SBO:promoter term is not linked to the SBO:particiption_role in the SBO ontology

[goksel]

According to the sbol3-11906 validation rule, the SBO:Promoter role (http://identifiers.org/SBO:0000598) should be a child term of the SBO:Participation_role (http://identifiers.org/SBO:0000003). However, the promoter term is not linked to any other term in SBO. As a result, the sbol3-11906 validation rule is not correct. We need to fix this issue in SBO. The validation rule will then be correct without any spec changes.

Validation rule:
sbol3-11906 Exactly one role in the set of role properties SHOULD be a URL from the participant role branch of the SBO (see Table 12).

SBO:Participation_role - SBO:0000003 tree view
https://www.ebi.ac.uk/ols4/ontologies/sbo/classes/http%253A%252F%252Fbiomodels.net%252FSBO%252FSBO_0000003?lang=en

SBO:Promoter - SBO:0000598 tree view
https://www.ebi.ac.uk/ols4/ontologies/sbo/classes/http%253A%252F%252Fbiomodels.net%252FSBO%252FSBO_0000598?lang=en

[jakebeal]

Looking at Table 12, it's very strange to me that "Promoter" is there as a special case. I can understand how we ended up with it, but it ignores other non-promoter methods of regulating genetic production.

It's also worth noticing (and worrying about) the fact that there is a second item also called Promoter in the SBO, which is "SBO:0000590"

What if, instead of asking them to link up the defective "SBO:0000598", you ask them to create a new term under SBO:0000003 that is a more general notion like "Regulator"?

PS: please add a link to the SBO term request when you've created it.

[goksel]

How about asking for both of the following items?

• A name change from Promoter to Regulator
• Adding the "SBO:0000598 subClassOf SBO:0000003" relationship.

[jakebeal]

That sounds like a good plan to me.