Training Course in Biomedical Ontology
Schloss Dagstuhl · 21-24 May 2006
Organized by Barry Smith in
collaboration with the European Network of Excellence SemanticMining and the US National Center for Biomedical
Ontology.
This three-day training course is
designed to provide a basic introduction to the field of biomedical ontology and
to enhance awareness of current developments and best practices in ontology in
the life sciences.
Intended Audience
Attendees who might find this
seminar worthwhile include:
developers and users of biomedical
ontologies, terminologies and coding systems,
developers and users of electronic
patient record systems,
biologists and physicians
interested in the possibilities of modern ontologies.
We are targeting advanced doctoral
students, but welcome interested post-doc and industrial participants as well.
The number of participants is restricted to about 30 to maximize possibilities
for intense discussion. All participants will receive from their attendance in
this tutorial hands-on training in ontology design and use.
Overview
Barry
Smith: Introduction to Biomedical Ontologies
Werner Ceusters: Biomedical Ontologies and
the Electronic Health Record
Olivier Bodenreider: On Mapping, Aligning and Integrating Biomedical Ontologies
Mark Musen: Case Studies in Ontology
Development
Program
I. Introduction to Biomedical
Ontologies
Barry
Smith
Biomedical Ontologies
have developed in an uncoordinated way, often reflecting mere relations of
'association' between what are called 'concepts', and serving primarily the
purposes of information extraction from on-line biomedical literature and
databases.
In recent years, we have
learned a great deal about the criteria which must be satisfied if an ontology is to allow true information integration and
automatic reasoning across data and information derived from different sources.
Such criteria would ensure that ontologies which satisfy them would be
automatically interoperable.
We will survey existing biomedical ontologies and show how they fall
short of meeting these criteria and how they can be reformed in such a way as to
allow true information integration. We also survey the current reform efforts
under the auspices of the Open Biological Ontologies (OBO)
consortium.
II. Biomedical Ontologies and the
Electronic Health Record
Werner
Ceusters
The future of biomedical
informatics, in an era of personalized, evidence-based medicine, will
increasingly involve reasoning with the sorts of temporally indexed instance
data we find in the Electronic Health Record (EHR). We will survey the problems
which confront us when we try to use current EHR systems as a basis for such
reasoning, and show how an adequate ontology of the biomedical domain can lead
to a new and better management of EHR data.
Current Electronic Health Records (EHRs) are organized around two kinds
of statements: those reporting observations made, and those reporting acts
performed. In neither case does the record involve any direct reference to what
such statements are actually about. They record not: what is happening on the
side of the patient, but rather: what is said about what is
happening.
In addition, existing EHRs embody information primarily in the form of
general concept codes, which are tied to instances in reality only indirectly,
via designations of persons and times. In contrast to this, we shall describe a
regime in which the EHR incorporates direct representations of all clinically
salient individuals as they are related together in reality. We show how this
will allow us to achieve interoperability among different EHR systems at the
level where it really matters: in regard to what is happening in the real world.
It will allow us to keep track of particular disorders and of the effects of
particular treatments in a precise and unambiguous way, and to engage in new
types of reasoning and error checking in relation to the data encoded. We will
also show a prototype implementation of an EHR/terminology system conforming to
our methodology for ontology design, focusing on how such an implementation can
be used to verify data entry in the EHR, to reason with the data, and to use the
resultant EHR / terminology system for statistical and other
purposes.
III. On Mapping, Aligning and Integrating Biomedical Ontologies
Olivier
Bodenreider
Unlike other domains, biomedicine
has a long tradition of developing terminological resources and ontologies for
organizing both documents and thoughts. With the increasing need to integrate
vast, disparate clinical and biological information resources, these efforts are
becoming increasingly important. One result is the development of repositories
of cross-referenced ontologies such as the Open Biomedical Ontologies (OBO)
library.
We will survey these developments in a critical manner, focusing on mappings, alignments and integrations in various domains of ontology, and paying attention also to the way biomedicine is currently being used as a testbed for Semantic Web technologies and on the associated formalisms for representing ontologies (RDF/S, OWL). Thus for example we will examine how relations among types in single ontologies can be detected from patterns of associations in annotations, and draw parallels between terminology integration in the UMLS and data integration through RDF in the Semantic Web.
IV. Case Studies in Ontology
Development
Mark Musen
We will examine a series of existing
biomedical ontologies, indicating how they were initially developed and
subsequently maintained, and outlining common problems and solutions. The
evolution of ontologies to represent clinical practice guidelines and protocols
will provide a foundation for much of the discussion. We will survey early
efforts to define entities of clinical care, and trace the expansion of the
corresponding models as investigators incorporated increasing numbers of
distinctions concerning clinical protocols and guidelines. We will discuss
trade-offs in modeling as well as work on ontology
evaluation.
We will discuss how the need to create biomedical ontologies has
stimulated the creation of new technology for ontology editing and management.
Special attention will be paid to the Protege ontology development environment,
and to its OWL plug-in, and also to the new technologies developed by the US
National Center for Biomedical Ontology.
Administration
Participants should plan to arrive
in Dagstuhl between 3 and
The registration fee is € 600 and
includes lodging and full board at Schloss Dagstuhl. A non-refundable
registration fee of € 20 is included in this amount. Doctoral students and other
academics may apply for a grant of up to €400 to assist their
participation.
Further details on the amenities at
Dagstuhl and getting there may be found here.
Inquiries about the course and
registration should be addressed to michelle.carnell@ifomis.uni-saarland.de.
Faculty
Barry Smith is Julian
Park Distinguished Professor of Philosophy in the University at
Werner Ceusters is Professor of
Psychiatry in the University at Buffalo and Director of the Ontology Research
Group in the New York State Center of Excellence in Bioinformatics and Life
Sciences. He has degrees in
medicine, neuropsychiatry, informatics and knowledge engineering and served as
coordinator of a series of international research projects in medical natural
language processing under the Third, Fourth and Fifth Research Frameworks of the
European Commission. Since then, he has also been active in standardisation
bodies related to medical terminology such as CEN/TC251/WG2 and ISO/TC215/WG3.
In April 1998, he started a new company - Language & Computing nv (L&C) - to exploit the results of his research. He
left L&C in 2004, his main interest being now applying and testing a new
theoretically-grounded approach to ontological
engineering.
Olivier Bodenreider, MD, PhD, leads Medical Ontology Research in the National Library
of Medicine,
Mark Musen is head of Stanford
Medical Informatics, an interdisciplinary research group at