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
Course URL: http://users.utu.fi/denshe/biodb
Course blog: biological database systems
Office hours: B6019, ICT at 15-18 on Wednesdays
Exam: Turku: February 27 at 9-12, B2039
Tampere: March 6 at 12-15, Histotechnology room
Lectures:

In Turku	Period II (four times): Tuesdays 10-12, classroom B2038(ICT), starting November 20 Period III (ten times): Mondays/Wednesdays 10-12, classroom B2039(ICT), starting January 9, 2008
In Tampere	Period II (two times): Thursdays 11-15, classroom Red Meeting Room, Finn-Medi 1; dates: 22.11 and 13.12 Period III (four times): Thursdays 11-16, classroom Histotechnology room, Finn-Medi 1; dates: 10.1, 7.2, 14.2, 21.2

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 Dec 12, 2007 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;
comparing performance of built databases;
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	ppt
2	Database concepts, overview of database design process, entity-relationship data model	ppt	Chapters 1 & 2 of [2] (use username/password specified in one of the emails or ask me for it)
3	E-R (cont.) model	ppt	Chapter 2 of [2], [5]
4	Relational data model, introduction to SQL	ppt	Chapter 3 of [2], any online SQL tutorial (e.g., w3schools, sqlzoo, 1keydata)
5	Introduction to SQL (cont.), SQLite Demo	ppt	Any online SQL tutorial (e.g., w3schools, sqlzoo, 1keydata); SQLite demonstration
6	XML and XML Schema	ppt	XML Schema tutorial, [3]
7	Design of biological database systems	ppt	[6]
8	Design of biological database systems (cont.)	ppt	[4], [7]
9	Entity-attribute-value (EAV) modeling	ppt	EAV/CR Model, [8]
10	Model organism databases	ppt	GMOD Project, [9], [10]
11	Web services, integrating biological databases	ppt.1 ppt.2	WABI, [11], [12]
12	Integration of biological data	ppt	[13], [1]
13	Analysis workflows, Taverna project	ppt.1 pdf.2m ppt.2s	[14]
14	Review lecture	ppt

Demo:

SQLite database engine (slides 187-192)

Literature

Slides
References in the end of slides
Books:
[1]   Bioinformatics: Managing Scientific Data by Lacroix & Critchlow, Morgan Kaufmann, 2003 (ISBN-10: 155860829X)
[2]   Database Systems Concepts, 5th edition by Silbershatz, Korth & Sudarshan, McGraw-Hill, 2005 (ISBN-10: 0072958863)
[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