Browsing the ontology

Browsing the eNM ontology with BioPortal, AberOWL and Protégé

Authors: Linda Rieswijk, Friederike Ehrhart and Egon Willighagen, Maastricht University


The field of engineered nanomaterials is exponentially growing as well as the demand to assure the safe use of this type of materials. Nanomaterials are defined as being materials with at least one external dimension in the size range from approximately 1‐100 nm. Nanoparticles are objects with all three external dimensions at the nanoscale. Engineered nanomaterials can be used within a numerous amount of application such as:

1. In the design of pharmaceuticals specifically targeting organs or cells in the body such as cancer cells which also enhances the effectiveness of therapies.
2. To make materials such as cloth or cement stronger and lighter.
3. Use in electronics, as environmental remediation or clean‐up to bind with and neutralize toxins, for their anti‐bacterial function in cosmetics etc.

The primary objective of WP2 within the FP7 EU‐funded eNanoMapper (eNM) project is to develop and disseminate a comprehensive ontology for the nanosafety domain, encompassing nanomaterials and all information relating to their characterization, as well as information describing relevant experimental paradigms, biological interactions, safety indications and experimental paradigms.

The current version of the eNanoMapper ontology 1,2,3 is based on the re‐usage of 18 existing ontologies (e.g. NanoParticle Ontology, BioAssay Ontology, Experimental Factor Ontology) (full details can be found in reference [1]) together with specialized engineered nanomaterials and nanotechnology vocabularies and definitions, which have been described by several national and international standardization committees (e.g. International Organization for Standardization, Joint Research Centre).

The re‐used ontologies (OWL file) were made slimmer 4, if necessary modified using the free, open‐source ontology editor Protégé 5 and new terms were added using the Issue Tracker within GitHub 6,7,8 .

The eNM ontology might be accessed through three different ways, namely online via BioPortal 2,9 and AberOWL 3,10 or locally using the open‐source Protégé 5 software. This tutorial focusses on browsing through the eNM ontology when one would be interested in finding a Unique Resource Identifier (URI) for mapping a term originating from for example a database schema. Using URIs for database schemas will facilitate the harmonization of data originating from different sources and will make them more comparable.

In order to generate an ontology for engineered nanomaterials which is covering all domains also instructions are provided within this tutorial on which steps should be taken when a term is not present within the eNM ontology.

You can download the tutorial >> here << or see it in the preview window below.