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I am thinking and exploring options on designing database for my new application. In general, I will have registered users and info about them. They will be able to do some things in app and that data will be in the sam DB as users data (so I can have FK's shared and stuff)

But, then I plan to have second database that will be in logic totally independent of the first database except it will share userID as FK.

I don't know should I even put that second logic in an extra DB or should I have everything in the same database. I plan to have subdomain in my app for second logic (it is like app in app) but what if I discover they should share more data? Will that cross querying drop my peformances? And is that a way to go actually, is there a real reason to separate databases ?

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As soon as you have two databases you have potential complexity. You have not given any particular reason why you need two databases. So keep it simple until you have a reason.

An example of what folks do: have a "current" database, small, holding just the data needed right now. That might be where orders are taken and fulfilled. Once the data is no longer current, say some days or weeks after the order is filled move the data to a "historic" database. There marketing and mangement folks can look at overall trends in the history without affecting performance of the "current" database, whose performance might be critical to keeping your customers happy.

As an example of complexity: any time you have two databases you need to consider consistency between them, this is much harder to ensure than it might appear. Databases do offer Two-Phase Transactional capabilities, or you can devise batch processes but there are always subtleties that are hard to catch.

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I would just keep all in one database. Unless you have dozens of tables there should be no real performance problems, imho. It will however facilitate your life greatly, only having to work with one database connection & not having to worry about merging information from two queries,

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Also agree that unless volume of your data is going to be huge (judging by the question, doesn't seem like that is the case here), you can use single database to store your data without performance issues.

For "visual" separation of data structure, you can always create tables in two schemas of single database.

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