title_body: What ebook format to choose?
upvoted_answer: I think epub3 is basically the standard format (especially now that Kindlegen is fairly well aligned with epub3 even though kindle doesn't support all features); what you have to decide is the toolchain to get the job done (especially regard to the editing process). You also have to decide whether you are going digital only or publishing digitally and print simultaneously. 
  
  I don't know what your content is or how many contributors or editors you will have. I also don't know your budget or what form your content currently is in; I assume it's in XML or in some SQL database. Maybe you'd be able to keep it in DITA http://en.wikipedia.org/wiki/Darwin_Information_Typing_Architecture .
   For collaborative XML Editing, you're talking about pretty pricey things; maybe you can have data input in a php/mysql form which later could be converted into custom HTML.  Even though this probably has a hefty price tag though it's easier to maintain. 
  
  The other option is a mobile app. I assume there are templates for multimedia book apps which you can purchase and customize. I generally shun those kinds of solutions, but depending on your content and audience, this might be attractive. Also, an app could connect to a constantly updated online db. 
  
  On android especially epub3 support on software seems to vary widely, and so apps tend to look more uniform across platforms. 
  
  I can't speak of compression or performance, but I'd wonder how you expect readers to browse through. Will they be starting by searching for the keyword? I guess you can stick some javascript up front for a reader-friendly search form. That means you'd need the ereader platform to support javascript.
  
  These are my superficial thoughts.