I'm creating a database for all human genes, bringing many disparate data sources together. I am using Hype to create a way to view the data for each gene. I'm making a generic Hype layout that I will then customize for each gene, if that makes any sense. When I have the generic layout, I use Perl to customize it for each gene (substituting folder name for gene name, and changing the names of the data files accessed, etc.). So, every gene will have its own Hype document/folder. Each document has a few scenes for each type of data being presented (and each of those has an HTML widget within it in which I use D3 to visualize the data).
So, say the scenes are: Publications, Disease Association, Pathways, etc.
It would be cleaner to have the HTML widgets named publications.html, diseases.html, pathways.html, etc.
It's not required, but it would make things easier down the road.
I hope that made some sense!