It's only just names... yEd uses the terms "node" and "edge" to refer to an "object" and a "connection line," respectively.
The terminology stems from graph theory (mathematics); but it's not dangerous at all ;-).
(Since there are so many different names one can think of instead of "node" and "edge" -- object, rectangle, box, element, vertex, point, etc. and arrow, connection, connection line, line, arc, etc. respectively -- yEd just sticks to the original ones.)