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-...

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Bibliographic Details
Published in:2006 International Conference of the IEEE Engineering in Medicine and Biology Society 2006, p.5751-5754
Main Authors: Wang, Y., Sunderraman, R., Tian, H.
Format: Article
Language:English
Subjects:
Bioinformatics
Biology
Buildings
Conference management
Database languages
Domain Specific Object-Oriented DataBase
Information retrieval
Lambda-DB Constraint Language
Object oriented databases
Protein Query Language
Proteins
Relational databases
User interfaces
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Summary: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
ISSN:1557-170X
DOI:10.1109/IEMBS.2006.259892