Integrating AOP-Knowledgebase components: Lessons learned from AOP-XML

Integrating AOP-Knowledgebase components: Lessons learned from AOP-XML, OpenTox Euro 2016

Ahmed Abdelaziz


Douglas Connect


Safety Scientist 


A glue for different components of the AOP Knowledgebase

The need for a mechanistic understanding of the toxicological pathways lead to the development of Adverse Outcome Pathway (AOP) program by OECD. AOPs are structural representations of biological key events initiatied by a stressor and leading to an adverse outcome. The AOP knowledgebase (http://aopkb.org) is an initiative by OECD to allow “close collaboration between the European Commission's Joint Research Centre (JRC), the United States Environmental Protection Agency (EPA), and the US Army Engineer Research & Development Center (ERDC)”. The involvement of multiple organizations in the large collaborative effort as well as the intention of allowing third parties to contribute and benefit from the AOP-KB platform, called for the development of an open standard for data exchange that can glue different component together (i.e., AOP-XML).

AOP-XML is sponsored by the JRC and aims to define a standard for data exchange between the AOP-KB modules, tracks the differences in data presentations between different KB modules, identify potential functionalities overlap between modules and results in the publication of XML Schema definition (XSD) that should be used by different stakeholders for AOP data exchange. The AOP-XML does not define ontologies for the vocabulary of different objects but uses the ones already available, it suggests how fields should be defined (not necessarily serialized) including the format and value restrictions.

In this presentation, the current stage of development of the AOP-XML will be discussed and the lessons learned from interacting with multiple partners within the international effort of AOP-KB will be highlighted.