Harnessing ontologies

eNanoMapper: Harnessing ontologies to enable data integration for nanomaterial risk assessment

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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.


Nanomaterials are materials in which the individual components are sized roughly in the 1-100 nanometer range in at least one dimension, although an exact definition is still being debated [1,2]. Particles in this size range display special properties having to do with their very large ratio of surface area to volume [3]. Natural nanomaterials include viral capsids and spider silk. Recent years have seen an explosion in the development of engineered nanomaterials (ENMs) aiming to exploit the special properties of these materials in various domains including biomedicine (e.g. as vehicles for drug delivery), optics and electronics [3].

Counterbalancing the many possible benefits of developed nanotechnology, nanoparticles also pose serious risks to human and environmental health [4]. Recognising these dangers, regulatory bodies are calling for systematic and thorough toxicological and safety investigations into ENMs with the objective of feeding knowledge into predictive tools which are able to assist researchers in designing safe nanomaterials. Evaluating and predicting the possible dangers of different nanomaterials requires assembling a wealth of information on those materials – the composition, shape and properties of the individual nanoparticles, their interactions with biological systems across different tissues and species, and their diffusion behaviour into the natural environment. These data are arising from different disciplines with highly heterogeneous requirements, methods, labelling and reporting practices. Regulatory descriptions of ENMs are not like those needed for nanoQSAR analyses. Safety requirements may also vary under different conditions, e.g. when developing vehicles for drug delivery in life-threatening diseases as compared to materials for use in the construction industry.

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. eNanoMapper aims to develop a comprehensive ontology and annotated database for the nanosafety domain to address the challenge of supporting the unified annotation of nanomaterials and their relevant biological properties, experimental model systems (e.g. cell lines), conditions, protocols, and data about their environmental impact. Rather than starting afresh, the developing ontology will build on existing work, integrating existing ontologies in a flexible pipeline. The establishment of a universal standardisation schema and infrastructure for nanomaterials safety assessment is a key project goal, which will support collaboration, integrated analysis, and discoveries from data organised within a knowledge-based framework.

In this paper, we survey the existing ontologies that were integrated into the unified eNanoMapper ontology, focusing on the challenges we experienced with the integration of diverse sources and our automated solution for seamless modular re-use of external content. Furthermore, we discuss challenges in the definition of key entities in the domain and give harmonised definitions for the core material and experimental entities in the domain.

Journal of Biomedical Semantics Sample (doi:10.1186/s13326-015-0005-)

AUTHORS:  Janna Hastings¹, Nina Jeliazkova², Gareth Owen¹, Georgia Tsiliki³, Cristian R Munteanu4,5, Christoph Steinbeck¹, Egon Willighagen5.

1 European Molecular Biology Laboratory – European Bioinformatics Institute
(EMBL-EBI), Cambridge, United Kingdom
2 IdeaConsult Ltd., 4.A.Kanchev str., Sofia, Bulgaria
3 National Technical University of Athens (NTUA), Athens, Greece
4 Computer Science Faculty, University of A Coruña, A Coruña, Spain
5 Department of Bioinformatics – BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands