More and more journals require authors to make their data available, as an increasing trend to open science and reproducibility. If I want to use some data openly accessible that is linked to a publication, do I just need to cite the data source in my manuscript or will I also need to contact the authors to let them know I am using their data or to ask for permission?
The future of scholarly research will be based on open data to ensure accountability, transparency and independent replication (e.g. Warren et al, New Engl J Med 2016). Thus, we need to be ready for similar scenarios.
Do I just need to cite the data source in my manuscript or will I also need to contact the authors to let them know I am using their data or to ask for permission?
Unless there is an explicit policy you need to follow (quite uncommon indeed), you just need to provide the precise citation to what you accessed. However, contacting the authors could be a smart choice: they could provide you additional data or collaborate with you more actively.
You can, at your choice. It depends on whether it is required by the authors (that is unlikely given that the data is already public), and your intentions. Do you need their inputs beyond the public data? In that case, feel free to contact them.
Otherwise, just cite them (the data sets as well as their primary research paper that describes the data sets).
ONCE your paper is accepted for publication, you can send a copy of your paper indicating that you have used their data sets in your work. They will be delighted to hear that their data set has contributed for yet another research work. This will be a win-win, as they will read your paper, and you can become collaborators.