ENanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.

Janna Hastings,Nina Jeliazkova,Christoph Steinbeck,Egon Willighagen,Cristian R Munteanu,Gareth Owen,Georgia Tsiliki

doi:10.1186/s13326-015-0005-5

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.

Highlights

Nanomaterials are materials in which the individual components are sized roughly in the 1-100 nanometer range in at least one dimension, an exact definition is still being debated [1,2]
Even dedicated ontologies such as the NanoParticle Ontology (NPO) need to be updated in the light of recent advances in the field of nanotechnology safety, including a growing diversity of novel nanomaterial types and new approaches to describing biological interactions
Much of the missing content that we have identified so far is in scope for one of the ontologies already targeted for import, e.g. the NPO, BioAssay Ontology (BAO) or Ontology for Biomedical Investigations (OBI), Chemical information ontology (CHEMINF), Chemical Entities of Biological Interest (ChEBI) or Chemical Methods Ontology (CHMO)

Summary

Introduction

Nanomaterials are materials in which the individual components are sized roughly in the 1-100 nanometer range in at least one dimension, an exact definition is still being debated [1,2]. Counterbalancing the many possible benefits of developed nanotechnology, nanoparticles 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. Safety requirements may vary under different conditions, e.g. when

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