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Gardening requests
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Test Methods
Forum: Desirable AOP-Wiki features
Last Post: Clemens Wittwehr
21 Feb 2022, 16:15
» Replies: 0
» Views: 249

 
  AOP-Wiki Release 2.4.1
Posted by: swedwards - 07 May 2022, 18:32 - Forum: Tool Developers - No Replies

Our most recent AOP-Wiki update fixed several errors with our XML downloads. With this release, we have synchronized the updates between the AOP-Wiki and the AOP-XML schema in order to avoid validation errors moving forward. The AOP-XML schema is available here: https://github.com/swandle06/AopXml (assets/schema/current.xsd). The version of the schema corresponding to the latest wiki release will be tracked here: https://github.com/swandle06/AopXml/releases.

There are still some controlled terms that are being processed, and those discrepancies will be fixed in our next release later this summer. With those exceptions, the wiki exports are now consistent with the defined schema here: https://github.com/swandle06/AopXml/releases/tag/v1.0.1. Moving forward, we will raise any new alterations to the schema and associated exports in this subforum prior to release of the AOP-Wiki code. This will allow an opportunity for feedback from developers using AOP-Wiki data in their applications as well as time for them to adjust their applications to accommodate the changes.


  <biological-organization-level> is not always visible in the rendered wiki page
Posted by: vasvir - 05 Apr 2022, 13:19 - Forum: AOP-Wiki Technical Assistance - Replies (4)

Hi,

We noticed an inconsistency between the latest XML and some key events and maybe you could help us a bit to understand what's going on.

Case in point are events 1043, 1492, 1493 which have a non-empty <biological-organization-level> like Cellular or Tissue but it is not rendered in the wiki page.


In contrast, in the  event 1847 that has the exact same value (Cellular) is visible.
There is a screenshot depicting the issue attached.

So why some in some key event <biological-organization-level> is rendered and in some it is not rendered?

Thanks in advance

  Vassilis



Attached Files
.png   event-1043-no-biological-context.png (Size: 132.51 KB / Downloads: 0)

  Taxonomic applicability TAG discrepancy between AOP, KE AND KER
Posted by: vasvir - 05 Apr 2022, 12:47 - Forum: AOP-Wiki Technical Assistance - Replies (3)

Hi,

I noticed that the containing tag in KER (as per XSD) is <taxonomic-applicability> (of appicability-type) while in AOP an KE the tag name is <applicability>.

In AOPs/KEs
<applicability>
  <sex></sex>
  <life-stage></life-stage>
  <taxonomy></taxonomy>
</applicability>


while in KERs
<taxonomic-applicability>
  <sex></sex>
  <life-stage></life-stage>
  <taxonomy></taxonomy>
</taxonomic-applicability>


Are these two tags different by design? Can we make them both 'applicability'? so Sex/Life Stage/taxonomy are not listed under taxonomic-applicability in KERs?

Thanks in advance

  Vassilis


  Taxonomic applicability discrepancy between XML and UI
Posted by: irenelopezs - 02 Mar 2022, 14:32 - Forum: AOP-Wiki Technical Assistance - Replies (4)

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


  Gardening requests
Posted by: DanV-AOP - 02 Mar 2022, 12:26 - Forum: AOP-Wiki Technical Assistance - Replies (1)

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


  Test Methods
Posted by: Clemens Wittwehr - 21 Feb 2022, 16:15 - Forum: Desirable AOP-Wiki features - No Replies

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. However, this loose and verbal description does not reflect the importance of the link between a specific key event and the test method(s) it can be measured with (and the other way round). In addition, the role of the "stressors" as triggers of key events was downgraded in the AOP-Wiki to that of "prototypical stressors", i.e. ones that e.g. a test method developer can use as positive control.

This means that the proper linkage between possible real-life stressors (beyond prototypical stressors) that can trigger a KE and that KE must be established via the test method:


- A stressor is tested using a certain test method
- In the AOP-Wiki, this test method is stored and earmarked as relevant for a certain Key Event
- Thereby the link between the stressor and the Key Event is established: Depending on the result of the test, the stressor is either implicated in the key event or not.


The management of test methods in the AOP-Wiki should therefore be enhanced:


- The data model should feature a distinct object "test method"
- The attributes of this object can be derived from various guidance documents on how to describe test methods
- In order to simplify the work for the AOP authors, a two level hierarchy might be appropriate: a more general "Type of Measurement" object (e.g. "Radioimmunoassay") with an 1:n relationship to a more concrete "Test Method" (in this example e.g. "Abnova", or "CreativeBiolabs")
- Note: The AOP-Wiki should only describe the method (and link it to Key Events), but not actual test results. That is done by third party systems, e.g. the Endocrine Active Substances Information System (EASIS), which provides OECD Harmonized Templates-formated NAM test results.


The following use cases must be supported:

- The AOP author can quickly create a Type of Measurement and link it to a Key Event.
- Test method developers can create actual Test Methods and link them to the Type of Measurement
- Links from the Test Methods and Types of Measurement to third party test method repositories must be possible

Advantages:

- More visible and actionable link between a test method and a key event
- Stressors are finally treated properly (via the test method link) and the AOP-Wiki still remains "chemical-agnostic"
- A whole new audience is attracted tot he AOP-Wiki: the test method developers


  Hidden, but Searchable AOP-Wiki elements
Posted by: Clemens Wittwehr - 20 Feb 2022, 09:00 - Forum: Desirable AOP-Wiki features - No Replies

AOPs are living documents and are co-created by a numerous people. AOPs run through a series of maturation, adoption and endorsement steps. Some authors prefer that their contributions remain invisible until a certain moment in that workflow. However, the re-use of already existing AOP components in the AOP-Wiki is a strong driver of building AOP networks, and potentially relevant content being “hidden” for a considerable time might be counterproductive. A compromise between the justified wish to “embargo” certain elements on the one hand and the necessity to have the latest knowledge available for re-use must be implemented.

A "Hidden but Searchable feature" is desirable which is intended as a compromise that could give authors the option to keep their own content hidden, while still allowing other users to understand what content is currently under development in the AOP-Wiki and to be able to utilize shared KE and KER pages.


This feature is planned for release 2.6 of the AOP-Wiki.

A tentative description of what is foreseen will become available soon.


  De-emphasizing the role of stressors
Posted by: Clemens Wittwehr - 20 Feb 2022, 08:53 - Forum: Desirable AOP-Wiki features - No Replies

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.


This will be addressed either in release 2.5 or 2.6 of the AOP-Wiki.

A description of what is foreseen is attached.



Attached Files
.pdf   How stressors will be treated in the AOP-Wiki.pdf (Size: 889.89 KB / Downloads: 0)

  Intuitive AOP Visualizations
Posted by: Clemens Wittwehr - 19 Feb 2022, 16:31 - Forum: Desirable AOP-Wiki features - No Replies

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.


This issue will be addressed in a series of Focus group meetings in spring 2022, and it is foreseen that first results will be implemented in version 2.6 of the AOP-Wiki.


  Modulating Factors
Posted by: Clemens Wittwehr - 19 Feb 2022, 16:11 - Forum: Desirable AOP-Wiki features - No Replies

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.


This feature is foreseen for release 2.5 of the AOP-Wiki.

A tentative description can be viewed in the attachment.



Attached Files
.pdf   Description - Strategy Fields.pdf (Size: 400.2 KB / Downloads: 2)