66557 - Biomedical Data Bases

Learning outcomes

At the end of the course, the student acquires expertise in designing, implementing and curating data bases. The student will also be trained on the major biologically and medically oriented public data bases and how to retrieve and extract information for problem solving. Major tools accessible from specific data bases will be also utilized in order to facilitate information retrieval and data analysis.

Course contents

Module 1 (3.5 CFU, 28 ore, docente: Prof. M. Paola Turina)

- Introduction to biomedical databases.

- Overview and training on the UniProt database.

- Overview and training on the molecular structure database PDB at RCSB. Training on molecular visualization software.

- Overview and training on the NCBI databases: Genbank, Refseq, dbSNP, Gene, PubMed/MeSH, OMIM.

- Overview and training on the EnsEMBL Genome database.

 

Module 2 (2.5 CFU, 20 ore, docente: Prof. Davide Salomoni)

- Introduction to databases; structure, contents, general features

- Relational databases

- Non-relational databases (including key-value and graph databases)

- Streaming biological data into databases

- How to programmatically interact with databases: data retrieval, annotation and analysis

- Create your own database

Readings/Bibliography

Online materials and other suggested readings will be indicated during the course.

Teaching methods

Lectures and hands-on activities.

 

Assessment methods

A written test, a personal project, and a final oral discussion.

Teaching tools

Slides of all lectures and hands-on sessions will be available.

Office hours

See the website of Maria Paola Turina

See the website of Davide Salomoni