Physical Map Assembler: an active OODB system for human genome applications

We describe the design and implementation of a scientific database for the map assembly tasks performed by the geneticists at the University of Michigan Human Genome Center. Our system manages complex genomic data and supports the automation of the associated map assembly tasks. For the former, we present a genomic object model that integrates both experimental and derived data. For the latter, we describe operators to automate some of the analysis steps. To develop a framework for implementing our rule-based approach to physical mapping, we have designed and implemented an active object-oriented database (OODB) system, called Crystal, on GemStone. Crystal seamlessly integrates inference capabilities with complex object modeling and other typical database capabilities as required for physical mapping. We also discuss the implementation of a physical map assembly tool on top of Crystal. In conclusion, we provide a walk-through example that demonstrates how our approach can be used to effectively support physical contig assembly