CS 395 Architecture and Applications of Biological Databases

Prof. Daniel P. Miranker

Spring ‘02

Content:

Introduction:

A database management system (DBMS) comprises a collection of integrated services on a database. Clearly Biologists have assembled a myriad of databases. Yet, there are no biological database management systems. What is clear is that biological data that must have first class treatmentdoes not receive that treatment if stored in a relational database management system, (e.g. DNA and Protein sequences, molecular structure, phylogenies).

In this seminar class we will read papers that,

1. Speak to other efforts working to rationalize biological data.

2. More mature database models that may inspire innovation in biological data.

3. Applications of existing databases, as to understand the requirements of the domain.

Topical Areas:

I have not yet enumerated a set of papers for the class to read. A few possible papers and/or specific topics are listed among the topics so that those of you who considering registering for this class and would like to look deeper may do so.

1. Rationalizing Biological Data

· “Inverting the Database”, Lee and Parker, VLDB 91

· "A data tranforamtion system for biological data sources", Buneman, Davidson, Hart, Overton and Wong, VLDB 95

2. Other Database Models

· Temporal Sequence Databases

· XML – semi-structured databases

· Recursive query processing

· Graph databases

3. Applications

· Structure-based query languages

· Data-driven structure prediction

· Protein Identification

· Comparative Molecular Biology