genetic area. The Gene Ontology is a collaborative effort to create a controlled vocabulary of gene and protein roles in cells, to consistently describe gene products in different databases. Many other efforts are currently being carried out at different institutions regarding ontological development in BMI. Some examples will be shown from the EC-funded INFOBIOMED and ACGT projects, carried out at the Biomedical Informatics Group, Universidad Politecnica de Madrid. We have used ontologies for different computational applications such as clinico-genomic database integration or ontology-assisted data preprocessing in distributed environments. Ontologies have proved to be an important component for Biomedical Informatics applications in the frameworkof Genomic Medicine.