High level programming environment system for protein structure data

Authors:
Yanchao Wang;Rajshekhar Sunderraman;Piyaphol Phoungphol
Affiliations:
Computer Science Department, Georgia State University, Atlanta, GA;Computer Science Department, Georgia State University, Atlanta, GA;Computer Science Department, Georgia State University, Atlanta, GA
Venue:
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Year:
2007

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Abstract

In this paper, we present an application system that extends the Object-Oriented Database (OODB) system by adding domain-specific layers to manage protein structure data. Protein-QL, a domain-specific query language, and Protein-OODB layers are added above the OODB. We have implemented this system for protein domain, but we can easily extend it into other biological domains to build a bio-OODBMS. We define protein's primary, secondary, and tertiary structures as internal data types to simplify queries in Protein-QL in such a way that the domain scientists can easily master the query language and formulate data requests. We use EyeDB as the base OODB to communicate with Protein-OODB. Our system uses Java RMI to return results back to the clients so that transactions can be conveniently executed by the clients.