The formatting of the flat files accepted by BridgeDb is as follows:

• Each column for one ID type
• Each row except the first one represents IDs of different types mapping to each other
• First row contains the name of the ID type. This name is significant, especially if you wish to combine the flat file with other mapping sources in a stack. The name should be equal to the full name of the datasource.
• Multiple IDs are allowed to be contained in one cell (One to many mapping, or IDs of the same type maps to each other). Use special character (e.g., ';', '/', etc, or user defined) to separate IDs.

(See  http://tinyurl.com/mergesvn/testData/yeast_id_mapping.txt for an example).