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partial draft of SEP 024

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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), Chris Myers (myers@ece.utah.edu), _probably others too_
**Editor** |
**Type** | Data Model
**SBOL Version** | 2.3
**Replaces** |
**Status** | Draft
**Created** | 3-Jul-2018
**Last modified** | 3-Jul-2018
**Issue** | [#2](https://github.com/SynBioDex/SEPs/issues/2)
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.
Table of Contents
---------------------
* [1. Rationale](#rationale) <or, if you prefer, 'Motivation'>
* [2. Specification](#specification)
* [2.1 Measurements](#measurements)
* [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)
* [3. Example or Use Case](#example)
* [4. Backwards Compatibility](#compatibility)
* [5. Discussion](#discussion)
* [6. Relation to Other SEPs](#relation)
* [References](#references)
* [Copyright](#copyright)
1. Rationale <a name="rationale"></a>
----------------
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.
2. Specification <a name="specification"></a>
----------------------------------------------
### 2.1 Measurements<a name="measurements"></a>
Numerical measurements SHOULD be specified using the "OM: Units of Measure" ontology ([http://www.ontology-of-units-of-measure.org/resource/om-2](http://www.ontology-of-units-of-measure.org/resource/om-2)).
### 2.2 Mixtures via ModuleDefinitions <a name="mixtures"></a>
Any ModuleDefinition can be interpreted as a mixture of the FunctionalComponents it includes (either directly or through included Modules).
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>
The components
### 2.4 Strains, Genomes, and Plasmids<a name="strain"></a>
### 2.5 Samples<a name="samples"></a>
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
Is it better to instantiate a titration with FunctionalComponents or sub-Modules?
### 2.6 Other experimental parameters<a name="otherparameters"></a>
How do we want to represent temperature, time?
### 2.1 optional sub-point
< sub-divide specification section if useful >
### 2.2 optional sub-point
< sub-divide specification section if useful >
3. Example or Use Case <a name='example'></a>
-------------------------------
Examples are presented in the subsections above.
4. Backwards Compatibility <a name='compatibility'></a>
-----------------
The best practices in this proposal do not affect backwards compatibility.
5. Discussion <a name='discussion'></a>
-----------------
_none yet_
6. Relation to Other SEPs <a name='relation'></a>
-----------------
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>
----------------
_none_
Copyright <a name='copyright'></a>
-------------
<p xmlns:dct="http://purl.org/dc/terms/" xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#">
<a rel="license"
href="http://creativecommons.org/publicdomain/zero/1.0/">
<img src="http://i.creativecommons.org/p/zero/1.0/88x31.png" style="border-style: none;" alt="CC0" />
</a>
<br />
To the extent possible under law,
<a rel="dct:publisher"
href="sbolstandard.org">
<span property="dct:title">SBOL developers</span></a>
has waived all copyright and related or neighboring rights to
<span property="dct:title">SEP 024</span>.
This work is published from:
<span property="vcard:Country" datatype="dct:ISO3166"
content="US" about="sbolstandard.org">
United States</span>.
</p>

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