Applications of Biomedical Ontologies and Resources
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  M. Scott Marshall   M. Scott Marshall
Assistant Professor of Bioinformatics, Dept. of Medical Statistics and Bioinformatics
Leiden University Medical Center
    Jeffrey Grethe
Co-Principal Investigator, Neuroscience Information Framework
Center for Research in Biological Systems, University of California, San Diego
  Mark Musen   Mark Musen
Professor of Medicine and Computer Science, Stanford Center for Biomedical Informatics Research
Stanford University


Thursday, June 24, 2010
02:00 PM - 03:00 PM
Level:  Practical Experience

Location:  Yosemite B

As steadily more structured vocabularies and ontologies are made available on the Web, attention is turning towards how to share and annotate data using these vocabularies. Meanwhile, the work on creating and extending ontologies continues, now with the new possibilities provided by OWL 2. Two complementary approaches are being applied: the former enhances the use of identifiers to link data and interoperates at the level of RDF, the latter stresses the benefit of OWL 2 ontologies and formal semantics in order to interoperate at a semantic and reasoning level. The authors will present the current state of work and discuss the benefits of these complementary approaches for Life Sciences.

  1. A new era of collaborative research is becoming possible, enabled by steadily increasing numbers of inter-linked resources. In order for these resources to add value to each other through 'linking', a sustainable and common system of shared identifiers, vocabularies, and data provenance practice is required. The W3C Health Care and Life Sciences Interest Group promotes the use of such identifiers and best practices by creating a translational medicine ontology and bridging the data of multiple disciplines in demonstrations of data federation across the enterprise.

  2. Moving life sciences ontologies to OWL 2 provides several advantages: interoperability, semantics, reasoning services. Interoperability is important for shared use across different domains. Once converted to OWL 2, ontologies become easier to be connected and combined with other ontologies. Semantics (meaning) of terms is formally specified thanks to the underlying logics, thus preventing possible errors of annotation. Another major practical benefit of converting biomedical ontologies to OWL 2 is that it makes ontologies amenable to the multitude of existing OWL tools and services, in particular powerful reasoners. Reference ontologies for Disease(SNOMED), Anatomy (FMA), the Gene Ontology and other OBO ontologies, which constitute the backbone of semantic applications in Life Sciences, are already available in OWL 2.

Dr. M. Scott Marshall is an Assistant Professor of Bioinformatics at the Leiden University Medical Center. As part of a split appointment, he is responsible for activities in the Adaptive Information Disclosure subprogramme of the Virtual Laboratory for e-Science project, where semantic e-Science applications for health care and life sciences are being developed. Previously, Dr. Marshall has worked at CWI, Glaucus Proteomics, Kiadis Pharma, and the microarray department at the University of Amsterdam in The Netherlands. He is a co-chair of the W3C Semantic Web Health Care and Life Sciences Interest Group and a Visiting Scholar at Stanford. Dr. Marshall received a Ph.D. for his work in graph visualization.

Dr. Jeffrey S. Grethe is co-Principal Investigator for the Neuroscience Information Framework (NIF; in the Center for Research in Biological Systems (CRBS; at the University of California, San Diego. NIF is an open source information framework enabling neuroscientists around the world to access a rich virtual environment identifying neuroscience-relevant data and resources, to advance scientific inquiry leading to new discoveries and treatments of human neurological disorders. Unlike more general search engines, NIF provides deeper access to a more focused set of resources that are relevant to neuroscience, provides search strategies tailored to neuroscience, and also provides access to content that is traditionally "hidden" from web search engines (i.e. the hidden or deep web). Following a B.S. in Applied Mathematics from the University of California, Irvine, he received a doctorate in neurosciences with a focus on neuroinformatics and computational modeling from the University of Southern California. After a post-doc in non-invasive human imaging (PET, MRI, fMRI) at Emory University he joined the fMRI Data Center (fMRIDC) at Dartmouth College. At the fMRIDC (, he was one of the core members responsible for bringing the Data Center online, the first publicly accessible repository of peer-reviewed fMRI studies. Dr. Grethe then transitioned to the BIRN Coordinating Center at the University of California, San Diego. As the Executive Director for the BIRN Coordinating Center he focused on enabling collaborative research, data sharing and discovery through the application of advanced informatics approaches. This focus continues with his work in NIF.

Dr. Musen is Professor of Medicine (Medical Informatics) and Computer Science (by courtesy) at Stanford University, where he is head of the Stanford Center for Biomedical Informatics Research. He holds an MD from Brown University and a Ph.D. from Stanford.  Dr. Musen conducts research related to intelligent systems, the Semantic Web, reusable ontologies and knowledge representations, and biomedical decision support. His long-standing work on a system known as Protégé has led to an open-source technology now used by thousands of developers around the world to build intelligent computer systems and new computer applications for e-commerce and the Semantic Web. He is known for his research of the application of intelligent computer systems to assist health-care workers in guideline-directed therapy and in management of clinical trials. Dr. Musen’s group has begun to explore the use of knowledge-based technologies to monitor a variety of data sources in an effort to detect incipient epidemics, including those caused by possible acts of bioterrorism. In 1989 Dr. Musen received the Young Investigator Award for Research in Medical Knowledge Systems from the American Association of Medical Systems and Informatics. He received a Young Investigator Award from the National Science Foundation in 1992. He has served on the Biomedical Library Review Committee of the National Library of Medicine and as an advisor to many academic and industrial groups concerned with the development of advanced information technology. Dr. Musen sits on the editorial boards of several journals related to medical informatics and computer science. He is co-editor of the Handbook of Medical Informatics (Springer-Verlag, 1997) and co-editor-in-chief of the journal Applied Ontology.

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