It is important that the mapping file is of a particular format. You get the correct format by downloading the file from http://www.geneontology.org/GO.current.annotations.shtml.
If you cannot find the file you are looking for there or you already have the information you need in a different file, you can create the mapping file if your file is in the format described in the next section.
The tabular file can be obtained from Source at Stanford http://genome-www5.stanford.edu/cgi-bin/source/sourceBatchSearch or must have the following format:
id \tab GO:#######GO:#######GO:#######...
The id in this file must be the same as the identifier in one of the columns in your data set. If you don't have the correct column in your data set, you can add one by using the Annotation Manager
1. Select Create mapping from tabular file from the File menu.
2. Select your tabular file and click Open
3. Type the name of the mapping file that is to be created. This file will automatically be placed in the <J-Express Pro>\resources\go\goassociations folder
4. Close the GO Tree window and open a new one. The newly created mapping file should now be available from the Mapping File combo box