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.
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References
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Wang, Y., Sunderraman, R., Phoungphol, P. (2007). High Level Programming Environment System for Protein Structure Data. In: Măndoiu, I., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2007. Lecture Notes in Computer Science(), vol 4463. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72031-7_20
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DOI: https://doi.org/10.1007/978-3-540-72031-7_20
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-72030-0
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