Open the NCI Thesaurus in Protégé 5.2.0

Biomedical researchers might find it challenging it open the ontology file of the NCI Thesaurus OBO Edition (NCIt), a core reference ontology for the cancer domain, even on computers with 8GB RAM. The huge size of the ontology file (417MB) triggers out-of-memory errors in Protégé, preventing ontology engineers from working with the file.

The root cause of the problem is the default heap size setting in Protégé‘s configuration. In olders versions (Protégé 3.x), the corresponding setting was available from the Protégé GUI under File > Preferences > Protege.lax, which has been changed from version 4, in which the user has to edit the Protege.lax file directly in a text editor [1].

In Protégé 5.2.0, however, there is no Protege.lax file anymore, and the setting can be changed in the Protege.l4j.ini configuration file in the Protégé installation directory instead. By increasing the heap size in this file, large OWL files can be opened in Protégé without running out of memory.


[1] Setting the Heap Size. Protege Wiki.