Genomics Algebra: A New, Integrating Data Model, Language, and Tool for Processing and Querying Genomic Information

The dramatic increase of mostly semi-structured genomic data, their heterogeneity and high variety, and the increasing complexity of biological applications and methods mean that many and very important challenges in biology are now challenges in computing and here especially in databases. In contrast to the many query-driven approaches advocated in the literature, we propose a new integrating approach that is based on two fundamental pillars. The Genomics Algebra provides an extensible set of high-level genomic data types (GDTs) (e.g., genome, gene, chromosome, protein, nucleotide) together with a comprehensive collection of appropriate genomic functions (e.g., translate, transcribe, decode). The Unifying Database allows us to manage the semi-structured contents of publicly available genomic repositories and to transfer these data into GDT values. These values then serve as arguments of Genomics Algebra operations, which can be embedded into a DBMS query language.