GDSII is a time honored format, used for data transfer of semiconductor physical layout between design tools, computers and mask fabricators. It is universally used and is the most frequently encountered file format in semiconductor work. GDSII was originally a format proprietary to GE Calma, before evolving into an industry standard.
GDSII format is a complete representation of a circuit with cells hierarchically placed on each fabrication layer. The format is binary and platform independent. Cells may contain geometrical objects such as polygons (2-dimensional boundaries), paths or other cells making the design hierarchical.
Databases for wafer level packaging or MCMs are limited in complexity, compared to the billion transistor interconnects common in contemporary wafers. Yet, they both rely on the same elements used to form cells, polygons, paths and arrays hierarchically forming cells and subcells.