Databases for Bioinformatics

Aim

The aim of this course is to give a thorough introduction to the theoretical and practical issues underlying the design and implementation of modern biological database systems that are used in bioinformatics research. After the completion of the course you should:

• understand and be able to use important terminology in text-based information management in a correct way.
• be able to design a data model using EER diagrams.
• be able to design and use a relational database.
• understand the theory behind the relational model and how this affects good design of databases.
• understand which file structures in the database management system can be used to implement a database system.
• know the basic principles for indexing a database.
• understand which problems can occur when several users use the database and solutions to this.
• understand how a database can guarantee persistence of data och how this is solved using recovery and back-up.
• understand which problems can occur when a user needs to integrate information from different databases and solutions to this.

Content

Methods for storage of information: text, semi-structured data, data models, rules. Text: basic issues in information retrieval, conceptual models, file models, query mechanisms, ranking. Semi-structured data: conceptual model, query mechanisms. Data models: relational model, object-oriented model. Databases: General database management systems (DBMS). Methods for data modelling and database design. Physical database. Data structures for databases. Query language. Multiple user issues: transactions, concurrency control and recovery. Integration of biological databases.