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SEP 048 -- Enhance Combinatorial Derivations

SEP
Title Enhance Combinatorial Derivations
Authors Jake Beal ([email protected])
Editor Hasan Baig
Type Data Model
SBOL Version SBOL 3.0.1
Replaces
Status Accepted
Created 17-July-2020
Last modified
Issue

Abstract

In SBOL3, combinatorial derivations can also represent things like the design of an experiment, e.g., test strains A, B, and C in media X, Y, and Z. Currently, however, it is not able to take advantage of the full succinctness offered by the new Feature class. This SEP proposes a generalization of the CombinatorialDerivation class to allow direct use of all features and measures.

1. Rationale

In SBOL3, combinatorial derivations can also represent things like the design of an experiment, e.g., test strains A, B, and C in media X, Y, and Z.

Currently, however, it is not able to take advantage of the full succinctness offered by the new Feature class. In particular:

  • LocalSubComponents and ExternallyDefined cannot be used as targets, only SubComponents.
  • Measures cannot be directly varied, but must be varied by varying components with the measure attached.

Thus, if we design a sample with 0.5 uM arabinose, we can express that directly as an ExternallyDefined with 0.5 uM concentration, but if we want to express a CombinatorialDerivation in which the dosage varies between 0.0, 0.2, and 0.5 uM, we need to use a SubComponent for the variable and then create 3 Component objects, one for each dosage.

I believe this was a simple oversight in our updating, because our discussions clearly envisioned using CombinatorialDerivation in these ways. I believe this can be fixed quite simply by:

  • Changing the range of VariableComponent:variable from SubComponent to Feature.
  • Adding a VariableComponent:variantMeasure field, with cardinality 0..* and range om:Measure

The first change will allow modulation of all component features, which I believe is appropriate. We want to be able to change the dose of small molecules (ExternallyDefined), fill in blank variables (LocalSubComponent), vary the type of junction or scar (SequenceFeature), and might want to vary something in a subsystem (ComponentReference).

The second change will allow direct specification of variation of dosages, temperatures, and other design properties.

2. Specification

The range of the VariableComponent property variable is changed from SubComponent to Feature.

A new variantMeasure property is added to VariableComponent, with cardinality 0..n (i.e., optional, and as many as desired can be added).

Given a set of values linked from a VariableComponent, it SHOULD be the case that all value are of type Measure or else all values are of type Feature. At present, it is explicitly left undefined how an algorithm ought to handle mixtures of Measure and Feature values.

Note that because a Measure is not a TopLevel, it is not possible to link to a variantCollection of Measure objects.

3. Example or Use Case

In order to specify an experiment that grows a modified strain of E. coli in LB media with varying levels of L-arabinose, the following CombinatorialDerviation can be used:

  • template is a Component with a three Features:
  • SubComponent for the E. coli strain, with a Measure for dose.
  • SubComponent for LB media, with a Measure for dose.
  • ExternallyDefined for L-arabinose, with no Measure
  • There is one VariableComponent, with the following contents:
  • variable linking to the L-arabinose ExternallyDefined
  • variantMeasure pointing to a set of measures for concentrations 0.0 uM, 0.1 uM, 0.3 uM, and 1.0 uM.

This thus encodes a set of four L-arabinose doses that can be enumerated into Component objects, e.g.:

  • SubComponent for the E. coli strain, with a Measure for dose.
  • SubComponent for LB media, with a Measure for dose.
  • ExternallyDefined for L-arabinose, a Measure of 0.3 uM

4. Backwards Compatibility

All CombinatorialDerivations that are legal in SBOL 3.0 will still be legal with this SEP. This SEP will allow the construction of CombinatorialDerivations that are prohibited by the current SBOL 3.0, however.

5. Discussion

6. Competing SEPs

None.

References

None.

Copyright

CC0
To the extent possible under law, SBOL developers has waived all copyright and related or neighboring rights to SEP 048. This work is published from: United States.