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SEP 024 -- Best practices for host context / ontologies for experiments

SEP 024
Title Best practices for host context / ontologies for experiments
Authors Jacob Beal (jakebeal@ieee.org), Nicholas Roehner (nicholas.roehner@raytheon.com), Bryan Bartley (bryan.a.bartley@raytheon.com), and Chris Myers (myers@ece.utah.edu)
Editor Curtis Madsen, Pedro Fontanarrosa
Type Data Model
SBOL Version 2.3.1 / 2.4
Replaces
Status Accepted
Created 3-Jul-2018
Last modified 8-Apr-2018
Issue #57, #84

Abstract

This SEP proposes adding a collection of best practices regarding the representation of host and environmental context, including sample designs for experiments, media, strains, inducers, and other environmental conditions.

Table of Contents

1. Rationale

The design-build-test extensions of SBOL 2.2 support linking of genetic designs with experimental data. To fully specify the sample that data is connected to, however, also involves specification of host and environmental context, such as media, strain, inducers, etc. Otherwise one cannot distinguish between clearly different circumstances, such as data for the same construct grown in E. coli with 1mM Arabinose in LB media versis in B. subtilis with no Arabinose in M9 media.

The SBOL model is already flexible enough to encode such information, but there are a number of different ways in which this might be approached. We thus recommend a set of best practices for encoding this information.

Certain of these best practices, however, suggest adding "role" and "measures" properties where they are not currently added, so this may be an SBOL 2.4 rather than SBOL 2.3.1 addition.

2. Specification

2.1 Mixtures via ModuleDefinitions

Any ModuleDefinition can be interpreted as specifying a mixture of the FunctionalComponents and Modules that it includes.

The amount of each such instance included in the mixture SHOULD be specified by attaching a Measure with a type set to the appropriate SBO term. The SBO terms that are RECOMMENDED as appropriate are members of the Systems Description Parameter (SBO:0000545) branch of SBO. Examples include:

  • SBO:0000540: fraction of an entity pool (e.g., 1/3 CHO cells, 2/3 HEK cells)
  • SBO:0000472: molar concentration of an entity (e.g., 1 mM Arabinose)
  • SBO:0000361: amount of an entity pool (e.g., 200 uL M9 media)

2.2 Media, Inducers, and other Reagents

An "atomic" reagent, which is not expected to be divided further in designs, SHOULD be represented as a ComponentDefinition. Examples: Arabinose, Kanamycin, Rainbow bead control

A "composite" reagent, which might be defined as a mixture of other reagents, SHOULD be represented as a ModuleDefinition that defines it as a mixture of other reagents. This might be recursive, with mixtures of mixtures of mixtures, etc. Examples: M9 media, LB broth

The roles of reagents may vary in context: for example, Arabinose may serve as an inducer or as a media carbon source. As such, role SHOULD be indicated by an NCI Thesaurus (NCIT) term in a role property of the FunctionalComponent or Module. Examples include:

  • NCIT:C64356: Positive Control
  • NCIT:C48694: Cell
  • NCIT:C85504: Media
  • NCIT:C14419: Strain
  • NCIT:C120268: Inducer

Note that this also implies that the role property should be promoted from Component to ComponentInstance (so it can be used for FunctionalComponent as well) and also added to Module.

2.3 Strains, Genomes, and Plasmids

A cell strain SHOULD be represented as a ModuleDefinition containing at least:

  • A FunctionalComponent for the cell, which is RECOMMENDED to have type cell (GO:0005623) and role physical compartment (SBO:0000290).
  • A representation of its genetic material (genome, plasmids, etc.) as a collection of FunctionalComponent and/or Module instances.
  • An Interaction of type FunctionalCompartment (SBO:0000289) with the cell participating as physical compartment (SBO: 0000290) and the genetic material participating as contained entity (SBO:0000664).

2.4 Samples

A complete specification of a sample SHOULD be a ModuleDefinition that includes at least:

  • A Module instantiating each strain in the sample
  • A Module or FunctionalComponent for the media or buffer
  • A Module or FunctionalComponent for each additional reagent added to the media (e.g., inducers, antibiotics)
  • Measures on each of these specifying the amount in the sample
  • Measures on the ModuleDefinition for each environmental parameter (e.g., temperature, pH, culturing time)

2.5 Other experimental parameters

In order to deal with parameters associated with the context in general but not specific instances, e.g., temperature, pH, total sample volume, we need to add a measures property to ModuleDefinition (in addition to the ones already on Module and ComponentInstance) and to ComponentDefinition.

The distinction is that the measures of a Definition provide context-free information (e.g., the pH of M9 media, the GC-content of a GFP coding sequence), while the measures on an instance provide a measurement in context (e.g., the dosage of Arabinose in a sample).

Values of these parameters SHOULD be specified by attaching a Measure with a type set to the appropriate SBO term. The SBO terms that are RECOMMENDED as appropriate are members of the Systems Description Parameter (SBO:0000545) branch of SBO. Examples include:

  • SBO:0000147: thermodynamic temperature (e.g., culturing at 27 C)
  • SBO:0000332: half-life of an exponential decay (e.g., decay rate of a gRNA)
  • SBO:0000304: pH (e.g., pH of M9 media)

2.6 Possible promotion of "measures" to Identified

Given the number of other classes with a potential "measures" property to add in the future, we should also consider changing it to be on Identified rather than on individual classes.

3. Example or Use Case

Examples are presented in the subsections above.

4. Backwards Compatibility

The best practices in this proposal do not affect backwards compatibility.

Adding a "roles" property to FunctionalComponent and Module is backward compatible.

Adding a "measures" property to ModuleDefinition and ComponentDefinition is also backward compatible, as would be promoting "measures" to be on Identified.

5. Discussion

none yet

6. Relation to Other SEPs

This SEP was originally much more complex, covering measurements and representation of cells. Those portions were pulled out and approved separately as SEP 028 and SEP 030, respectively.

No other SEPs currently propose best practices in the same space: SEP 020 and SEP 021 are complementary and non-conflicting.

References

none

Copyright

CC0
To the extent possible under law, SBOL developers has waived all copyright and related or neighboring rights to SEP 024. This work is published from: United States.