Biomedicine and bioinformatics databases (2016/2017)



Course code
4S004549
Credits
12
Coordinator
Carlo Combi
Other available courses
Other available courses
    Academic sector
    ING-INF/05 - INFORMATION PROCESSING SYSTEMS
    Language of instruction
    English
    Teaching is organised as follows:
    Activity Credits Period Academic staff Timetable
    Fundamentals of database systems 6 I sem. Alberto Belussi
    Biomedical and bioinformatic data management 6 II sem. Carlo Combi

    Lesson timetable

    II sem.
    Activity Day Time Type Place Note
    Biomedical and bioinformatic data management Tuesday 11:30 AM - 1:30 PM lesson Lecture Hall G  
    Biomedical and bioinformatic data management Friday 11:30 AM - 2:30 PM lesson Lecture Hall G from Mar 24, 2017  to Jun 9, 2017
    Biomedical and bioinformatic data management Friday 2:30 PM - 3:30 PM lesson Lecture Hall G  
    I sem.
    Activity Day Time Type Place Note
    Fundamentals of database systems Wednesday 10:30 AM - 12:30 PM lesson Lecture Hall G from Oct 6, 2016  to Oct 11, 2016
    Fundamentals of database systems Wednesday 10:30 AM - 12:30 PM lesson Hall Verde from Oct 12, 2016  to Nov 11, 2016
    Fundamentals of database systems Wednesday 10:30 AM - 12:30 PM lesson Lecture Hall G from Nov 12, 2016  to Jan 31, 2017
    Fundamentals of database systems Friday 10:30 AM - 1:30 PM lesson Lecture Hall G  

    Learning outcomes

    This course provides students with the knowledge about the basic concepts of database systems and their application in the modeling and management of biomedical data and information. Students will be able to understand the needs related to the management of biomedical information and will be able to autonomously propose suitable solutions for these complex biomedical domains. Students will be able to interact with different stakeholders, within a multidisciplinary community. He will also be able to acquire and use knowledge about all the future advances both in methodologies and technologies for the management of data and their application in the biomedical domain.
    ------------------------
    MM: Fundamentals of database systems
    ------------------------
    This module of the course provides the student with the main theoretical concepts of the relational data model, of object and object-relational data models, and of the semistructured and XML data models. Related query languages will be introduced and some related technical issues will be discussed.
    ------------------------
    MM: Biomedical and bioinformatic data management
    ------------------------
    The main aim of this course is introducing the students to manage biomedical and bioinformatics databases. In particular, object-oriented modeling techniques will be considered, together with the management of semistructured data. Attention will be paid to information retrieval techniques.

    Syllabus

    ------------------------
    MM: Fundamentals of database systems
    ------------------------
    * The relational data model: relational calculus, functional dependencies, normal forms and decompositions.
    * Conceptual data modeling in UML
    * Object and object-relational databases: data model and query language of SQL 3, UML for modeling object oriented databases.
    * Semistructured databases: basic concepts, XML, XML Schema, UML for modeling semistructured datasets.
    * Spatio-Temporal databases: basic concepts, data models, query languages (TSQL2, Simple Feature Specification for SQL OGC).
    ------------------------
    MM: Biomedical and bioinformatics data management
    ------------------------
    * Temporal databases: advanced topics
    * Temporal Clinical Databases
    * Querying biomedical XML data: Xpath and Xquery
    * Electronic Medical Record systems
    * Information retrieval techniques (a survey)

    Assessment methods and criteria

    The final score of the exam is the average of the scores obtained in the exams related to the modules.
    ------------------------
    MM: Fundamentals of database systems
    ------------------------
    The exam for this module consists of a written test of about 2.5 hours containing: (i) some exercises requiring the specification of queries and database design using one of the database models included in the program and (ii) open questions about the theory. During the semester, in a date to be decided with the students, an intermediate test will be proposed on the part of the program regarding: the relational calculus, the functional dependencies and the normalization.
    ------------------------
    MM: Biomedical and bioinformatics data management
    ------------------------
    The exam consists of an oral examinations with exercises and questions related to the different parts of the module, with the goal of verifying whether the student is aware of the theoretical content of the module and is able to apply it in real-world contexts.

    Reference books
    Activity Author Title Publisher Year ISBN Note
    Fundamentals of database systems R. Elmasri, S. B. Navathe Fundamentals of Database Systems (Edizione 1) Addison-Wesley 1994 0805317481
    Fundamentals of database systems J. D. Ullman Principles of Database and Knowledge-base Systems Computer Science Press  
    Biomedical and bioinformatic data management S. Abiteboul, P. Buneman, D. Suciu Data on the Web: from relations to semistructured data and XML (Edizione 1) Morgan Kaufmann 1999 155860622X
    Biomedical and bioinformatic data management C. Combi, E. Keravnou-Papailiou, Y. Shahar Temporal Information Systems in Medicine (Edizione 1) Springer 2010 978-1-4419-6542-4

    Student opinions - 2016/2017