Engineered nanomaterials (ENMs) are being developed to meet specific needs in diverse domains across the engineering and biomedical sciences drug delivery). However, accompanying the exciting proliferation of nanomaterials is a challenging race to understand and predict their detrimental effects on human health and the environment. The eNanoMapper (www.enanomapper.net) is creating a pan-European computational toxicological data management for ENMs, based on semantic web standards ontologies. Here, we describe the development of the eNanoMapper on adopting and extending existing ontologies of relevance for the domain. The resulting eNanoMapper ontology is available at http://purl.enanomapper.net/onto/enanomapper.owl. We aim to make the re- external ontology content seamless and thus we have developed a library automate the extraction of subsets of ontology content and the assembly subsets into an integrated whole. The library is available (open source) http://github.com/enanomapper/slimmer/. Finally, we give a comprehensive of the domain content and identify gap areas. ENM safety is at the between engineering and the life sciences, and at the boundary between granularity and bulk granularity. This creates challenges for the key entities in the domain, which we also discuss.