Prototype Details

Prototyping to Improve the AOP-Wiki Data Model

The most recent prototype extends a series of AOP-Wiki data model prototyping efforts, which started in summer of 2022. These efforts were presented in a poster at the meeting in Montreal in July of 2024. The poster is available on FigShare at: Integrated Application and Transformation of the Adverse Outcome Pathway (AOP) Framework for Modeling Evidence and Advancing New Approach Methodologies (NAMs), doi: https://doi.org/10.6084/m9.figshare.26390980.v1.

M2AOP v1.0 This prototyping effort is fiscally supported by US-EPA and driven by a collaboration with the Methods2AOP initiative, an effort led by Clemens Wittwehr from the European Commission Joint Research Centre (JRC).

As outlined in the AOP Developer’s Handbook, AOPs link molecular initiating events triggered by a stressor to adverse outcomes through a sequence of linked Key Events. A Key Event describes a measurable change in a biological or physiological state. Within the production AOP-Wiki, all Key Events have a free text field for authors to describe how a Key Event was measured or detected. The data model prototyping work hosted on this site replaces the single free text field with a collections of methods data objects – including assays, study designs, and observations - to better describe how Key Events are measured in a structured manner. Adding more structure to methods information in the AOP-Wiki will enhance the computability of the information, which can help with identifying areas where better methods might be needed.

Links to the new method data objects and content that has been submitted by Methods2AOP stress testers is available on the Prototypes Landing Page.

To learn more about the Methods2AOP initiative, please visit the links below:

• Methods2AOP featured on the US National Toxicology Program Adverse Outcome Pathways page
• Poster presented at 2023 Society of Toxicology meeting Methods2AOP: An International Collaboration to Integrate Assay Annotations into the AOP Key Event Descriptions

The design and content of this EMOD protype site does not necessarily represent US EPA policy.

M2AOP v1.1

The top priority for this first round of stress testing is to evaluate the suitability of the data model for adding Methods information to the AOP-Wiki. We are interested in your feedback on the user interfaces and content submission processes, because we are planning to continue to iterate in this area, but we want to keep the focus on getting feedback on how well the new data objects support mapping evidence to AOPs through Key Events.

In this context, Methods broadly encompasses both assay and measurement information. We are currently using the term Observation to refer to contextualized measurements that can be linked to Key Events (KE). "Suitability of the data model" encompasses the data objects (assays, study designs, observations, etc), the relationships between those objects, and the properties on those objects.

Before starting, consider your goals.

• Are you interested in contributing Assays?
• Are you interested in adding Observations for a KE that you've alredy selected?
• Define a discrete set of information that you plan to submit – suggested scopes include:
  • A set of assays
  • Multiple observations from a single study that map to different Key Events
  • Multiple observations from different studies that map to the same Key Event

Importance of the Feedback Form

Your feedback is incredibly important and possibly more important than the details you submit to the prototype forms. Before you begin submitting information, read through the questions on the feedback form. Feel free to fill in the Feedback form while you are submitting content to the prototype.

Adding Assay information

If you are only interested in submitting information for Assays, but not intereested in submitting measurements collected with those assays that link to Key Events, you should start on the Assays Homepage. Keep in mind that there are other repositories and data bases that have been developed for storing assay information.

• As part of stress testing, what aspects of an assay are most critical for the AOP-Wiki?
• Are the existing Assay form fields adequate to capture information that is critical to support an AOP?

Adding Observational Information for a Key Event

You need to create a study design to hold the contextual information for the Observation that will be linked to the Key Event. After you've created the Observation, you'll have the option to link an Observation and a Key Event from the Study Design view. Observations also depend upon samples and assays. Since the workflow has not yet been fully optimized to enter all nested information within a single form, here are some details that are important to know in advance of submitting information.

1. Submitted references already in the prototype wiki will be available through a drop-down menu on both the assay and study design creation forms. There will be a button to link out to create a new reference and then return.
2. Similarly, samples that have already been submitted will be available through a drop-down menu on the observation creation form. There will be a button to link out to create a new sample and then return, but there's a risk of losing other information in the form. We recommend either:
   • adding samples before creating observations OR
   • create an observation, and then add the sample from the observation edit form
3. As indicated above, there is no way to add an observation without first creating a study design.