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SynBioDex / SBOL-specification

The Synthetic Biology Open Language (SBOL)
http://sbolstandard.org
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Higher-level interactions? #399

Closed jakebeal closed 3 years ago

jakebeal commented 3 years ago

We have been considering the question of higher-level interactions in SBOL Visual, such as aTc repressing the repression of a TetR CDS on pTet. (See discussion on: https://github.com/SynBioDex/SBOL-visual/issues/73).

The key question that we are hung up on right now is whether something can simultaneously be both an occurring entity and a participant role (e.g., both Inhibition (SBO:0000169) and Inhibited (SBO:0000642). I have come to believe this may be reasonable.

If we allow this, we will definitely be making a choice that is incompatible with the current SBOL data model, which does not support higher-level interactions at present. That might, however, instead be indicating a thing that we'd want to change in the data model, and indeed I've recently seen an example where it might make sense, in which an operator is regulating a genetic production relationship. This was indicated by giving a role to the operator, but it might be more elegantly represented by the operator controlling the interaction.

If we allowed this in SBOL3, the change would be to allow a Participant to be either a Feature or an Interaction. What do people think of this possibility?

jakebeal commented 3 years ago

SEP is open: https://github.com/SynBioDex/SEPs/issues/104

jakebeal commented 3 years ago

SEP 049 changes have been approved and merged in #427.

Validation rules are pending in #424

jakebeal commented 3 years ago

424 is merged.