Most manufacturers of embroidery machines and publishers of needlecraft books such as DMC are marketing their own collection of threads. A specific thread may be uniquely identified by a colour-ID, or a colour name, both of which are manufacturer specific.
There is no fundamental difference between hand embroidery thread, machine embroidery thread, or any other sewing thread for that matter.
Proprietary embroidery file formats such as Brothers PES implicitly refer to the manufacturers's thread palettes. Therefor every embroidery file conversion software must also be able to do thread conversion.
Home embroiderers are sometimes intimidated by thread conversion, thinking it to be some kind of magical science of its own. The only way to get out of thread hell is to standardize the relevant thread parameters, such as thread color, thickness, etc. The BLF is currently working on an open standard known as YarnML.