An active OODB system for Genome physical map assembly

摘要

In this paper, 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 this purpose, we have developed an overlap refinement hierarchy characterizing the types of overlap and ordering relationships between DNA fragments. Based on this model, we designed an associated set of inference operators to automate some of the contig assembly steps, such as inferring overlap information using transitivity rules. In order to realize this map inferencing approach and to take advantage of the modeling power offered by object-oriented database technology, we have developed an active object-oriented database (OODB) system, called Crystal, on the GemStone OODB. Crystal seamlessly integrates rule inferencing with object modeling and other typical database capabilities, thus avoiding the overhead in moving data between systems for rule processing and data management, and eliminating data mismatch in these different representations. We also discuss the implementation of the physical map assembly (PMA) tool on top of Crystal, which includes the realization of the genome information model and the map assembly inferencing process. PMA executes inferencing automatically, without explicitly having to initiate rule execution, and thus can respond to the incremental addition of new experimental data. In conclusion, we provide a walk-through example and several experimental results that demonstrate how our approach can be used to support physical contig assembly.