Training
Course in Biomedical Ontologies, Dagstuhl, 21-24 May 2006
Programme
Sunday 21 May,
2006
15:00-19:00
Arrival
Monday 22 May,
2006
7:30 Breakfast buffet
8.45 Mark Musen: Ontologies in
Biomedicine
The past 15 years has seen a surge of interest in the use
of ontologies in biomedicine. Along with this popular groundswell has been
some confusion about what an ontology is. We will
explore the nuances of what different groups refer to as an ontology, and
discuss the need for a
National
Center for Biomedical
Ontology.
Stevens, R., et
al. Ontologies in bioinformatics. In: Staab, S. and Studer,
R., eds. Handbook on Ontologies, Springer-Verlag,
2004.
10:15 Coffee
10:45
Mark Musen: The Use of Ontologies in Knowledge
Engineering
One of the earliest drivers in the development of
biomedical ontologies was the need to structure the knowledge bases of
intelligent systems. We explore mechanisms of knowledge engineering, the
manner in which ontologies provide guidance in knowledge elicitation, and the
use of ontologies to build intelligent computer systems.
Musen MA. Ontology-oriented design and programming. In: Cuena, J. et
al., eds. Knowledge Engineering and Agent Technology. IOS Press,
Amsterdam,
2002. http://www.mindswap.org/~aditkal/research/papers/ontoSW/ont-oriented-design-prog.pdf
Crubézy,
M., and Musen, M.A. Ontologies in support of problem
solving. In: Staab, S. and Studer, R.,
eds. Handbook on Ontologies, Springer-Verlag, 2004.
12:15 Lunch
14:30
Barry Smith: Biomedical
Ontologies: A Critical Survey
Ontologies, terminologies and thesauri are now in common
use in the domain of biomedical informatics. Their goal is to support search and
retrieval, but also to advance genuine reasoning about biomedical phenomena and
to enable re-use of heterogeneous data through the use of common systems of
annotations. We examine a representative collection of biomedical ontologies in
light of these criteria, and draw (somewhat sad) conclusions as to the current
state of the field.
Ceusters W, Smith B, Goldberg L. A terminological and
ontological analysis of the NCI Thesaurus, Methods Inf Med, 2005;44:498-507.
http://ontology.buffalo.edu/medo/NCIT_Smith.html
16:00 Coffee
16:30
Olivier Bodenreider:
Enhancing Ontologies Through Annotations
Relations among types in single ontologies can be
detected from patterns of associations in an annotated corpus. Examples are
taken from MeSH/MEDLINE and GO/model organism databases. We describe how this
approach can be extended in order to discover relationships between ontologies.
Examples are taken from FMA-GALEN and Metathesaurus/Semantic
Network.
Bodenreider O, Aubry M, Burgun A. non-lexical approaches
to identifying associative relations in the Gene Ontology.
In: Altman RB, et al (eds.), Pacific
Symposium on Biocomputing 2005, 91-102.
http://helix-web.stanford.edu/psb05/bodenreider.pdf
18:00 Dinner
19:30
Barry Smith: The Ontology
of Biomedical Reality
Ontologies to support
scientific research and clinical medicine have special characteristics, which we
shall outline in terms of a distinction between three levels: (1) the level of
reality; (2) the level of cognitive representations; and (3) the level of the
publicly accessible concretizations of such cognitive representations for
example in ontologies. Against this background we shall clarify the relations
between ontologies, terminologies, information models, databases, and similar
artifacts.
Barry Smith and Werner Ceusters “Towards a Coherent
Terminology for Principles-Based Ontology”, Proceedings of Annual Symposium of
American Medical Informatics Association,
submitted.
http://ontology.buffalo.edu/bfo/Terminology_for_Ontologies.pdf
Tuesday 23 May,
2006
7:30 Breakfast buffet
8:45 Mark Musen: Case Studies in Ontology
Engineering: Getting the Models Right
We
will explore the evolution of ontologies such as GO, EON, and HyBrow, and
discuss the manner in which the developers of those ontologies made steps (and
missteps) toward their final formulation. We will discuss ways in which
ontology builders can evaluate modeling choices and work to eliminate design
errors.
Guarino, N., and Welty, C. Evaluating ontological decisions with OntoClean.
Communications of the ACM. 45:(2)61–65, 2002.
http://delivery.acm.org/10.1145/510000/503150/p61-guarino.pdf?key1=503150&key2=5055556411&coll=GUIDE&dl=GUIDE&CFID=74961924&CFTOKEN=23571491
10:15 Coffee
10:45
Werner Ceusters: The
Role of Terminologies and Ontologies in the Context of the
Electronic Health Record
Electronic patient records increasingly involve the use
of standardized terminologies and ontologies, and tremendous efforts are being
devoted to the creation of terminology resources that can meet the needs of a
future era of personalized medicine, in which genomic and clinical data can be
aligned. We describe these efforts and show the problems of information
integration which arise when nurses, physicians, biologists and medical
researchers each use their own tailor-made terminologies.
Barry Smith and Werner Ceusters, “Ontology as the Core
Discipline of Biomedical Informatics: Legacies of the Past and Recommendations
for the Future Direction of Research”, forthcoming in
Computing, Philosophy,
And Cognitive Science, Gordana Dodig
Crnkovic and Susan Stuart (eds.),
Cambridge: Cambridge Scholars Press, 2006.
http://ontology.buffalo.eduhttps://buffalo.box.com/shared/static/lp1aubydzupxnxqygt6ivsfru0r0xx1s.pdf
12:15 Lunch
14:30
Werner Ceusters:
Referent Tracking: The New Paradigm
Current Electronic Health Records (EHRs) record not what
is happening on the side of the patient, but rather what is said about what is
happening. We show how this creates obstacles for reasoning with the information
contained in the EHR and for creating interoperability between different EHR
systems. We show how these obstacles can be overcome if we move to an EHR regime
in which all clinically salient particulars – from the concrete disorder on the
side of the patient and the body parts in which it occurs to the concrete
treatments given – are uniquely identified.
Referent Tracking
Literature: http://www.org.buffalo.edu/RTU/papers.html
16:00 Coffee
16:30
Werner Ceusters: Ontology and
the Future of Evidence-Based Medicine
The future of biomedical
informatics, in an era of personalized, evidence-based medicine, will
increasingly involve reasoning with the sorts of instance data we find in the
Electronic Health Record (EHR). We show how an adequate ontology of the
biomedical domain can lead to a new and better management of EHR
data.
Ceusters W, Smith B.
Strategies for Referent Tracking in Electronic Health Records.
Journal of Biomedical Informatics. In press.
http://wings.buffalo.edu/cogsci/Activities/Colloquium/CLLQf05/FinalCeustersRome4BS.pdf
18:00 Dinner
19:30
Olivier Bodenreider: Experience
in Aligning Anatomical Ontologies
We first describe a direct alignment technique developed
for FMA-GALEN, and its application to other pairs of ontologies, including Mouse
Adult Anatomical Dictionary-NCI Thesaurus and
FMA-SNOMED CT. We then describe an indirect
alignment technique – through a reference ontology –
and its application to mapping the following ontologies pairwise: FMA, Mouse
Adult Anatomical Dictionary and NCI Thesaurus.
Bodenreider O, Hayamizu TF, Ringwald M, de Coronado S,
Zhang S. Of mice and men: Aligning mouse and human anatomies. Proceedings of
AMIA Annual Symposium 2005:61-65.
http://lhncbc.nlm.nih.gov/lhc/docs/published/2005/pub2005027.pdf
Zhang
S, Bodenreider O. Alignment of multiple ontologies of anatomy: Deriving indirect
mappings from direct mappings to a reference. Proceedings of AMIA Annual
Symposium 2005:864-868.
http://lhncbc.nlm.nih.gov/lhc/docs/published/2005/pub2005039.pdf
Wednesday 24 May,
2006
7:30 Breakfast buffet
8:45
Olivier Bodenreider:
Ontologies for data integration: A Semantic Web
perspective
We describe how mapping across terminologies is
effected in the UMLS Metathesaurus for indexing purposes, and
draw parallels between terminology integration in the UMLS and data integration
through RDF in the Semantic Web. We sketch applications and limitations, and
include a brief presentation of the Semantic Web.
Fung
KW, Bodenreider O. Utilizing the UMLS for semantic mapping between
terminologies. Proceedings of AMIA Annual Symposium 2005:266-270.
http://lhncbc.nlm.nih.gov/lhc/docs/published/2005/pub2005031.pdf
10:15 Coffee
10:45
Barry Smith: The OBO Foundry
Project: Towards Scientific Standards and Principles-Based Coordination in
Biomedical Ontology Development
The OBO Foundry is a collaborative experiment,
involving a group of ontology developers who have agreed in advance to the
adoption of a growing set of principles specifying best practices in ontology
development. The primary objective is to establish gold standard reference
ontologies, one for each core domain of biomedical science. We shall describe
how this objective is already being realized, and show
how it can not only help solve the problems of data retrieval and re-use but
also foster the development of the powerful tools that will be needed to reason
with biomedical data in the future.
Michael Ashburner, Suzanna Lewis, Barry Smith: The OBO
Foundry. A New Paradigm for Biomedical Ontology Development,
http://obofoundry.org/
12:15 Lunch
13:00 Smith, Ceusters, Bodenreider: The Future of Biomedical
Ontology