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SEP 024 full draft

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jakebeal
jakebeal committed Apr 13, 2019
1 parent 2d865a2 commit 1dd0784edda005067f726c99a7a67dae5e793111
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  1. +64 −33 sep_024.md
@@ -7,33 +7,30 @@ SEP | 024
**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** |
**Type** | Data Model
**SBOL Version** | 2.3
**SBOL Version** | 2.3.1
**Replaces** |
**Status** | Draft
**Created** | 3-Jul-2018
**Last modified** | 14-Aug-2018
**Issue** | [#2](https://github.com/SynBioDex/SEPs/issues/2)
**Last modified** | 8-Apr-2018
**Issue** | [#57](https://github.com/SynBioDex/SEPs/issues/57)

Abstract
-----------

This SEP proposes adding a collection of best practices regarding the representation of sample designs for experiments, including media, strains, inducers, and other environmental conditions.
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](#rationale) <or, if you prefer, 'Motivation'>
* [2. Specification](#specification)
* [2.1 Measurements](#measurements)
* [2.1.1 Measure](#measure)
* [2.1.2 Unit](#unit)
* [2.1.1 Prefix](#prefix)
* [2.2 Mixtures via ModuleDefinitions](#mixtures)
* [2.3 Media and Inducers](#media)
* [2.4 Strains, Genomes, and Plasmids](#strain)
* [2.5 Samples](#samples)
* [2.6 Other experimental parameters](#otherparameters)
* [2.1 Mixtures via ModuleDefinitions](#mixtures)
* [2.2 Media, Inducers, and other Reagents](#media)
* [2.3 Strains, Genomes, and Plasmids](#strain)
* [2.4 Samples](#samples)
* [2.5 Other experimental parameters](#otherparameters)
* [2.6 Possible promotion of "measures" to Identified](#measure)
* [3. Example or Use Case](#example)
* [4. Backwards Compatibility](#compatibility)
* [5. Discussion](#discussion)
@@ -52,44 +49,73 @@ The SBOL model is already flexible enough to encode such information, but there
## 2. Specification <a name="specification"></a>
----------------------------------------------

### 2.1 Measurements<a name="measurements"></a>
### 2.1 Mixtures via ModuleDefinitions <a name="mixtures"></a>

Moved to SEP 028.
Any ModuleDefinition can be interpreted as specifying a mixture of the FunctionalComponents and Modules that it includes.

### 2.2 Mixtures via ModuleDefinitions <a name="mixtures"></a>
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:

Any ModuleDefinition can be interpreted as a mixture of the FunctionalComponents it includes (either directly or through included Modules).
* 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)

The quantity of any FunctionalComponent in the mixture is specified by an OM:measure property linking it to an OM:Measure TopLevel object.

### 2.3 Media and Inducers<a name="media"></a>
### 2.2 Media, Inducers, and other Reagents<a name="media"></a>

The components
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

### 2.4 Strains, Genomes, and Plasmids<a name="strain"></a>
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

### 2.5 Samples<a name="samples"></a>
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:

A complete sample is specified with a ModuleDefinition that includes at least:
* A Module instantiating the strain (including any constructs)
* A Module or FunctionalComponents instantiating media and inducers
* NCIT:C64356: Positive Control
* NCIT:C48694: Cell
* NCIT:C85504: Media
* NCIT:C14419: Strain
* NCIT:C120268: Inducer

Is it better to instantiate a titration with FunctionalComponents or sub-Modules?
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 name="strain"></a>

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

### 2.6 Other experimental parameters<a name="otherparameters"></a>
* 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).


How do we want to represent temperature, time?
### 2.4 Samples<a name="samples"></a>

### 2.1 optional sub-point
A complete specification of a sample SHOULD be a ModuleDefinition that includes at least:

< sub-divide specification section if useful >
* 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)

### 2.2 optional sub-point

< sub-divide specification section if useful >

### 2.5 Other experimental parameters<a name="otherparameters"></a>

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<a name="measure"></a>

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 <a name='example'></a>
@@ -102,6 +128,10 @@ Examples are presented in the subsections above.

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 <a name='discussion'></a>
-----------------
@@ -111,9 +141,10 @@ _none yet_
## 6. Relation to Other SEPs <a name='relation'></a>
-----------------

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.

The specification of strains with modified genomes recommended in this SEP is simplified by the use of sequence insertion and replacement as proposed in SEP 013.

References <a name='references'></a>
----------------

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