With the advent of Wiki 2.6 we dusted off a bit our XML parser to make it ready for the new AOP-Wiki features.
We discovered 3 possible inconsistencies and I thought it would be best to report them here.
So here there are:
1) No tag in the XML for "Strategy" subsection (under "AOP Development Strategy" section).
How to reproduce:
Example is AOP 423. Go to https://aopwiki.org/aops/423 and https://aopwiki.org/aops/423.xml Note that while "Context" is listed in the XML unde "/aop/background" the "Strategy" content although visible in the wiki is not found in the XML. Search for "In this stud" to verify.
2) No tag in the XML for "Known Modulating Factors" subsection (under "Overall Assessment of the AOP" section).
3) Duplication of content under "/aop/essentiality-support" and "/aop/overall-assessment/key-event-essentiality-summary".
Hello all - this thread is intended to collect ideas from the AOP Community of Practice regarding features and functions to be implemented as part of AOP-Wiki 3.0. Ideas presented here will be considered for invitation to present and discuss your idea over the course of several SAAOP-sponsored 1/2 day workshops to take place in July, August, September, 2023.
If you have an idea you'd like to post, please create a Thread in this sub-forum. If you see an idea you like, please click the stars to up-vote. Topics with the most stars, or discussion activity will be selected for presentation and/or discussion at the workshop.
In summary, the FAIR principles support machine-readability and reuse of data/information/knowledge. The acronym stands for: Findability - facilitated e.g. by rich annotation of (meta)data using persistent identifiers and ontologies Accessibility - facilitated e.g. by standardized communication protocols Interoperability - facilitated e.g. by formal, accessible and broadly shared languages and vocabularies (e.g. ontologies), as well as qualified references to related information (links to other databases) Reusability - facilitated e.g. by clear reuse licenses and detailed provenance
Some initial low-hanging fruit can be suggested to support increased FAIRness of the AOP-Wiki, including:
- researcher ORCID:s for AOP developers and coaches
- doi:s for references
- KE component use broadened
- annotation of e.g. genes/proteins with commonly accepted identifiers or vocabulary, e.g. HUGO Gene Nomeclatur (HGNC)
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.
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
Don't worry about the all caps labels at the beginnings of most of the features in this forum. We will insert them as necessary:
FORESEEN = a desirable feature 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
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
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.
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.
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?
