The API is the tool to access information about the data at the Allen Institute.
General help information about the API is here:
http://help.brain-map.org/display/api/
Something that may help the novice user are these example queries for experiment metadata:
Examples are included for download of a list of ISH experiments (genes) for Developing Human Brain, Mouse Brain (adult), Developing Mouse Brain, and Human Brain ISH Autism Study.