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Harmonised terminology, ontologies development and semantic annotation

Semantic annotation of data and generally of scientific output across all areas of nanosafety and nanoinformatics still requires large effort to define and build the required terminologies/ontologies, to provide the support infrastructure for data input and curation and also training to foster general uptake. Many different competences (domain experts, ontology experts, software development experts,…) are needed and many tools have to be made available to support the ontology development as well as then the users willing to annotate their data, protocols and standard operation procedures, results and publications all leading to more open science and FAIRness. To help all stakeholders understand their roles and how to communicate with each other, this area of the user handbook provides general introductions, tutorials and training materials as well as links to a collaborative research platform for terminology development.

Table of contents

The Ontology universe

First, it is important to place yourself into the ontology universe. Are you a data produced who wants to annotate your data, a domain expert who wants to provide your expertise to clearly define the terms or an ontology developer in the nano or neighbouring area.

Annotate your science Create a defined terminology with clear definitions Create semantic relationships to improve the ontologies Organise and harmonise ontologies within and across disciplines (to be established)

The Ontology universe: Click on one area to view relevant guidance and tools.

Nanosafety-specific ontologies and project contributions

This section includes information on specific nanosafety ontologies or ontology development projects.

eNanoMapper

The eNanoMapper ontology is one of the largest collections of nanosafety and nanoinformatics terminology. It was developed first in the eNanoMapper project and is now maintained and extended by the NanoCommons and NanoSolveIT projects and supported by many other projects providing new terms and community-agreed definitions.

An introduction to the ontology is available in this short video:

ACEnano

Due to its focus on physico-chemical characterisation, the ACEnano project collected terminology specifically in this area and proposed it to be added to the eNanoMapper ontology.

Guidance and tools

For data producers and curators annotating data

Semantic annotation is needed for understanding and evaluating the data as well as finding, accessing and integrating it in a more automatic way. Nanosafety and nanoinformatics produce many different types of data, all needing specific terminology for their annotation. Currently no single ontology is able to cover all these areas. Therefore, multiple ontologies have to be used for the time being, which, fortunately, follow similar concepts with respect to searching and using of terms. Training material was generated for the eNanoMapper ontology, which is generally helpful when annotating data.

The eNanoMapper ontology can be accessed through three different ways, namely online via BioPortal and AberOWL or locally using the open-source Protégé software.

BioPortal is also useful to search across many different ontologies in the life sciences:

Put this all into action

Have a look at the NanoCommons Workshop “Annotating Your Experimental Data Workshop” by Egon Willighagen providing hands-on training to participants in how to enrich their (published) data to give it more impact, by linking the description of the experimental data to community terminology (ontology terms) and making their research articles findable to other researchers.

For domain experts generating harmonised terminologies including clear definitions

The most time consuming part of ontology development is the collection of the needed terms and agree on the preferred synonym and clear definition. This is done in different projects as described above. However, with the tools described here, everybody is able to participate and provide expert knowledge.

EU NanoSafety Terminology Harmonizer (also known as GRACIOUS WIKI)

Provided by the GRACIOUS project this is a tool to work collaboratively on a collection of well defined terms to be used across the complete nanosafety community. Separate but harmonised areas exist at the moment for physicochemical characterisation, nanoinformatics and simulations, bio-nano interactions, Safe-by-Design, regulation and manufacturing. More areas can always be added. Everyone is welcome to contribute to these area. Besides these public areas, also project specific areas exist. EU NanoSafety Terminology Harmonizer

For ontology developments integrating collections of terms into a semantic model