<![CDATA[AOP Forum - Portal]]> https://forum.aopwiki.org/ Thu, 23 Apr 2026 08:58:02 +0000 MyBB <![CDATA[Pdf attachments]]> https://forum.aopwiki.org/showthread.php?tid=220 Mon, 20 Jan 2025 09:48:41 +0000 Claudia Torero Gutierrez]]> https://forum.aopwiki.org/showthread.php?tid=220 Have any of you have problems uploading pdf attachments to your AOP? I have done it previously, but in the recent days the system it is not allowing me to upload PDF files, only image-type files. Any suggestions?

Thank you!

Claudia]]> Have any of you have problems uploading pdf attachments to your AOP? I have done it previously, but in the recent days the system it is not allowing me to upload PDF files, only image-type files. Any suggestions?

Thank you!

Claudia]]> <![CDATA[Ontology versions in KE Components]]> https://forum.aopwiki.org/showthread.php?tid=219 Tue, 08 Oct 2024 08:47:39 +0000 marvin.martens]]> https://forum.aopwiki.org/showthread.php?tid=219 My colleague and I are trying to work with the ontologies that were used to annotated KEs, specifically under the KEC Biological Process. First going through all GO (gene ontology) terms, we are struggling to find all mappings of GO terms to genes (which is frequently done for gene set enrichment studies). Out of the 600-ish GO terms, we can not find about 10% of the terms using conventional mapping tools (GO package, MSigDb, ...). Manual searching indicates that GO terms might be obsolete and not anymore in the current versions of GO. Is there a way to find out which version of the ontology is used in AOP-Wiki, or whether there are updates to the ontologies used in the AOP-Wiki? For completeness, it would be great if such information can be found in the help page (https://www.aopwiki.org/info_pages/2/inf...ed_pages/7).]]> My colleague and I are trying to work with the ontologies that were used to annotated KEs, specifically under the KEC Biological Process. First going through all GO (gene ontology) terms, we are struggling to find all mappings of GO terms to genes (which is frequently done for gene set enrichment studies). Out of the 600-ish GO terms, we can not find about 10% of the terms using conventional mapping tools (GO package, MSigDb, ...). Manual searching indicates that GO terms might be obsolete and not anymore in the current versions of GO. Is there a way to find out which version of the ontology is used in AOP-Wiki, or whether there are updates to the ontologies used in the AOP-Wiki? For completeness, it would be great if such information can be found in the help page (https://www.aopwiki.org/info_pages/2/inf...ed_pages/7).]]> <![CDATA[AOP Developers Handbook Version 2.7]]> https://forum.aopwiki.org/showthread.php?tid=218 Fri, 24 May 2024 21:56:38 +0000 Travis Karschnik]]> https://forum.aopwiki.org/showthread.php?tid=218 <![CDATA[3y post-doc vacancy for AOP based IATA for DNT within EFSA funded project]]> https://forum.aopwiki.org/showthread.php?tid=217 Fri, 01 Mar 2024 17:30:12 +0000 mpaparella]]> https://forum.aopwiki.org/showthread.php?tid=217 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]]> 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]]> <![CDATA[post-doc vacancy for MUI Regulatory Science Group in Innsbruck/Austria]]> https://forum.aopwiki.org/showthread.php?tid=216 Fri, 18 Aug 2023 08:53:41 +0000 mpaparella]]> https://forum.aopwiki.org/showthread.php?tid=216 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]]> 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]]> <![CDATA[Inclusion of evidence for domain of applicability]]> 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

.pptx   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

.pptx   AOP-Wiki_DOA proposal.pptx (Size: 285.88 KB / Downloads: 8) ]]> <![CDATA[Different types of stressor tables]]> 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)]]> <![CDATA[SAAOP Workshop Registration]]> 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!]]]> <![CDATA[Standardization, Ontologies and Visualization]]> 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)
]]> <![CDATA[Built in AOP network statistics tools and visualizations]]> 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