Biomedicine and bioinformatics databases (2018/2019)



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
    Biomedical and bioinformatic data management 6 II semestre Carlo Combi

    Go to lesson schedule

    Fundamentals of database systems Teoria 5 I semestre Alberto Belussi

    Go to lesson schedule

    Fundamentals of database systems Lab. 1 I semestre Alberto Belussi

    Go to lesson schedule

    Learning outcomes

    Knowledge and understanding:
    The goal of this course is to provide the student with the knowledge and understanding of the theoretical, methodological and technological main concepts related to database systems and their use for the management of biomedical and bioinformatics data and information.

    Applying knowledge and understanding:
    The student will be able to a) define through a formal model the structure and the features of complex data collections; b) specify queries on complex data through different query languages; c) understand the advanced requirements for the management of biomedical information.

    Making judgements:
    The student will acquire the capability of autonomously evaluate different design options for complex systems, and of autonomously propose effective solutions in the application domain related to biomedicine and bioinformatics.

    Communication:
    The student will be also able to interact with different stakeholders in multidisciplinary teams, having different skills and backgrounds in biomedicine and bioinformatics.

    Lifelong learning skills:
    The student will acquire the capability of learning new methodologies and technologies related to data management and applying them in the biomedical/bioinformatics domain.

    Syllabus

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    MM: Biomedical and bioinformatic data management
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    * Temporal databases: advanced topics * Temporal Clinical Databases * Querying biomedical XML data: Xpath and Xquery * Electronic Medical Record systems * Information retrieval techniques (a survey)
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    MM: Fundamentals of database systems Teoria
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    - 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, mapping towards SLQ 3. - Spatio-Temporal databases: basic concepts, data models, query languages (TSQL2, Simple Feature Specification for SQL OGC). - Big data systems: Hadoop
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    MM: Fundamentals of database systems Lab.
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    - training on SQL 3 with postgreSQL - training on spatio-temporal queries with PostGIS

    Assessment methods and criteria

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    MM: Biomedical and bioinformatic data management
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    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.
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    MM: Fundamentals of database systems Teoria
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    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.
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    MM: Fundamentals of database systems Lab.
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    See the description of the theory module

    Reference books
    Activity Author Title Publisher Year ISBN Note
    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 Don Box, Aaron Skonnard, John Lam Essential XML: Oltre il Markup Addison Wesley 2001 8871921186
    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
    Fundamentals of database systems Teoria R. Elmasri, S. B. Navathe Fundamentals of Database Systems (Edizione 1) Addison-Wesley 1994 0805317481
    Fundamentals of database systems Teoria M. N. DeMers Fundamentals of Geographic Information Systems (Edizione 1) Jhon Wiley & sons, Inc. 1997 0471142840
    Fundamentals of database systems Teoria M. F. Worboys GIS: A Computing Perspective (Edizione 1) Taylor & Francis 1995 0748400656
    Fundamentals of database systems Teoria J. D. Ullman Principles of Database and Knowledge-base Systems Computer Science Press  
    Fundamentals of database systems Teoria P. Rigaux, M. Scholl and A. Voisard Spatial Databases with Application to GIS Morgan Kaufmann  
    Fundamentals of database systems Teoria C. Combi, E. Keravnou-Papailiou, Y. Shahar Temporal Information Systems in Medicine (Edizione 1) Springer 2010 978-1-4419-6542-4
    Fundamentals of database systems Teoria R. G. G. Cattell The Object Data Standard: ODMG 3.0 Morgan Kaufmann 2000 1-55860-64

    STUDENT MODULE EVALUATION - 2017/2018