Biomedicine and bioinformatics databases (2020/2021)



Course code
4S004549
Credits
12
Coordinator
Carlo Combi
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, I semestre Carlo Combi

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Fundamentals of database systems Teoria 5 II semestre, I semestre Carlo Combi

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Fundamentals of database systems Lab. 1 II semestre, I semestre Carlo Combi

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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: Fundamentals of database systems - Theory
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- The relational data model: relational calculus, functional dependencies, normal forms and decompositions.
- Conceptual data modeling in UML (modelling non relational data)
- Object and object-relational databases: data model and query language of SQL 3, UML for modeling object oriented databases, mapping towards SQL3 3.
- Temporal databases: basic concepts, data models, query languages (TSQL2, SQL:2011).

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MM: Fundamentals of database systems Lab.
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- training on SQL 3 with postgreSQL

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MM: Biomedical and bioinformatic data management
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* Electronic Medical Record systems
* Temporal databases: advanced topics
* Temporal Clinical Databases
* Querying biomedical XML data: Xpath and Xquery
* Information retrieval techniques in Medicine

Assessment methods and criteria

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MM: Fundamentals of database systems Theory
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he 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.
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MM: Fundamentals of database systems Lab.
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See the description of the theory module

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MM: Biomedical and bioinformatic data management
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The exam consists of oral 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.