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Does SBOL support timing and threshold value parameters?

Bioinformatics Asked by Hasan Baig on May 9, 2021

Like the propagation delay and threshold value parameters in electronic circuits, does SBOL format support any such parameters/glyph to represent the propagation delay (time to trigger the output protein once the input is provided) and threshold value (minimum input concentration required to trigger the model’s output) of genetic models?

If currently not supported, can these parameters be incorporated in the SBOL visual representation which would give reader an idea (just by looking at the schematic diagram) about the timing behavior of a model?

One Answer

Note: I will use SBOL3 in my descriptions; the answer can be equivalently translated to SBOL2

At present, SBOL doesn't have any explicit recommendations for how to represent these types of timing parameters. This is because there is not yet a clear scientific consensus on whether or not such parameters are a good way to represent genetic circuits.

That said, one of the advantages of using SBOL is that its extensible RDF-based model allows additional information like this to be added into a model. Two good ways of doing so are:

  1. If the parameters are simple and can stand alone as measurements, then they can be added to designs as a Measure object with appropriate units and type. For example, if you have biological devices with a 90 minute propagation delay, then on the Component representing the device you can add a Measure with numerical value 90, units of om:minute. You'd likely want two types, one of SBO:0000225 (Delay), and a custom type for your own notion of propagation delay, since I don't think that's included in any ontology yet.
  2. If the parameters are more complex and/or inter-related, e.g., a full data-sheet, then you'd likely want to instead create one or more extension classes that are used to represent the information. A library that makes this easy is sbol_factory, though one can do it with any of the SBOL libraries.

This becomes more complicated if you want to talk about behavior in different environmental contexts, but the basic principles are still the same.

Finally, as for SBOL visual: again, there's no explicit representation, but the model is extensible, and this information can be added as any sort of text or custom glyph as long as it doesn't conflict with ones already in the standard.

Correct answer by jakebeal on May 9, 2021

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