When taking about x-axis, y-axis and z-axis direction, you actually refer to the right, up and forward vectors which compose the basis of a matrix.
If you want to convert a coordinate system (e.g. from IFC) to the one of three.js, I highly recommend the following topic: Convert from one coordinate system to another?
I don’t know the conventions of IFC but three.js uses a right handed coordinate system with +Y up.