Biological Database Systems, BIOI4330

MSc programme in Bioinformatics, University of Tampere/Turku

General Information

Lecturer: Denis Shestakov, email: firstname.lastname at utu dot fi
Course structure: lectures, project work, exam
Credits: 5 ECTS
Language: English
Lectures: Mondays at 12-14 in B4080 and Fridays at 10-12 in B2039; first lecture will be held on Friday, October 31, at 10-12 in B2039
Office hours: B6019, ICT at 15-18 on Mondays
Exam: December 12, 2008 (Friday) at 10-13, B2039; Example of exam questions
Course URL: http://users.utu.fi/denshe/biodb08
Course blog: biological database systems

Project work: See assignments
The project task is to design and build a database that combines data from several biological sources.
~~You may suggest your own project before Nov 7, 2008 by sending to my email the description of a database you interest to design and implement.~~
The project will include:

designing E-R, relational, and XML schemas;
writing data converters;
building relational and XML-based databases based on the corresponding schemas;
creating a program-friendly interfaces to databases.

Course Description

The course is devoted to database systems (existing and developing) designed for storing and accessing biological data with concentration on the database aspects of designing and managing biological data.

Course Content

	Topics	Slides	Suppl.Materials
1	Introduction	pdf (two slides per page)
2	Database concepts, overview of database design process	pdf	Chapters 1 of [2a] (use username/password specified in one of the emails or ask me for it)
3	Entity-Relationship data model	pdf	Chapter 2 of [2a], [5]
4	Relational data model, introduction to SQL	pdf (four slides per page)	Chapter 3 of [2a], Chapter 2 of [2b], any online SQL tutorial (e.g., w3schools, sqlzoo, 1keydata)
5	Introduction to SQL (cont.)	pdf	Any online SQL tutorial (e.g., w3schools, sqlzoo, 1keydata), [2a], [2b]
6	XML data model	pdf	XML Schema tutorial, [3]
7	SQLite Demo, Design of biological database systems	pdf	[6]
8	Design of biological database systems (cont.)	pdf	[4], [7]
9	Web services and analysis workflows, integration of biological data	pdf	WABI, [11], [12], [14], [15], [1], [13]
10	Review lecture, exam questions	pdf
*	Supplemental: model organism databases	pdf	GMOD Project, [9], [10]

Demo:

SQLite database engine (slides 265-269)

Literature

Slides plus references in the end of slides
Books:
[1]   Bioinformatics: Managing Scientific Data by Lacroix & Critchlow, Morgan Kaufmann, 2003 (ISBN-10: 155860829X)
[2a]   Database Systems Concepts, 5th edition by Silbershatz, Korth & Sudarshan, McGraw-Hill, 2005 (ISBN-10: 0072958863)
[2b]   Database Systems: The Complete Book, 2nd edition by Garcia-Molina, Ullman & Widom, Prentice-Hall, 2008 (ISBN-10: 0130319953)
[3]   XML Schema by Eric van der Vlist, O'Reilly Media, 2002 (ISBN-10: 0596002521)
Articles:
[4] Biological database design and implementation by Birney & Clamp (the Ensembl project), Briefings in Bioinformatics, 5(1):31-38, 2004

Supplementary:
[5]   Genomic data modeling by Chen & Carlis, Information Systems, 28(4):287-310, 2003
[6]   Designing databases to store biological information by Nelson et al., BIOSILICO, 1(4):134-142, 2003
[7]   Editorial: What makes a good database? by Batemen, NAR, 35(Database issue):D1-D2, 2007
[8]   Guidelines for the effective use of entity-attribute-value modeling for biomedical databases by Dinu & Nadkarni, Int.J. of Med.Informatics, 76(11-12), 769-779, 2007
[9]   The Generic Genome Browser: A Building Block for a Model Organism System Database by Stein et al., Genome Research, 12(10), 2002
[10]   A Chado case study: an ontology-based modular schema for representing genome-associated biological information by Mungall & Emmert, Bioinformatics, 23(13), 2007
[11]   Biological SOAP servers and web services provided by the public sequence data bank by Sugawara & Miyazaki, NAR, 31(13), 2003
[12]   Web Services at the European Bioinformatics Institute by Labarga et al., NAR, 35(Suppl 2), 2007
[13]   Integration of life science databases by Kohler, Drug Discovery Today: BIOSILICO, 2(2), 2004
[14]   Taverna: a tool for the composition and enactment of bioinformatics workflows by Oinn et al., Bioinformatics, 20(17), 2004
[15]   Integrating biological databases by Stein, Nature Reviews Genetics, 4(5), 337-345, 2003