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AOP-Wiki 3.0 Workshop Recap and Path Forward

As previously shared here in July, the Society for the Advancement of Adverse Outcome Pathways hosted a workshop series to collect perspectives and input from AOP community stakeholders. The third and final session of the series will be held on Thursday, September 28th, 2023, 9:00-11:00 am EST (GMT -4:00).

During this final session, the AOP-Wiki development team will present connections between workshop topics and our vision for how a redesign of the AOP-Wiki data model and information workflows can address and accommodate ideas and challenges that have been presented by AOP community members. Following the recap presentation, there will be one hour of plenary discussion time.

To join the meeting, please click the link to: Register here!

Lastly, if you missed the earlier sessions or would simply like a refresher, the recordings have been posted to YouTube and can be accessed at the links below:

  • Session 1: July 26, 2023
    • Session 1a                                  View Presentations
      • AOP Networks
      • AOP Grouping and Tagging
      • Methods2AOP 
  • Session 2: August 16, 2023
    • Session 2a                                  View Presentations   
      • Mystery of ROS (reactive oxygen species)
        • Shihori Tanabe (0:00)
      • Umbrella Kes
      • Domain of Applicability
      • AOP-Wiki as Registry
      • Umbrella Key Events break out report (47:30)
      • Domain of Applicability break out report (52:35)
      • AOP-Wiki as a Registry break out report (57:00)  
    • Session 2b                                                  View Presentations       View Breakout Room Report 
      •  Unfortunately, due to technical problems, the opening comments and the presenters were not included in the recording.  
      • Interoperability
      • Re-envisioning the AOP Page
      • Emerging AOPs and Semantic Analysis
        • Nathan Pollesch (31:35)
      • Interoperability, break-out summary (00:40)
      • Emergent AOPs and semantic analysis, break-out summary (06:00)
      • Re-envisioning the AOP Page, break-out summary (11:15)

SAAOP 2023 Workshop Series

The Society for the Advancement of Adverse Outcome Pathways (SAAOP), is hosting a workshop webinar series to obtain perspectives and input from AOP community stakeholders in an effort to define the features and functions (requirements) to be implemented as part of AOP-Wiki 3.0, with as much specificity as possible. The dates, times and registration links for the workshops are below.

As workshop session topics take shape, this post will be updated with more details.

Please visit the AOP-Wiki Forum and propose or “pitch” ideas for features that you desire. Vote for the ideas to be discussed during the workshop sessions using the star and discussion features in the forum. 

Register for either proposed time for each session following the registration links.

  • Session 1: July 26, 2023
  • Session 2: August 16, 2023

AOP-Wiki Upgrade

New version of the Adverse Outcome Pathway Wiki (AOP-Wiki): More features, better help, updated concepts

  AOP-Wiki release 2.5, launched on 16 July, comes with a series of added functionalities, provides better access to background information, and rethinks the role of stressors.

The AOP-Wiki is the central web-based application for capturing, disseminating and reviewing Adverse Outcome Pathway (AOP) knowledge, both for AOPs on the official OECD work plan and AOPs spontaneously suggested and inserted by the scientific community. The OECD working group managing the AOP-Wiki is happy to announce the brand new AOP-Wiki version 2.5, which comes with lots of highlights:

  • Improved and seamless integration of OECD AOP guidance into the Wiki: The official “AOP Developers’ Handbook” is now an integral part of the AOP-Wiki, and context sensitive help is never far away. It is always possible to check under which version of the guidance a particular version of an AOP was developed, which is essential when endorsement and validity of an AOP are discussed.
  • Information about available AOP(-Wiki) training material is at the users’ fingertips: A new AOP Training page provides a summary of the online training options with links to the appropriate material.
  • The AOP-Wiki has opened its doors to third party tools: As the Wiki cannot possibly cover all functionalities that the stakeholder community might request, a series of pilot collaborations with outside software providers was initiated. Connections to their systems are now integrated into the AOP-Wiki: Novel ways of graphical AOP depictions, and support in identifying literature that strengthens the evidence behind AOP elements are now provided by third party tools. Based on these pilot experiences, more possibilities for such collaborations will be identified in the future.
  • The AOP-Wiki now reflects the fact that the AOP Framework is “stressor-agnostic”: AOPs are triggered by the interaction of a “stressor” (e.g. chemical, nanomaterial, radiation, virus, …) with the organism on molecular level, leading to the Molecular Initiating Event (MIE). The scope of the AOP Framework starts with the MIE and does not explicitly include the stressor - in other words, AOPs are “stressor-agnostic”. However, in the AOP-Wiki, it is possible to enumerate stressors that were used when the AOP evidence was collected. By emphasising the fact that these stressors are just “prototypical” examples, the false impression that the Wiki provides any kind of risk assessment concerning them is now avoided.
  • More structured information about the strategy with which an AOP was authored: Transparency about the way an AOP was assembled is of utmost importance: Stakeholders will trust – and ultimately apply in a regulatory context - AOP knowledge only when they can fully comprehend why, how and by who an AOP was put together. This need for traceability is now implemented with dedicated “strategy fields” in the Wiki in which AOP authors can provide information about their motivations when working on the AOP.
  • More structured information about Modulating Factors: Modulating factors are extrinsic or intrinsic variables that, while not a direct causal element of an AOP, influence the response to the perturbation(s) represented in the AOP. They can be factors that convey greater or lesser sensitivity, can result in more, or less, severe effects, can alter time to effect(s) etc. In the new AOP-Wiki, modulating factors information is now highlighted in tabular form allowing authors to give a precise overview of how, when and to what extent an AOP is influenced by such factors.
  • New features improve the user experience: Tables (AOPs, KEs, …) can now be sorted and filtered, which helps users to always have control of the aspects they want to see in the AOP-Wiki at any given moment.

The AOP-Wiki is in constant evolution. By the end of 2022, the next release is expected, which - among other things - will feature an improved licensing model for AOP-Wiki content, helping authors to protect their content while they are in the process of peer-reviewed publication.

Later (2023 to 2024) a series of more profound changes is foreseen, like better integration of test method information in the Wiki, better traceability of who exactly contributed which element to a particular AOP, and improved AOP visualisation. Based on the new strategy fields, systematic approaches will be incorporated into the AOP development process. The role of ontologies when naming AOP elements will be strengthened in order to better link the AOP Framework to neighbouring domains.

The AOP-Wiki currently features 390 AOPs, and it has 800 registered users, 280 of which with AOP authoring privileges. These numbers are constantly increasing, but the AOP-Wiki’s scalability allows for significant growth in the future.

The AOP Framework, which is steered by the OECD Extended Advisory Group for Molecular Screening and Toxicogenomics (EAGMST), aims at mechanistically describing toxicity as a series of Key Events that lead from an organism’s first molecular interaction with a stressor towards an Adverse Outcome like cancer, reproductive problems, or death. The framework’s central ICT system, the AOP-Wiki, is managed by the EAGMST AOP-KB subgroup in association with the Society for the Advancement of AOPs (SAAOP); members of the subgroup include staff from the European Commission Joint Research Centre (JRC), the United States Environmental Protection Agency (US EPA), Environment and Climate Change Canada (ECCC), the Organisation for Economic Cooperation and Development (OECD), the US Army Engineer Research and Development Center (ERDC), RTI International, Maastricht University, University Paris Cité, and others.

Greetings

Interested in Developing or Using AOPs, but not sure how to get started?

E-mail:  aopwiki@googlegroups.com and we will try to provide help.  Really, we will.  It's free.