Schloss Dagstuhl · 20-23 June 2007
Reasoning with Biomedical Information:
Training Course in Logic for Biomedical Research
Organized by
Barry Smith in collaboration with
·
European Network of Excellence SemanticMining,
·
NCBO – US
National Center for Biomedical Ontology,
·
RIDE
– A Roadmap for Interoperability of eHealth Systems,
·
ECOR – European Centre for
Ontological Research,
·
ACGT –
EU 'Integrated Project' Advancing Clinico-Genomic Trials on Cancer,
·
IFOMIS – Institute for Formal
Ontology and Medical Information Science.
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, focusing on logical and computational aspects. It will feature a special debate on the future of OWL DL in biomedical ontology development.
Intended
Audience
Attendees
who might find this training course 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.
Overview
Barry
Smith: Introduction to Terminology, Ontology, and the Philosophy of Language for Biomedical Researchers
Deborah
McGuinness: The Future of the Semantic Web
Fabian Neuhaus: Introduction to Logic and Semantics for Biomedical Researchers
Alan Rector: Introduction to Programming with OWL and
Its Problems
Nigam Shah:
Introduction to OWL and its Alternatives for Biomedical Researchers & Varieties of Reasoning
Administration
Participants
should plan to arrive in Dagstuhl in the
morning of Wednesday, June 20, 2007. The program will begin after lunch and
conclude on Saturday morning, June 23, with breakfast, the last plenary session
finishing Friday, 6 pm.
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
Deborah McGuinness is the acting
director and senior research scientist at the Knowledge Systems, (KSL) Artificial Intelligence Laboratory
at Stanford University. She is a leading expert in knowledge representation and
reasoning languages and systems and has worked in ontology creation and
evolution environments for over 20 years. Most
recently, Deborah is best known for her leadership role in semantic web
research, and for her work on explanation, trust, and applications of semantic
web technology, particularly for scientific applications. Deborah is co-editor
of the Ontology Web Language
which has emerged from web ontology
working group of the World Wide Web (W3C) semantic web activity and has now
achieved W3C Recommendation status. She helped start the web ontology working
group out of work as a co-author of the DARPA
Agent Markup Language program's DAML
language. She helped form the Joint
EU/US Agent Markup Language Committee which evolved the DAML language into
the DAML+OIL description
logic-based ontology language. She is a co-author of one of the more widely
used long-lived description logic systems (CLASSIC) from Bell
Laboratories. Her work on languages (including OWL, DAML+OIL,
OIL, CLASSIC, etc.) is aimed at
providing languages that enable the next generation of web applications moving
from a web aimed at human consumption to the semantic web aimed at machine
consumption in support of intelligent assistants and web agents. Deborah is a
leader in ontology-based tools and applications. She is a co-author and
technical leader of the Stanford KSL ontology evolution
environment. She also consulted to help VerticalNet design and build its Ontobuilder/Ontoserver
ontology evolution environment. She also provided technical leadership for the
Stanford project to help Cisco systems form its ontology evolution plan for its
meta data formation work.
Fabian Neuhaus is a postdoctoral fellow at the University at Buffalo.
Alan Rector is Professor of Medical Informatics in the
Department of Computer Science
at University of Manchester. He received his BA in Philosophy and Mathematics
from Pomona College, his
medical training at the universities of Chicago and Minnesota where he obtained
his MD, and his PhD in Medical Informatics from the University of Manchester.
Over the past twenty-five years he has led a series of
projects on clinical decision support, medical records, and medical terminology
including the ground breaking PEN&PAD
project on intelligent medical records sponsored jointly by the UK Medical
Research Council and Department of Health.
During the 1990s his work focused on medical terminology and
ontologies, and he led the EU sponsored GALEN programme (www.opengalen.org) and the UK Drug Ontology project sponsored by the Department of Health
in conjunction with the Prodigy Programme for decision support in prescribing
in general practice.
Since 2002 he has led the MRC sponsored Cooperative Clinical
E-Science Framework (CLEF) consortium of seven UK universities, NHS trusts,
and Cancer Networks which aims to provide "joined up" information
solutions for clinical care and clinical and bioscience research in cancer.
>From 2003 he leads the JISC and EPSRC funded Co-ODE and HyOntUse
projects, working with Stanford University and Epistemics to create a new
platform for cooperative ontology development.
His work on clinical terminology and ontologies provided a
key stimulus for the technologies underpinning the use of ontologies for the
Semantic Web. He has been a visiting senior scientist at Stanford University
and consultant to the NHS
Information Authority, Hewlett Packard, the Mayo Clinic, and a variety of smaller companies. He is a
member of the JISC Committee for the Support of Research, the National Cancer
Research Institute Board for Bioinformatics, the Joint NHS/Higher Education
Forum on Informatics, and the Board of the Academic Forum of the UK Institute
for Health Informatics. He is also active in HL7, the main standards body for health informatics, and on
the board of HL7-UK.
He currently leads the CO-ODE and HyOntUse
projects developing user oriented ontology development environments under the
JISC and EPSRC Semantic Web and Autonomic Computing initiatives as well as the CLEF project,
developing secure and ethical methods to collect live patient record data in
research repositories, under the MRC eScience initiative.
Nigam Shah is a postdoctoral fellow with the National Center for Biomedical Ontology. He received his MBBS degree from M.S. University in India followed by a PhD in Integrative Biosciences from Penn State University. His thesis work was focused on developing formal methods for the representation, manipulation and integration of diverse biological data - such as gene expression, protein interactions & annotations - with prior biological knowledge for the purpose of evaluating alternative hypotheses. The prototype system is available at www.hybrow.org.
He has conducted tutorials on 'How to make and use ontologies in biomedicine' and lectures on the 'Uses of ontologies' in BMI courses at Stanford. His current research is focused on developing ontology-based reasoning applications in the biomedical sciences.