Admission requirements
Not applicable
Description
This course explores the use, reuse and reproducibility of data in biomedical science. Biomedical data exists in large and ever-growing distributed data repositories. Generally, it is produced to answer a specific research question, but it can be reused and integrated to find new insights. As the amount and variety of biological data grows, we face new challenges in recording, publishing and sharing scientific results in a way that will allow further integration and exploitation. Consequently, data integration, management and reuse are central concerns in bioinformatics.
The FAIR data principles, which state that data should be Findable, Accessible, Interoperable and Reusable, provide a conceptual framework for enabling easier discovery and reuse of biomedical data.
The course will cover 1) the principles and applications of FAIR data (i.e. that data should be Findable, Accessible, Interoperable and Reusable), 2) the use of semantic web tools and technologies which facilitate making data FAIR (i.e. standards, ontologies and knowledgebases), 3) the importance of provenance in FAIR data collection, analysis and aggregation, and 4) computational methods to improve reuse and also reusability in science.
Course objectives
Make use of global public bioinformatics data resources, identifying and linking data to answer biomedical research questions
Explain the FAIR data principles (i.e. that data should be Findable, Accessible, Interoperable and Reusable) and the role FAIR plays in data reuse in bioinformatics
Explain the role of ontologies and the semantic web in FAIR data integration
Explain the role of workflows in reproducible and FAIR analyses
Discriminate between different data collection and management approaches
Timetable
To access the timetables for all courses and degree programs at Leiden University, please use the [MyTimetable] (https://rooster.universiteitleiden.nl/schedule) tool (login required). Any teaching activities that you have successfully registered for in MyStudyMap will automatically be displayed in MyTimetable. Additionally, any timetables you manually add will be saved and shown the next time you log in.
MyTimetable offers the convenience of integrating your timetable with popular calendar apps such as Outlook, Google Calendar, Apple Calendar, and other smartphone calendar apps. Any changes made to the timetable will be automatically synced with your calendar. If desired, you can enable email notifications for timetable changes in the "Settings" section (after logging in).
For more information, please watch the instructional video or visit the "help-page" within MyTimetable. Note that Joint Degree students from Leiden/Delft will need to merge their two separate timetables into one. A video tutorial is available to guide you through the merging process.
Mode of instruction
Lectures
Practical classes
Presentations
Assessment Method
Two practical assignments (30% and 40%)
Practical classes (10%)
Presentation (20%)
Students are required to pass each element of the assessment with at least a 5.5
Reading list
- Scientific papers from journals and conferences
Registration
All students have to register for courses with the enrollment tool MyStudyMap. There are two registration periods per year: registration for the fall semester opens in July and registration for the spring semester opens in December. Please see this page for more information.
Please note that it is compulsory to preregister your participation for every exam and retake. Not being registered for a course means that you are not allowed to participate in the final exam of the course.
Extensive FAQ's on MyStudymap can be found here.
Contact
Coordinator: Dr. K.J. Wolstencroft
Email: k.j.wolstencroft@liacs.leidenuniv.nl