MoBIoS: A Metric-Space DBMS to Support Biological Discovery

MoBIoS is a specialized database management system whose storage manager is based on metric-space indexing, and whose query language entails biological data types. When relational database management systems are used to support biological data, important data types are relegated to blob and unstructured text fields. Consequently, even simple, but critical queries are executed by sequentially dumping the data to utilities outside the database. Metric-space indexing exploits the intrinsic clustering of a dataset without regard to a mapping of the data to a coordinate system. It is clear from an abundance of bioinformatic discoveries that biological data is not random and exhibits interesting structure with respect to clustering. Just as Geographic Information Systems have been enabled by spatial databases, we argue that Biological Information Systems will be enabled by metric-space databases. We show that both biological sequence data and mass-spectrometry protein signatures can be effe...

• Type: Conference
• Year: 2003
• Where: SSDBM
• Authors: Daniel P. Miranker, Weijia Xu, Rui Mao
• Keywords: Biological Data, Data Types, Database, Database Management Systems, SSDBM 2003