The most important parameter influencing the performance is the number of database pages, which H2 can keep in the main memory. By default this value is set to 100000 pages of 8KB. To change this value, add the CACHE_SIZE option to the H2.URL.
H2.URL = jdbc:h2:file:data/edb;CACHE_SIZE=500000
Furthermore, you may change the following configuration values in OntoConfig.prp:
H2.TermCacheSize = 100000
These parameters set the cache size for the translation between term ids used in the database and term objects in OntoBroker. There are two caches, one used mainly for the first argument of predicates and one for all other arguments. If you have lots of main memory, you may increase these cache sizes.