S6: AOP extended Ontology
EC Joint Research Centre, Ispra, Italy
Scientific/technical support officer
The views expressed in this abstract or proposed presentation are purely those of the authors. They may not in any circumstances be regarded as an official position of the European Commission or any of its services and they do not necessarily reflect EPA policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.
The Adverse Outcome Pathway Knowledge Base (AOP- KB, http://aop-kb.org) is a crowdsourcing multi-module platform aimed to support the collaborative development, sharing, and dissemination of AOP-related knowledge. The AOP- KB Wiki module provides a user-friendly interface for AOP development with a series of closed vocabulary and free text fields to describe mechanistically linked events at different level of biological organisation leading to adverse health or ecotoxicological effects. Modularity of the AOP elements, such as key events (KEs), is a key feature that promotes the reuse of key events and resulting emergence of AOP networks. Currently, however, the increasing number of AOPs in the Wiki and lack of controlled vocabularies for naming these KEs results in poorly retrievable or cross-referenceable information.
The AOP-KB project is currently undergoing a joint effort to incorporate ontology-based information in a harmonised way across all modules (Oki et al, Curr Environ Health Rep, 2016; Edwards at al, J Pharmacol Exp Ther, 2016). For this purpose, a core ontology has been developed that allows the components of the AOP to be described in terms of entities from existing biological ontologies (https://github.com/DataSciBurgoon/aop-ontology).
To provide a controlled vocabulary for naming KEs that will improve the reuse of KEs and identification of similar KEs, the AOP-KB Wiki will introduce the possibility to "tag" KEs with ontology terms. Together with their verbal extensive description, KEs will feature standardised terms describing additional properties: process, object, action and context. This tagging approach will facilitate the use of appropriate controlled vocabularies from a set of suitable existing biomedical ontologies and in accordance with the level of biological organisation of each event. Overall, the use of ontology driven information to describe AOP KEs will play a key role in promoting the systematic reuse of AOP elements to streamline multi-party AOPs development and enhance AOP network interoperability. Furthermore, use of standard naming will also facilitate AOP application in regulatory context.
The presentation will cover the scientific background of AOPs, the AOP-KB and the ontology effort and will also show hands-on examples of how ontologies will be applied to and AOP the new version of the AOP-KB Wiki.