Efficient incremental maintenance of derived relations and BLAST computations in bioinformatics data warehouses

Abstract

In the data driven field of bioinformatics, data warehouses have emerged as common solutions to facilitate data analysis. The uncertainty, complexity and change rate of biological data underscore the importance of capturing its evolution. To capture information about our database's evolution, we incorporate a temporal dimension in our data model, which we implement by means of lifespan timestamps attached to every tuple in the warehouse. This temporal information allows us to keep a full history of the warehouse and recreate any past version for purposes of auditing. Equally importantly, this information facilitates the incremental maintenance of the warehouse. We maintain the warehouse incrementally not only for relations derived by applying the standard relational operators but also for computed relations. In particular, we consider computed relations obtained through external BLAST sequence alignment computations, which are often identified as a bottleneck in the integrated warehouse maintenance process. Our experiments with subsets of protein sequences from the NCBI non-redundant database demonstrate at least 10-fold speedups for realistic target space size increases of 1% to 5%. © 2008 Springer-Verlag Berlin Heidelberg.