References added, the authors primarily used Open Babel but others were used in places.
Pull request https://github.com/MolSSI/QCSchema/pull/23 remains unmerged as of August 18, 2020, but I see the merge of connectivity in May of 2018. Thank you for spotting this, it is only in one example at this stage. Removed language about no agreed upon representation for bonding, and added in an example of equivalent bonding to the QCSChema JSON.
Added a comment to highlight that recent work has added support for the basis set exchange format.
Jupyter had already been cited (Thomas Kluyver, Benjamin Ragan-Kelley, Fernando Pérez, Brian Granger, Matthias Bussonnier, Jonathan Frederic, Kyle Kelley, Jessica Hamrick, Jason Grout, Sylvain Corlay, Paul Ivanov, Damián Avila, Safia Abdalla, Carol Willing, Jupyter development team. Jupyter Notebooks ? a publishing format for reproducible computational workflows. 87–90 In Positioning and Power in Academic Publishing: Players, Agents and Agendas. IOS Press, 2016), added citation to jupyter.org as well, added missing citations to JupyterLab, PubChem and ChemSpider, thank you for spotting these.
Added some further explanation of what a RESTful interface is to the first paragraph of "Flexible Data Server Platform"
It reuses a number of Python frameworks, it provides some capabilities that can be found in Django, while offering a smaller more focused codebase with more convenience functions than lower level frameworks such as Flask and FastAPI. Added a further sentence explaining some of these advantages such as authentication, HPC queuing integration, etc.
It is a simple ORM, added some text but at its core it maps from the underlying database modelto and from the RESTful API providing a clear separation from the RESTful endpoint code. They were mentioned in the text, added some additional detail to avoid vagueness.
This platform has been developed as a forward looking platform, and we chose to integrate with NERSC early on where containers have been available for some time in the form of Shifter. A little more detail added to highlight this choice, while the platform could be adapted to function without containers it is our belief that next generation supercomputers will offer first class support for containers.
ANI is mentioned in the third paragraph of the "Machine Learning" section, and cited there. A TorchANI paper has since been published, added that to the citations. Added Binder and QCArchive citations that were missing, thank you for pointing out the omissions.

Referee #2 (Report openly available here after publication of the article)