InterMine includes a cost-based query optimiser that attempts to rewrite SQL queries to make use of precomputed tables. This involved parsing SQL strings into a Java representation, which is normally very fast but if multiple OR constraints are found in large queries can be slow.
There is a timeout to prevent query parsing from taking too long, if the time is exceeded a query will run as normal without possible optimisation. The default can be overridden by setting os.query.max-query-parse-time in *mine.properties to an integer value defining a number of milliseconds.
