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  3y post-doc vacancy for AOP based IATA for DNT within EFSA funded project
Posted by: mpaparella - 01 Mar 2024, 17:30 - Forum: Announcements - No Replies

Interested to evolve Next Generation Risk Assessment within our new EFSA funded DNT-RAP4 project? Apply now for a 3-years post-doc contract within our growing MUI Regulatory Science Group in Innsbruck/Austria!
Please follow the link for detailed information and send your full application by mail to the addresses indicated therein: https://www.i-med.ac.at/karriere/jobs/dr..._eng2.html


  post-doc vacancy for MUI Regulatory Science Group in Innsbruck/Austria
Posted by: mpaparella - 18 Aug 2023, 08:53 - Forum: Announcements - No Replies

Interested to join a growing team developing regulatory science as a new discipline? 
Apply now for a 4-years post-doc contract in Innsbruck/Austria
.pdf   
2024_01 PostDocEN MUI RegScienceGroup.pdf (Size: 392.94 KB / Downloads: 1) supporting two European research projects!

https://www.i-med.ac.at/karriere/jobs/dr...e_eng.html


  Inclusion of evidence for domain of applicability
Posted by: clalone - 29 Jun 2023, 14:19 - Forum: Desirable AOP-Wiki features - No Replies

See pptx for visual description and Jensen et al., 2023 for details:

Jensen, M. A., Blatz, D. J., & LaLone, C. A. (2023). Defining the biologically plausible taxonomic domain of applicability of an adverse outcome pathway: A case study linking nicotinic acetylcholine receptor activation to colony death. Environmental Toxicology and Chemistry, 42(1), 71-87.

Domain of applicability for Key Events (KE) in AOP-Wiki Tables:
List species, sex, life stage from empirical studies (in vitro and in vivo)
Define list of species for biologically plausible taxonomic domain of applicability (in silico) - can be pulled from 3rd party tools (e.g., SeqAPASS)

Domain of applicability for Key Event Relationships (KER) in AOP-Wiki Tables with evidence in free text:
Define Plausible Taxonomic Domain of Applicability where KEup list of species matches KEdown list of species (narrowest DOA; Jensen et al., 2023) 
-This info is derived from empirical studies that support the KEs and through lines of evidence toward structural and functional conservation for plausible taxonomic DOA
-Life stage and Sex can be combined with taxonomic tDOA
-Machine readable tables with links out to details for evidence calls in free text
-Ensure DOA categories are linked



Attached Files
.pptx   AOP-Wiki_DOA proposal.pptx (Size: 285.88 KB / Downloads: 8)

  Different types of stressor tables
Posted by: DanV-AOP - 16 Jun 2023, 12:32 - Forum: Desirable AOP-Wiki features - Replies (1)

To help the AOP-framework to better accommodate and apply to different stressor types (e.g., chemicals, radiation, viruses, immunotherapies...), consider adding additional types of stressor tables that would allow descriptors of non-chemical stressor types to be added.

(Idea proposed during a SKIG meeting)


  SAAOP Workshop Registration
Posted by: jabedini@rti.org - 15 Jun 2023, 17:03 - Forum: Desirable AOP-Wiki features - Replies (1)

The SAAOP is hosting an online workshop series to obtain perspectives and input from a broad range of AOP community stakeholders in an effort to define the features and functions (requirements) to be implemented as part of AOP-Wiki 3.0, with as much specificity as possible. 

Please “pitch” your desired features here prior to the sessions. Vote for the ideas to be discussed during the workshop sessions using the star and discussion features in the forum.


Session 1: July 26, 2023 
• 9:00-12:00 (GMT-4:00) North America and Europe [Register here!
• 20:00-22:00 (GMT-4:00) North America and Asia [Register here!

• Session 2: August 16, 2023 
• 8:00-10:00 (GMT +2:00) Europe and Asia [Register here!
• 15:00-18:00 (GMT +2:00) Europe and North America [Register here!]


  Standardization, Ontologies and Visualization
Posted by: vasvir - 07 Jun 2023, 13:58 - Forum: Desirable AOP-Wiki features - Replies (2)

Hi all,

here are a couple of points discussed in today's webinar with regards to term standardization, ontologies and visualization for making the AOP-Wiki more intuitive.

Issues

  • People do not fill in important information in tables. Instead, they put information in free text
  • People use generic terms
  • Although the process is driven by ontologies, sometimes inappropriate terms are inserted
  • Duplicated concepts exist
  • Data ossification: who maintains older AOPs, KEs when a new functionality is added
  • Ontology proliferation or custom-made vocabularies
  • Missing terms from major Ontologies
  • Standardization of KE names
  • Stressors may be linked to more than one chemical (eg stressor 57).
  • Stressors may not be Chemicals, e.g SARS-COV-2 . Also allow for other types of stressors to be added, e.g radiation
  • Increase Interoperability with regulator world

Here is a list of suggestions in order to tackle some of these issues above.

Low hanging fruit
  1. AO names could be mapped to MedDRA
  2. Standardize and fix terms in categories/Stressors
  3. Standardize and fix terms in categories/Organisms
  4. OLS-like interface for ontology consolidation
  5. Visualization of AOP networks will help identify duplication and hubs (already implemented for 3rd party tool page, but ideally needs to be in every AOP/KE page)

Mid-term
  1. Liaise with ontologies that are open to term suggestions, e.g UBERON
  2. Treat the project in an open-source way/Bug tracking for missing or incomplete information
  3. Treat the project in an open-source way/CI Reports for automatically identified common problems
  4. Treat the project in an open-source way/Governance: Create a body that may authorize proposed changes in case the AOP author is unresponsive

Requiring policy changes
  1. Standardize and fix terms in categories; Stressors must have only a PubChem ID and not Name, Preferred Name, User Term
  2. Put Biological Organization, Cell, Organ in KE component table (allows for multiple rows)
  3. Allow for Tissue and Subcellular location (relevant for MIE)


  Built in AOP network statistics tools and visualizations
Posted by: DanV-AOP - 02 Jun 2023, 16:27 - Forum: Desirable AOP-Wiki features - No Replies

Since 2018 we have been monitoring the growth of the AOP-Wiki in terms of user defined AOPs, relationships, events, emergent AOPs, etc.  This information is reported out at least biannually, but requires an expert user to extract this information from the XML using custom R code.  Would be nice to build in functions that calculate these statistics automatically and can provide real-time read out and cumulative plots, etc. on an on-going basis.


  Tag AOPs in wiki with application domains
Posted by: DanV-AOP - 01 Jun 2023, 14:30 - Forum: Desirable AOP-Wiki features - No Replies

AOPs are envisioned as a way to organize information not just relevant to chemical safety assessment, but also relative to radiation, disease/viruses, even economic stress.  As more of these examples get populated into the wiki, it may be useful to have ways to sort/filter based on general application domain areas.


  Review of AOPs should also be made "modular"
Posted by: JasonOBrien - 26 May 2023, 18:44 - Forum: Desirable AOP-Wiki features - Replies (1)

We need a solution for the review of AOP that have shared KEs and KERs.

This is especially important if these KEs/KERs have been borrowed from AOPs that have already been reviewed.

One suggestion is that during the review, each KE and KER gets reviewed independently of each other, and each have their own "review documentation" attached to them.

This way, any review conducted will "follow" that KE/KER wherever they go. This is the same as all the other information related to KEs and KERs

i.e. We should consider making AOP reviews "modular" as well. Or rather, a "review" is an attribute/property for each KE, KER and AOP in KB.

just like AOPs are make up of KEs and KERs, the "AOP Review" can be "made of" its component "KE Reviews" and "KER reviews", along with any higher level synthesis that occurs at the AOP level.

All of these "sub-reviews" can be conducted by the same group of reviewers (as is currently done) or can optionally be conducted individually, as needed.

I've included an image describing this idea (hope it makes sense :))


.png   modular review.png (Size: 232.63 KB / Downloads: 3)


  Umbrella Key Events
Posted by: DanV-AOP - 26 May 2023, 13:07 - Forum: Desirable AOP-Wiki features - Replies (1)

Create umbrella key events that could encompass multiple KEs that encompass a set of related KEs.



Attached Files
.pdf   umbrellaKE-3-11-21-lightest.pdf (Size: 1.05 MB / Downloads: 6)