Unfortunately, at this time, the term enrichment tool and slimmer both suffer from timeout and load issues on their They are limited in the amount of work that they can accomplish before a timeout event occurs either on the client or server. Due to these limitations, the current tool is not really designed to work on sets beyond a certain size. Unfortunately, this size is hard to pinpoint: depending on input type, size, and database warmup, the results available may be very different. If you get a timeout error, or see a phrase like "Query execution was interrupted", you have probably reached the time resource limit.
In the fairly near future we'll be moving to a Galaxy based workflow system that will not have these same limitations in size and time. Until then, you may wish to take a look at other available third-party tools:
Or look at a tool like Ontologizer: