Citation:

Campia, I., C. Ives, C. WITTWEHR, AND S. Edwards. AOP Extended Ontology: A new approach to categorise AOP Key Events. OpenTox EU 2016, Rheinfelden, GERMANY, October 24 - 25, 2016.

Impact/Purpose:

This work describes efforts to expand the AOP ontology developed as part of the international AOP-KB effort via the incorporation of existing biological ontologies. This work is essential for the long-term sustainability of AOP development and use. First, the expert-derived AOPs housed in the AOP-KB must be identifiable by controlled terminology to promote interoperability among the different modules of the knowledgebase and to facilitate the emergence of AOP networks. Second, having key events tied to biological ontologies is necessary for the incorporation of computationally predicted AOPs derived from data mining of toxicological databases. Finally, having the key events within an AOP tied to formal biological ontologies will promote direct use of the AOP information by computational methods and should facilitate the development of computational models describing the AOPs and AOP networks.

Description:

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 result in poorly retrievable or cross-referenceable information, as well as inadequate support for computational inferencesThe 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 concepts and properties 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 (Entity-Quality relationships). 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, enhance AOP network interoperability, and facilitate computational reasoning. 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. It will also show hands-on examples of how ontologies will be applied to AOP and the new version of the AOP-KB Wiki.[This is an abstract or a proposed presentation and does not necessarily reflect EPA policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.]

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