Bioinformatics databases Frank Olken   View Paper (PDF)   Return to Advanced Technology Seminars Abstract We are witnessing the industrialization of molecular biology research - its transformation over the past decade from manual cottage industry organization into large industrial scale automated, instrumented operations. This has resulted in an explosion of bioinformatics data (DNA sequences, protein structures, gene expression data) and databases, which will continue for the forseeable future. This explosion of data has generated demands for tools (and staff) to manage this data. The unusual nature of much of this data and queries has spawned new problems for database research and reignited interest in some old topics. The tutorial is intended to introduce database folk to database issues which arise in bioinformatics, i.e., molecular biology, genetics, and biochemistry. We will commence with a very brief introduction to molecular biology and genetics and the requisite vocabulary. However, this is NOT intended to be a biology tutorial, so attendees would be well advised to read a biology tutorial prior to attendence. We will be largely concerned with those data types, queries, and constraints which are frequently encountered in bioinformatics, but relatively unusual in conventional database applications. Specifically, we shall address the storage and retrieval of sequence data (DNA, RNA, and protein sequences), 3D protein structures, and biological pathways (metabolic, signaling, genetic control) and micro-array gene expression data. Less attention will be given to physical and genetic maps, taxonomies and phylogenies. We shall emphasis similarity-based queries for sequence and protein structure data. We shall also address issues of similarity and differential queries on pathway data. Brief mention will be made of LIMS (lab info. management) issues and scientific workflow management. We will conclude the technical portion with a brief overview of some of the issues in constructing federated biological DB and biological data warehouses. We will conclude with some pointers to major journals, conferences, standards efforts, professional societies, and funding sources for bioinformatics database research. DiSC'03 © 2003 Association for Computing Machinery