The export of the protein search results is available in Tab-limited Text format. The downloaded file is appropiate for further manipulation in Excel as well. More details about the Search page here.
The Downloads page contains three kind of prepared datasets:
The full database of the current and previous releases is available on the Downloads page in SQL format.
Note that in the downloadable full database the nodes are identified by ComPPI IDs. These IDs are not stable, they may change in every release. If you use ComPPI to build a network, you may want to consider using the protein names as node IDs, otherwise networks of different ComPPI versions may not be compatible with each other.
The downloaded files are compressed using the Gzip package to improve the speed of the downloads.