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Update SEP 028 by renaming measure property to measures and adding ty…

…pes to Measure objects in example.
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nroehner committed Oct 22, 2018
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@@ -76,12 +76,12 @@ The purpose of the `Prefix` class is to describe a standard factor for defining
### 2.2 SBOL Class Extensions<a name="sbol_extension"></a>
In order for relevant SBOL classes to be linked to parameters or measurements and their associated units, we propose adding an OPTIONAL `measure` property to the `FunctionalComponent`, `Module`, `Interaction`, and `Participation` classes. This property MAY specify a set of `Measure` objects contained by the parent. For example, an `Interaction` that represents a chemical reaction may have parameters added to it and each `Participation` it contains to capture its chemical kinetic rate and the stoichiometries of its reactants and products. A `ModuleDefinition` that represents growth media recipe may have measures added to each `FunctionalComponent` "ingredient" it contains and/or each `Module` "sub-media" that it includes.
In order for relevant SBOL classes to be linked to parameters or measurements and their associated units, we propose adding an OPTIONAL `measures` property to the `FunctionalComponent`, `Module`, `Interaction`, and `Participation` classes. This property MAY specify a set of `Measure` objects contained by the parent. For example, an `Interaction` that represents a chemical reaction may have parameters added to it and each `Participation` it contains to capture its chemical kinetic rate and the stoichiometries of its reactants and products. A `ModuleDefinition` that represents growth media recipe may have measures added to each `FunctionalComponent` "ingredient" it contains and/or each `Module` "sub-media" that it includes.
## 3. Example or Use Case <a name='example'></a>
-------------------------------
Figure 2 shows an example of using instances of the `Measure` and `Unit` classes in conjunction with instances of the SBOL `ModuleDefinition` and `ComponentDefinition` classes to specify a growth medium recipe. Note that this specification for M9 Glucose CAA media is partly composed from the specification of another growth medium, Teknova M1902. Namespace abbreviations used in this example include `om` for `http://www.ontology-of-units-of-measure.org/resource/om-2/`, `obo` for `http://purl.obolibrary.org/obo/`, and `chebi` for `http://identifiers.org/chebi/`. C85504 codes for the term "growth medium" in the National Cancer Institute Thesaurus (NCIT).
Figure 2 shows an example of using instances of the `Measure` and `Unit` classes in conjunction with instances of the SBOL `ModuleDefinition` and `ComponentDefinition` classes to specify a growth medium recipe. Note that this specification for M9 Glucose CAA media is partly composed from the specification of another growth medium, Teknova M1902. Namespace abbreviations used in this example include `om` for `http://www.ontology-of-units-of-measure.org/resource/om-2/`, `obo` for `http://purl.obolibrary.org/obo/`, `chebi` for `http://identifiers.org/chebi/`, and `sbo` for `http://identifiers.org/biomodels.sbo/`. C85504 codes for the term "growth medium" in the National Cancer Institute Thesaurus (NCIT). For specifying `Measure` `types` with SBO, 0000196 codes for "concentration of an entity pool", 0000226 codes for "density of an entity pool", and 0000470 codes for "mass fraction."
![Media recipe diagram](images/sep_028_media_recipe_example.png "Media recipe diagram")
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