Standardization, Ontologies and Visualization

[vasvir]

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)
   

[Julija4CIAO]

thumbs up for - OLS-like interface for ontology consolidation, all mid term goals and policy changes

[vasvir]

Apparently the forum theme does not properly display list (bullets) and numbering items so I suppose that makes our suggestions a bit difficult to read.

After the SAAOP meeting we created a mural workspace with our suggestions. Hopefully this will be easier to digest.

The numbered green items are the issues identified and the somewhat yellow / cream numbered items are the proposed solutions. The links show what actions need to taken to fully attack an issue. There rest is input from other people. As you can see it is somewhat complicated where an action may have positive impact to more than one issue.

Anyway, without further ado:




  SAAOP-AOP-Wiki-v3.0-mural.png (Size: 246.61 KB / Downloads: 11)