I am working with your latest released (https://aopwiki.org/downloads/aop-wiki-xml-2022-01-01.gz) dump and I've noticed missing or different information in it when compared to your website.

As an example, the AOP nº 69(https://aopwiki.org/aops/69#taxonomic_applicability) lists to be applicable on rats and humans.
On the XML, this AOP ID only has a taxonomic reference:

"<taxonomy-reference id="3cf5bab0-bfa0-48db-9347-ebd8fdbaea9e" aop-wiki-id="69"/>"

pointing to rats:
```
<taxonomy id="3cf5bab0-bfa0-48db-9347-ebd8fdbaea9e">
    <source-id>10116</source-id>
    <source>NCBI</source>
    <name>rats</name>
```

Another example is AOP nº 202(https://aopwiki.org/aops/202#taxonomic_applicability)for which there is no taxonomic reference at all in the XML whereas the webpage says it has humans applicability.

Could you please tell me if I am processing the data in an incorrect way or what is the source of this difference?


Many thanks for your help.
Best,
Irene López

I have created a new thread for forum users to identify issues for the gardeners to look into:

The ultimate goal of the AOP framework is to mechanistically explain and depict toxicity in a way that allows New Approach Methods (NAMs) to detect and measure AOP Key Events so that that their results be accepted in regulatory contexts – which in turn will lead to a better association of stressor chemicals to the AOPs they are involved in. AOP Key Events must be measurable and detectable in order to play a role in an AOP. That is also the reason why there is a free text section "How it is measured or detected" on the Key Event page (e.g. https://aopwiki.org/events/265#measured). However, in this current free text form, the AOP-Wiki does not focus enough on the role of relevant test methods, which makes the desired association between chemicals and AOPs scientifically difficult, and impossible in a regulatory context.

The international project Methods2AOP is currently addressing these issues, and the team envisions:

- A change to the AOP-Wiki data model and functionality reflecting the importance of test methods,
- ways to open the AOP framework up to the test method developers community,
- and plans to incorporate the suggestions into the OECD plans for the AOP program.

The attached PowerPoint Slides (PDF) give a short introduction to the Methods2AOP project.

Attached Files

  Methods2AOP overview.pdf (Size: 1.01 MB / Downloads: 0)

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, currently the AOP-Wiki includes a data object “Stressor”. This needs to be addressed by de-emphasising the role of stressors in the AOP-Wiki.

The recently published Science for Policy Report “Addressing evidence needs in chemicals policy and regulation” points out a series of steps to be taken in order to increase trust between the various stakeholders in chemicals regulation. It also shows a strong appetite for visual rendering of knowledge to make it more navigable and digestible. This is what is greatly appreciated by users of the AOP Wiki, as emerged from the focus groups and user studies conducted. These visualisations mediate between the different perspectives brought by different studies, approaches and interests: they are literally a medium for bringing them together, and at the same time, they play an intermediary role between perspectives, supporting steps towards greater agreement and productive discussions. In this sense, they are bridging technologies. Because they play such a pivotal role, their design is extremely important. In fact, the design of the visualisation frequently goes hand-in-hand with the design of the framework, as it focuses attention on the component parts, relationships between them, and the definitions and classifications of terms that will be used by each of these.
It is therefore desirable that the way AOPs are visualized is revisited and the diagrams be aligned with the expectations of the user community and the recommendations of the report.

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. Modulating factors act on one or more key event relationships (KERs) along the pathway. While they do not alter the causal connection between a pair of events, they do affect the quantitative attributes of the response-response relationship between those KEs.  However, because neither response-response relationships, nor the effect of modulating factors are always precisely defined in quantitative terms, the description of a modulating factor in the KER descriptions can range from qualitative to quantitative. Regardless, modulating factors should be supported by specific scientific evidence that establishes their overall effect on a given KER, which can include non-adjacent KERs (for example, linking the molecular initiating event directly to the adverse outcome).

Modulating factors are viewed as important information to capture with regard to an AOP, as they can be critical for application and interpretation. However, to date very little information about relevant modulating factors has been captured in the KER descriptions. This is thought to be, in part, because the text field for modulating factors is embedded as a sub-field under the heading of “Quantitative Understanding”.  Given that “Quantitative Understanding” is a section that is often left blank in KER descriptions, moving “Known Modulating Factors” to a separate section, independent of the “Quantitative Understanding” may increase visibility and lead to more information about modulating factors being captured in the AOP-Wiki.

A feature is therefore desirable in the AOP-Wiki to improve the capture of relevant modulating factor information during AOP development and, in the long term, increase the utility of that information for AOP users.

An important aspect of evaluating the quality and fit-for-purpose of an AOP is understanding how that AOP was developed and the overall approach to evidence assembly and evaluation that was employed. Additionally, other potential contributors to an AOP page can better understand what gaps might be filled through additional literature search or experimentation if there is some description of what strategies and approaches previous contributors have taken to assembling and evaluating supporting evidence. However, at present there are no text fields for describing the overall AOP development strategy on the AOP pages, nor the evidence collection and evaluation strategy on Relationship pages. A feature is desirable that provides free text fields for providing an overview of the strategies taken by the contributors.

The AOP Handbook is currently a static document on the OECD website.
This static document should be converted into an electronic handbook (e-Handbook) and published on the AOP-Wiki. It should always be clear under which handbook version a specific AOP was created/endorsed.

Third party organizations have been developing tools that can add functionality to the AOP-Wiki. However, the AOP-Wiki is not currently designed for the integration of third party tools. In order to facilitate their use, the AOP-Wiki should allow users to seamlessly launch third party tools.

A feature is desirable for the display of tabular information where the user is able to filter the display of tabular information similar to the function in Excel. This feature is especially important for the main AOP table.