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Add KER numbers to Relati...
Forum: Desirable AOP-Wiki features
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Rules for this forum
Forum: Desirable AOP-Wiki features
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  Invitation to publish AOP work in special issue
Posted by: mpaparella - 04 Nov 2022, 10:36 - Forum: Announcements - No Replies

Nunzia Linzalone and Gabriele Donzelli are planning a special issue "The Impact of Exposure to Environmental Toxic Chemicals on Human Health: Integration of Epidemiological and Toxicological Evidence” for the International Journal of Environmental Research and Public Health: https://www.mdpi.com/journal/ijerph

We think that this special issue could be a good match for publications related to AOP development, please see the attachment for further specification.

In case of interest, please contact Nuniza or Gabriele.

with kind regards

Martin



Attached Files
.pdf   IJERPH-SI.pdf (Size: 264.91 KB / Downloads: 1)

  Add KER numbers to Relationship Table on AOP
Posted by: Travis Karschnik - 23 Aug 2022, 15:48 - Forum: Desirable AOP-Wiki features - No Replies

User request to add KER ID to the relationship table on the AOP.  See attachment.



Attached Files
.jpg   KER ID.JPG (Size: 74.69 KB / Downloads: 3)

  Rules for this forum
Posted by: Clemens Wittwehr - 11 Aug 2022, 19:44 - Forum: Desirable AOP-Wiki features - No Replies

Have your say!

  • Please use the commenting function for any desirable AOP-Wiki feature that already has its dedicated thread - tell us what you think!
  • Please feel free to start discussion threads with features you would like to see implemented in the AOP-Wiki and do not yet have their own discussion thread

Features that we have put on our workplan have all caps labels at the beginning of their subjects:

FORESEEN = a desirable feature we are we are aware of, and which is on our workplan for the mid to long term future
IMMINENT = a desirable feature that will become available soon
IMPLEMENTED = a feature that was "desirable" in the past and has now been made available


  IMMINENT - AOP-Wiki Content Licensing
Posted by: Clemens Wittwehr - 11 Aug 2022, 15:21 - Forum: Desirable AOP-Wiki features - No Replies

Originally, there was a feature “Hidden but searchable” foreseen, meaning that part of the AOP-Wiki content should be hidden from public viewing for a period of time that would suit the authors (embargo before peer reviewed publication or similar). In the meantime, the OECD body governing the AOP framework and the AOP-Wiki has decided that the current way of licensing AOP knowledge be modified and that this new license model would replace the “hidden but searchable” feature.

The implementation for the new licensing model is foreseen for AOP-Wiki release 2.6, scheduled for the end of 2022.

A description of what is foreseen can be found in the attachment AOP-Wiki Content Licensing.pdf



Attached Files
.pdf   AOP-Wiki Content Licensing.pdf (Size: 602.03 KB / Downloads: 0)

  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:


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

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, 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 recent AOP-Wiki version 2.5 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 particular 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.
In summer 2022, an international and interdisciplinary initiative called "Methods2AOP" was created with the aim of delivering
  • a series of actionable test method related recommendations to the OECD EAGMST
  • a collection of implementable ICT requirements to the OECD EAGMST AOP-KB subgroup

The draft Terms of Reference of this initiative can be found in the attachment.



Attached Files
.pdf   Methods2AOP - Terms of Reference v1-0 anonymized.pdf (Size: 1.28 MB / Downloads: 0)