Adverse Outcome Pathway Knowledge Base (AOP-KB)

Background

Adverse Outcome Pathways (AOPs)

An Adverse Outcome Pathway (AOP) is a conceptual framework that portrays existing knowledge concerning the linkage between two anchor points - the Molecular Initiating Event (MIE), and an Adverse Outcome (AO), connected by a chain of Key Events (KE) and the relationships between them (KER).

The Adverse Outcome Pathway Knowledge Base (AOP-KB)

To enable the scientific community, in one central location, to share, develop and discuss their AOP related knowledge, the OECD has launched a project to develop the "Adverse Outcome Pathway Knowledge Base" (AOP-KB). The AOP-KB allows all stakeholders to build AOPs by entering and then linking information about MIEs, KEs, AOs and Chemical Initiators. Knowing that pathway elements are not necessarily unique to a single AOP, value is added to existing knowledge by facilitating the re-use of MIE, KE and AO information in multiple AOPs, which prevents redundancy and make the collective knowledge about those entities available in all AOPs in which they appear.

The AOP-KB is a combination of individually developed platforms, synchronised and orchestrated in a way that gives users the possibility to capture, review, browse and comment on AOPs shared by the AOP stakeholder community.

The AOP-KB project brings these four independently developed platforms – AOP-Wiki, Effectopedia, AOP Xplorer and Intermediate Effects DB - together so that stakeholders can benefit from having a shared knowledge base. The four systems have quite different emphasis on the type of the captured information:

• The AOP-Wiki provides a system that organises, via crowd-sourcing, the available knowledge and published research into a verbal description of individual pathways, using a user friendly Wiki interface. Controlled-vocabulary drop-down lists from which to select Methods, Actions, Biological Objects, Life stages, Species etc. related to the AOP simplify the entry of ontology-based information. The AOP-Wiki is ready to be used!
• Effectopedia will be a modelling platform designed for collaborative development and utilization of AOPs. It uses visually expressed modular structure to capture semantically annotated knowledge and algorithms together with all the supporting evidences.
  A beta release of Effectopedia is currently available for testing.
• The Intermediate Effects DB will host chemical-related data (following the OECD Harmonised Templates (OHT) format), derived from non-apical endpoint methods, and inform how individual compounds trigger Molecular Initiating Events (MIE) and/or Key Events (KE). Cross-referencing these empirical observations with AOP descriptions within the AOP-KB will link directly to the underlying evidence supporting the AOPs. The Intermediate Effects DB is currently being developed.
• The AOP Xplorer is a computational tool that enables automated graphical representation of AOPs and networks among them. The Xplorer is currently being developed.

AOP-KB will offer the opportunity for third party software developers to connect to the Knowledge Base via the AOP-KB Hub. Application Programming Interfaces (API) and format standards are currently being developed.

All four modules (and potentially also compatible third party systems) will share, exchange and synchronise information via the AOP-KB Hub.

The AOP-KB project is an OECD initiative, which is executed as 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).