The GenAlg Project: Developing a New Integrating Data Model, Language, and Tool for Managing and Querying Genomic Information

摘要

We have described the GenAlg project developing the Genomics Algebra as a new data model, language, and tool for representing, storing, retrieving, querying, and manipulating genomic information. Our integrated Genomics Algebra in conjunction with a DBMS will cause a fundamental change in the way biologists analyze genomics data and will allow them to pose questions using biological terms instead of low-level programs. Biologists should, and indeed want to invest their time being biologists, not computer scientists. Biologists are freed of the responsibility of managing their data and can concentrate on what they can do best, namely analyse the data. Due to the integration of genomic data types as abstract data types into databases and query languages, the Genomics Algebra can be embedded, for example, in a relational, object-relational, or object-oriented DBMS equipped with appropriate extensibility mechanisms throughout the whole system architecture. For example, in the case of a relational DBMS, our GDTs and their operations can be implemented as user-defined data types (UDTs) and functions (UDFs) inside a DBMS-specific adapter. We have defined an initial set of genomics data types and are in the process of identifying the corre-' spending operations and their semantics so that we can design suitable algorithms for their implementation. Our next goal is the implementation of the Genomics Algebra and its integration into a relational DBMS.