Karen L. Eilbeck , Ph.D.
Research Assistant Professor,
Department of Human Genetics

Contribution to Society

Bioinformatics is a branch of biological research that uses principles from mathematics and computer science to understand biological data. One bioinformatics technique is to develop ontologies to structure biological data in order to make it accessible to both people and computers. An ontology is a description of our knowledge about a subject. It contains the concepts and the relationships that hold between them. I am interested in developing ontologies and ontology-enabled software to enhance biological research—doing so is essential for analyzing and managing the massive volumes of genomic and health-care data that exist today.

Research Summary

I am a member of the Gene Ontology Consortium. As part of this project I am responsible for the development of the Sequence Ontology (SO), an ontology for describing genome annotations. Genome annotations combine biological sequence, the results of bioinformatics analyses, and the knowledge of human curators into models of gene structure. Despite their potential as a resource for such studies, to date genome annotations have proven difficult to use. A major reason for this has been the lack of community standards for describing them, which has resulted in the proliferation of arbitrary file formats and database schemas. The Sequence Ontology project aims to solve this problem by providing the means to unify the descriptions of genomic annotations. The SO project provides a standardized set of terms and relationships with which to label stretches of sequence; it therefore provides a community resource that will allow the standardization of genome annotation file formats, and model organism database schemas. This, in turn will facilitate the exchange and visualization of genome annotations as well as comparison of and computation upon their contents

The Gene Ontology (GO) is a related ontology that I am also involved with. GO is used to describe gene products. It is divided into three aspects, cellular location, biological process and molecular function. A gene product may be described by terms from each of the aspects. GO is used to describe what gene products do, e.g. the antennapedia gene encodes a protein with transcription factor activity, located in the nucleus, involved with the process of segment specification. The Sequence Ontology on the other hand is used to describe the structural features of the antennapedia gene, e.g. its transcripts, exons, UTRs, etc. Genome databases use both SO and GO to describe their genes and they naturally complement one another.

Recent Publications

The Gene Ontology Consortium. (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Research ;34:D322-D326.

Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M. (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biology.6(5):R44. Epub 2005 Apr 29.

Karen Eilbeck and Suzanna E. Lewis (2004) Sequence Ontology Annotation Guide. Comparative and Functional Genomics 5:642-647

Harris M.A. et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32 Database issue:D258-61

Venter J.C. et al. (2001) The Sequence of the Human Genome.Science 291, 1304 – 1351

Cornell M., Paton N. W., Wu S., Goble C., Miller C., Kirby P., Eilbeck K., Brass A., Oliver S. (2001) GIMS –A Data Warehouse for storage and analysis of genome sequence and functional data.2 nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001 ) pp15-22.

Paton, N.W., Khan S., Hayes A., Moussouni F., Brass A., Eilbeck K., Goble C.A., Hubbard S., Oliver S. (2000) Conceptual Modelling of Genomic Information. Bioinformatics 16, 548-557
Also selected for inclusion in the Yearbook of Medical Informatics 2002.

Karen Eilbeck, Andy Brass, Norman Paton, Charlie Hodgman. (1999) Interact: An object oriented protein-protein interaction database.ISMB 99Proceedings 87-94