Full description of KLayout database is in the API documentation. Here is a short summary.
Cell : Every structure that contains shapes or other cells inside is called a cell.
PCell : Every cell that is parameterizable and contains shapes, cells or PCells inside is called a PCell.
Shape : KLayout geometry primitive, such as point, box, line, polygon etc.
Point : The most basic Shape of KLayout. By using multiple points, it is possible to create Boxes and Polygons.
Macro : A script you can run in KLayout environment. Can use definitions from libraries. Can appear in KLayout GUI menus.
Chips : Chip corresponds to a single quantum circuit we can embed in the package for experimentation. Preferably implemented by a PCells, but some are manually drawn Cells.
Mask : Mask is an object used in optical lithography when producing an array of Chips onto a silicon wafer. If a physical mask is produced, exported design files are archived and code revision is tagged for traceability.
Top Cell : top_cell is the cell that works as a main container for the other cells and for instance masks can be thought of top cells that contain other Pcell structures such as pixels/chips.