Discussion  - 
Should I be using Ember Data for database for ember based web application? Can I use mongo db?
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Ember-data is for the client side for locally managing model data in your app. You can use different persistence storage mechanisms, although you might need to brower/write a custom adapter (I've done this for parts of my app to contect to a legacy API).

So yes you probably should be using ember-data. But do can mix and match. And you can always 'just' do Ajax calls and parse things yourself, but that will just make you appreciate the out of box experience. And I have seen references to ember data and mongodb.
If you're having problem understanding the difference between backend and frontend then you should really start with something more easier than ember.
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