A domain specific data management architecture for protein structure data.

In this paper, we propose an architecture that extends the Object-Oriented Database (OODB) system architecture by adding domain specific additional layers to manage protein structure data. The two layers introduced above OODB are Protein-QL, domain-specific query language and Protein-OODB, a domain-specific data layer. This architecture is designed specifically for the protein domain, but it is the first step in building a general Bio-OODBMS for biological applications. Three internal data types are defined for the primary, secondary, and tertiary protein structures, respectively, to simplify queries in Protein-QL. This enables the domain scientists to easily formulate data requests. We use lambda-DB as the back-end database to implement Protein-QL. Queries in Protein-QL are compiled into OQL which are then executed against the database. In order to make the underlying OODB system (lambda-DB) more powerful, we introduce additional constraints to check the integrity of protein data.