https://forum.aopwiki.org/ Fri, 15 May 2026 19:31:11 +0000 MyBB https://forum.aopwiki.org/showthread.php?tid=215 Thu, 29 Jun 2023 14:19:51 +0000 clalone]]> https://forum.aopwiki.org/showthread.php?tid=215
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

  AOP-Wiki_DOA proposal.pptx (Size: 285.88 KB / Downloads: 8) ]]>
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

  AOP-Wiki_DOA proposal.pptx (Size: 285.88 KB / Downloads: 8) ]]> https://forum.aopwiki.org/showthread.php?tid=214 Fri, 16 Jun 2023 12:32:46 +0000 DanV-AOP]]> https://forum.aopwiki.org/showthread.php?tid=214
(Idea proposed during a SKIG meeting)]]>
(Idea proposed during a SKIG meeting)]]> https://forum.aopwiki.org/showthread.php?tid=213 Thu, 15 Jun 2023 17:03:37 +0000 jabedini@rti.org]]> https://forum.aopwiki.org/showthread.php?tid=213
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!]]]>
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!]]]> https://forum.aopwiki.org/showthread.php?tid=212 Wed, 07 Jun 2023 13:58:11 +0000 vasvir]]> https://forum.aopwiki.org/showthread.php?tid=212
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)
   

]]>
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)
   

]]> https://forum.aopwiki.org/showthread.php?tid=211 Fri, 02 Jun 2023 16:27:57 +0000 DanV-AOP]]> https://forum.aopwiki.org/showthread.php?tid=211 https://forum.aopwiki.org/showthread.php?tid=210 Thu, 01 Jun 2023 14:30:28 +0000 DanV-AOP]]> https://forum.aopwiki.org/showthread.php?tid=210 https://forum.aopwiki.org/showthread.php?tid=209 Fri, 26 May 2023 18:44:07 +0000 JasonOBrien]]> https://forum.aopwiki.org/showthread.php?tid=209
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 :))


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


  modular review.png (Size: 232.63 KB / Downloads: 3) ]]> https://forum.aopwiki.org/showthread.php?tid=208 Fri, 26 May 2023 13:07:57 +0000 DanV-AOP]]> https://forum.aopwiki.org/showthread.php?tid=208
  umbrellaKE-3-11-21-lightest.pdf (Size: 1.05 MB / Downloads: 6) ]]>
  umbrellaKE-3-11-21-lightest.pdf (Size: 1.05 MB / Downloads: 6) ]]> https://forum.aopwiki.org/showthread.php?tid=207 Fri, 26 May 2023 13:02:04 +0000 DanV-AOP]]> https://forum.aopwiki.org/showthread.php?tid=207 https://forum.aopwiki.org/showthread.php?tid=206 Fri, 26 May 2023 13:00:31 +0000 DanV-AOP]]> https://forum.aopwiki.org/showthread.php?tid=206 https://forum.aopwiki.org/showthread.php?tid=205 Fri, 26 May 2023 12:57:58 +0000 DanV-AOP]]> https://forum.aopwiki.org/showthread.php?tid=205 https://forum.aopwiki.org/showthread.php?tid=204 Thu, 25 May 2023 22:03:51 +0000 jabedini@rti.org]]> https://forum.aopwiki.org/showthread.php?tid=204
This data model should also facilitate the reuse of this shared information among those related KEs to avoid increasing the burden on KE authors.]]>
This data model should also facilitate the reuse of this shared information among those related KEs to avoid increasing the burden on KE authors.]]> https://forum.aopwiki.org/showthread.php?tid=203 Thu, 25 May 2023 21:53:51 +0000 jabedini@rti.org]]> https://forum.aopwiki.org/showthread.php?tid=203

• Identify the appropriate level for each piece of information
  
• For concepts defined at a higher level, enforce compliance with those constraints when entering information at lower levels.
  
• For concepts defined at lower levels, roll up information at higher levels rather than capturing the information separately
  
• Reduce the number of free text inputs for all entities except the AOP and capture information through more structured forms
  

]]>

• Identify the appropriate level for each piece of information
  
• For concepts defined at a higher level, enforce compliance with those constraints when entering information at lower levels.
  
• For concepts defined at lower levels, roll up information at higher levels rather than capturing the information separately
  
• Reduce the number of free text inputs for all entities except the AOP and capture information through more structured forms
  

]]> https://forum.aopwiki.org/showthread.php?tid=202 Thu, 25 May 2023 21:45:36 +0000 jabedini@rti.org]]> https://forum.aopwiki.org/showthread.php?tid=202
For this, the new wiki data model should support three major features.

• Make it clear who contributed which content. While this information is currently available, it can be laborious to identify all the contributions from a single user using the edit history associated with each page.
  
• Document the strategy used to assemble literature when evaluating the evidence. This requires not only that contributions from individual users are tracked, but the individual references used must be tracked and tied to the strategy used to assemble the literature.
  
• Provide a more consistent format for the information in the AOP-Wiki. Users don’t have time to decipher many different ways of capturing the information. If the provenance of the wiki knowledge is not readily apparent, it will be invisible to most consumers of that information.
  

]]>
For this, the new wiki data model should support three major features.

• Make it clear who contributed which content. While this information is currently available, it can be laborious to identify all the contributions from a single user using the edit history associated with each page.
  
• Document the strategy used to assemble literature when evaluating the evidence. This requires not only that contributions from individual users are tracked, but the individual references used must be tracked and tied to the strategy used to assemble the literature.
  
• Provide a more consistent format for the information in the AOP-Wiki. Users don’t have time to decipher many different ways of capturing the information. If the provenance of the wiki knowledge is not readily apparent, it will be invisible to most consumers of that information.
  

]]> https://forum.aopwiki.org/showthread.php?tid=198 Mon, 03 Apr 2023 14:59:11 +0000 DanV-AOP]]> https://forum.aopwiki.org/showthread.php?tid=198
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.]]>
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.]]>