title: eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.
abstract: Engineered nanomaterials (ENMs) are being developed to meet specific application needs in diverse domains across the engineering and biomedical sciences (e.g. drug delivery). However, accompanying the exciting proliferation of novel nanomaterials is a challenging race to understand and predict their possibly detrimental effects on human health and the environment. The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. Here, we describe the development of the eNanoMapper ontology based on adopting and extending existing ontologies of relevance for the nanosafety domain. The resulting eNanoMapper ontology is available at http://purl.enanomapper.net/onto/enanomapper.owl. We aim to make the re-use of external ontology content seamless and thus we have developed a library to automate the extraction of subsets of ontology content and the assembly of the subsets into an integrated whole. The library is available (open source) at http://github.com/enanomapper/slimmer/. Finally, we give a comprehensive survey of the domain content and identify gap areas. ENM safety is at the boundary between engineering and the life sciences, and at the boundary between molecular granularity and bulk granularity. This creates challenges for the definition of key entities in the domain, which we also discuss.
authors: European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom.
authors: Janna
authors: J
authors: Hastings
authors: IdeaConsult Ltd., 4.A.Kanchev str., Sofia, Bulgaria.
authors: Nina
authors: N
authors: Jeliazkova
authors: European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom.
authors: Gareth
authors: G
authors: Owen
authors: National Technical University of Athens (NTUA), Athens, Greece.
authors: Georgia
authors: G
authors: Tsiliki
authors: Computer Science Faculty, University of A Coruña, A Coruña, Spain ; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.
authors: Cristian R
authors: CR
authors: Munteanu
authors: European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom.
authors: Christoph
authors: C
authors: Steinbeck
authors: Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.
authors: Egon
authors: E
authors: Willighagen
keywords: Nanomaterial; Ontology; Safety