Keynote Speakers: Michael Ashburner and Eric M. Meslin

PSB 2006

Michael Ashburner Professor of Biology Department of Genetics, University of Cambridge & EMBL - EBI Hinxton, Cambridge, England.

Ontologies for biologists - A community model for the annotation of genomic data

The representation of biological knowledge in databases is a necessity for modern biomedical research. Historically, there has been very little collaboration or coordination between different database providers. Although many grandiose schemes for the "integration" of biological databases have been proposed over the years, none have been practical to the point of implementation. Yet the need for integration remains, as many biologists, both those at the bench and those who analyse data computationally, wish to integrate data from a diversity of sources. The Gene Ontology Consortium (GOC) began, some eight years ago, to develop a resource that could be used by both the model organism databases (e.g. FlyBase, WormBase, Mouse Genome Database, The Arabidopsis Information Resource) and the large "horizontal" databases (e.g. UniProt, GeneDB, TIGR Gene Index) as a standard for the annotation of gene products. The GOC now maintains several structured controlled vocabularies for the annotation of gene products. The first three of these are used for the annotation of gene products with respect to these domains: their molecular function, their cellular location and the biological processes in which they are involved. This database of over 18,000 terms is now used for the annotation of the gene products of all of the major experimental eukaryotes and many prokaryotes.

The philosophy of the GOC is now being extended to cover further domains of biological knowledge. Under the umbrella of "obo" (open biological ontologies) structured controlled vocabularies are now available, or are being developed, for sequence annotation, anatomies and development, cells and tissues, mouse pathology and experimental treatments. These developments are being greatly aided by the newly funded National Center for Biomedical Ontologies (cBIO).

In this talk I will discuss how the concept of ontologies can be used for the intelligent design of database schema, and for the development of common tools for data exchange. I will also discuss some of the major limitations of the current models of data representation used by the GO Consortium, and proposals that will make the design of ontologies for shared use both more flexible and powerful.

URLs:
http://www.geneontology.org/
http://obo.sourceforge.net/
http://bioontology.org/

Biography:
Michael Ashburner (1942-) is Professor of Biology at the University of Cambridge and is the former Joint-Head of the European Bioinformatics Institute (EBI).

He was educated at the Royal Grammar School, High Wycombe and the University of Cambridge, where he received his undergraduate degree (1964) and Ph.D. (1968), both in genetics. He then went to the California Institute of Technology as a postdoctoral fellow with Hershell Mitchell. In 1979, he returned to the Department of Genetics in Cambridge where he has been based since, as Assistant in Research, University Demonstrator, University Lecturer, Reader in Developmental Biology and Professor (Ad hominem) of Biology (since 1991). He has been Miller Professor at the University of California at Berkeley and visiting professor at the University of California Medical School, San Francisco; University of Crete, Greece; and University of Pavia, Italy. For the period 1994-2001 he was first Research Coordinator and then Joint-Head of the European Molecular Biology Laboratory - European Bioinformatics Institute at Hinxton, Cambridge. During this period he was on 50% leave from the University of Cambridge.

His major research interests are now the structure and evolution of genomes. Most of his research has been with the model organism Drosophila melanogaster, about which he has written the standard research text (Drosophila: A Laboratory Handbook, Cold Spring Harbor Press, New York, 1989, 2nd ed. 2005). His research has covered a range of subjects, from classical genetics, developmental biology, cytogenetics to evolution, at both molecular and organismal levels. He was a member of the consortium which recently sequenced the entire genome of this fly. He has had a strong interest in the provision of databases for biologists for about 15 years. He is a founder of FlyBase, a major database for researchers using Drosophila as a model organizer, and of the Gene Ontology Consortium, a project to provide infrastructure for biological databases by a defined taxonomy of gene function. Ashburner is a Fellow of the Royal Society of London and of the Academia Europeae; he is a foreign honorary member of the American Academy of Arts and Sciences, a member of the European Molecular Biology Organization, and past president of the British Genetical Society. He also is a Professorial Fellow of Churchill College, Cambridge.

Eric M. Meslin Director, Indiana University Center for Bioethics Assistant Dean for Bioethics, Indiana University School of Medicine Professor of Medicine, Medical & Molecular Genetics, and Philosophy

The Moral Status of U.S. Science and Science Policy: Lessons from the Stem Cell Research Wars

It has been more than seven years since the successful isolation and culturing of human embryonic stem cells (hESCs) by University of Wisconsin scientists. These results were followed by other phenomenal scientific breakthroughs, including the recent announcements that a human embryo had been successfully cloned and that techniques have been used to extract single cells from a blastocyst. As impressive as the science of hESC research, it takes a backseat to the ethics and policy debates that have arisen. In 1999 President Clinton's National Bioethics Advisory Commission recommended that federal government support should be provided for research that both created and used stem cells obtained from excess embryos, a recommendation rejected by the White House and the NIH in favor of a more conservative position in which only the use of ES cells would be eligible for federal funding. The current Bush administration adopted an even more conservative position: permitting research on a limited number of hESC lines produced prior to August 2001. Meanwhile the US Congress has been unable to pass a single piece of federal legislation-even one that enjoys near unanimous support in the US and abroad: banning of reproductive cloning: Why is this? Part of the problem can be explained by recognizing that the hESC research touches on sensitive moral issues. But this is more than a debate about the moral status of embryos. At its core, it is a debate about the proper role of science in society and how the White House and Congress acquire and use science advice when making science policy. Indeed, there is growing concern that science itself is under threat, especially when it touches on socially (or politically) sensitive topics. Science policy is becoming less about science and more about politics and policy. If true, the damaging implications for scientists and the scientific enterprise may be felt for years to come.

Biography:
Dr. Eric Meslin is Director of the Indiana University Center for Bioethics, Professor of Medicine, and of Medical and Molecular Genetics in the Indiana University School of Medicine, and Professor of Philosophy in the School of Liberal Arts. He is also Assistant Dean for Bioethics at the Indiana University School of Medicine.

He came to Indiana University in July 2001 from the U.S. National Bioethics Advisory Commission (NBAC), where he had been Executive Director since 1998. NBAC was appointed by President Bill Clinton in 1995, and was charged with advising the White House and the federal government on a range of bioethics issues including cloning, stem cell research, international clinical trials, and genetics studies.

Born in Canada, Dr. Meslin received his B.A. in Philosophy from York University (Toronto), and both his M.A. and Ph.D. from the Bioethics Program in Philosophy at the Kennedy Institute of Ethics, Georgetown University in Washington, D.C.

He has held academic positions at the University of Toronto and at the University of Oxford. From 1996-98 he was Program Director for Bioethics Research in the Ethical, Legal and Social Implications (ELSI) Research Program at the National Human Genome Research Institute in Bethesda, Maryland. He has authored (or co-authored) more than 80 articles and book chapters, with most focusing on various topics in research ethics and health policy. He has been a consultant to the World Health Organization, the US Observer Mission to UNESCO, the Canadian Institutes of Health Research and is a member of a number of advisory boards including the Board of Directors of the Canadian Stem Cell Network (of which he is also chair of the Ethics Committee).

His research interests include the ethics of research involving human subjects; the conduct of research and treatment in economically developing countries; the use of federal advisory committees as mechanisms for constructing public policy; the collection, storage, and use of human tissues for genetics research; stem cell research; and ethical and policy issues arising from the human genome project. He is also Co-Editor of the "Bioethics and the Humanities Series" published by Indiana University Press.