module 21: Github, GDPR and research data management

module 21: Github, GDPR and research data management

  • module 21: Github, GDPR and research data management
    9:30 am - 5:00 pm
    Mon 16/09: 9.30 am - 5.00 pm | S8 room 2.036

Course details

week 2


"Reproducibility in Biomedical Natural Language Processing: Challenges and opportunities" Rigor and reproducibility of biomedical research has been the topic of much debate in recent years. While the increasing complexity of computational environment creates new challenges for reproducibility, cases of replication failures lead to a lack of confidence in published findings. This lecture will review a few examples of reproducibility challenges in Biomedical Natural Language Processing. We will subsequently analyze these experiences to understand what challenges impact reproducibility and which methods can be leveraged to learn from them.
"Tools for Reproducibility & Collaborative Information Management: an introduction to Git."
Reproducibility is challenging in today's complex computational and collaborative environment. This tutorial will present version control, a systematic method for managing and tracking changes to documents, computer programs and other collections of information. After a brief overview of different version control methods and tools, a particular version control system will be presented into more details, with practical exercises to learn the basics of Git.

This section on GDPR will focus on the implementation of privacy and GDPR throughout the entire research life cycle.
Starting off by setting out the main aspects of the GDPR that should be considered when assessing privacy aspects in a research project, such as the importance of the legal difference between anonymous data and pseudonymised data. This course then continues by analyzing the legal grounds for processing under GDPR such as consent and public interest. Special attention will be given to the legal framework for data collection and its implications for both researchers and the involved data subjects. After this, a set of tools will be explained that could help to enhance data security and what to do in case of a data breach. Considering that researchers will somehow encounter publication and archiving during their career, this presentation will conclude by offering an outline on the legal aspects of this area and why it is important to ensure compliance. This course will be open for questions from the audience and participants will be fully encouraged to engage in the debate by asking GDPR questions that may rise in their field of expertise.

Course structure

An interactive lecture on the general topic and a tutorial on git combined with a practical hands-on session.


No specific background required.


Aurélie Névéol is a Senior Staff Scientist at the Centre National pour la Recherche Scientifique (CNRS, LIMSI). She received an MSc in Linguistics in 2002 and a PhD in Computer Science in 2005. She has more than 10 years experience in biomedical Natural Language Processing Research and has addressed the analysis of biomedical text from the literature and from Electronic Health Records in French and in English. Recently, she has been focusing on clinical NLP for languages other than English. She has contributed to the development of representations of clinical information to support information extraction from EHR text, which can then be used for high throughput phenotyping. In the course of her work she has also contributed to the evaluation of research methods and workflows through her participation in the H2020 MiRoR project and international evaluation campaigns such as CLEF and WMT.

Hanne Elsen graduated in legal practice in Diepenbeek, Master in Laws in Antwerp and Master of Laws in Notarial Law in Ghent.
In 2016 she started her professional career as a business lawyer at Hasselt University, focusing on the legal aspects of academic research. While doing so, she developed a particular interest and expertise in ethics, integrity and privacy. She therefore continued her career at Ghent University, where she is currently appointed as Data Protection Officer. She has also been assigned as an independent Ethics Expert to the European Commission and is an avid member of several working groups concerning privacy and ethics, such as the Flemish Interuniversity Council (VLIR) on GDPR.


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