A massive effort is underway to map the structure of the nervous system and to genetically dissect its function. Virtual Fly Brain (VFB; http://www.virtualflybrain.org) is a popular, OWL-based resource providing neuroinformatics support for this work. It provides: curated descriptions of brain regions and neurons; queries for neurons based on their relationship to gross neuroanatomy; and queries for reagents based on their expression patterns. Query results are enriched by OWL axiomatisation allowing basic mereological reasoning. To keep reasoning fast and scalable, VFB confines expressiveness to the EL profile of OWL. As a result, VFB does not provide queries involving negation, despite there being both demand and sufficient information to support them. Recent developments in reasoning technology may make more expressive queries practical. Here we present design patterns to support queries with negation that are compatible with the mereological reasoning used in VFB.
