Review

gistfile1.txt

All criticized points were considered in the revision. I think the paper substantially improved. The distinction between `Kvik` and `Kvik Pathways` is made clear. A list of contributions makes it easier to follow the structure. I think you should consider putting the requirement analysis into a dedicated section.

I see nothing in the paper that gives me a reason to not approve it.

I have noticed two minor typos:
Abstract
Typo: Missing whitespace after sentence „Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.“
Implementation
Missing verb? „Kvik Pathways Cytoscape.js to create a pathway visualization from the list of nodes and edges and overlay the nodes on the pathway image.“
Apart from the paper, I have one comment on your response on my review w.r.t. the differences regarding the NIK paper. You stated that
"we removed the security since we believe that data should be publicly available, [...]"
I completely agree with the notion of open data. In my experience though, epidemiologists are often bound to contracts enforcing confidentiality of the data to protect the privacy of the subjects. Our project partners legally must not use a system, which does not allow for secure data handling.
This has no consequence for your paper at all, I just think that this is a observation from our collaboration with epidemiologists you might appreciate.