§ Is GI track part of the body system?

 No, GI track is GI track, its part of the digestion System. You have other systems like

    Nerve systems

    Circulation systems

    Lymph systems

    Reproduction system

My middle school textbook at least saying all that. 

Is there a breathing system?

That would be at circulation system. Its not called breathing system.

Are there bones systems?

Like teeth and your spine? No, They are anatomy when you go to University to learn something about the body, they tell you its Skeleton study = anatomy, or physiology = biochemistry inside your body study. 

Why they separate the anatomy from the system study?

That is not exactly the correct way to say it, but I understand what you try to say. The skeleton is the entire body structure of the bone, holding you up to walk straight, to talk straight. Without skeleton, you will be flat and kneel on the ground crawling 24 hours.

So physiology is not the system neither?

If you mean the skeleton, no. Why you keep thinking the skeleton is the system. They are not the system. Physiology is your internal body many things. Bones are internal things too, except, you just really seeing it through, there are distinquishedly different.

Skeleton, is you go to gym nurse room, where they hang a skeleton there, at least I seen cartoon their nurse doctor has one of those in the room. 

I don't really understand the entire things DNA, bone, blood, muscle.

Flesh. Use flesh you know that words better in New Age. Bone, blood, flesh.