| SEP | 028 |
|---|---|
| Title | Measurements/Parameters and Units |
| Authors | Jacob Beal ([email protected]) and Nicholas Roehner ([email protected]) |
| Editor | Curtis Madsen ([email protected]) |
| Type | Data Model |
| SBOL Version | 2.3 |
| Replaces | |
| Status | Accepted |
| Issue | #62 |
| Created | 3-Jul-2018 |
| Last modified | 22-Oct-2018 |
This SEP recommends the use of classes from the Ontology of Units of Measure (OM) to represent measurements/parameters and their associated units. This SEP also proposes adding a new OPTIONAL measure property to relevant classes in the SBOL data model, including Interaction, Participation, FunctionalComponent, and Module.
- 1. Rationale
- 2. Specification
- 2.1 Measurements/Parameters
- 2.1.1 Measure
- 2.1.2 Unit
- 2.1.3 Prefix
- 2.2 SBOL Class Extensions
- 3. Example or Use Case
- 4. Backwards Compatibility
- 5. Discussion
- 6. Relation to Other SEPs
- References
- Copyright
There are currently several use cases that warrant the inclusion of measurements/parameters and their associated units. These use cases include specification of genetic circuit designs and environmental conditions. In the first case, there is a need to specify the basic parameters of a genetic circuit (such as in a data sheet) to permit the generation of fully-fledged models of circuit behavior. In the second use case, there is a need to specify concentrations and other measures of environmental factors such as growth media that are conducive to design function or characteristic of an experimental condition.
Numerical measurements and parameters SHOULD be specified as members of the Measure, Unit, and Prefix classes from the Ontology of Units of Measure (OM). As incorporated into the SBOL data model, Measure is a subclass of Identified, while Unit and Prefix are subclasses of TopLevel (Figure 1).
Figure 1: Diagram of the Measure, Unit, and Prefix classes and their associated properties.
The purpose of the Measure class is to link a numerical value to a unit of measure. The hasNumericalValue property is REQUIRED and MUST contain a single xsd:float. Its hasUnit propery is also REQUIRED and MUST contain a single URI that refers to a member of the Unit class. Typically this URI will refer to a specific Unit that is already documented by OM, such as "gram per liter", but it can also refer to a custom Unit that is not covered by OM but is still useful for synthetic biology, such as "molecules of equivalent fluorescein", or "MEFL" for short. Finally, the types property is OPTIONAL and MAY contain a set of URIs. It is RECOMMENDED that these URIs identify terms from the Systems Biology Ontology (SBO). Note that this types property is added by SBOL and is not native to OM.
The purpose of the Unit class is to describe a particular unit of measure. The symbol property is REQUIRED and MUST contain a String. This String is commonly used to abbreviate the unit of measure's name. For example, the unit of measure named "gram per liter" is commonly abbreviated using the String "g/l". Alternative abbreviations can be specified using the alternativeSymbols property, which is OPTIONAL and MAY contain zero or more Strings. Similarly, alternative common names can be specified using the alternativeLabels property, which is OPTIONAL and MAY contain zero or more Strings. Finally, the longcomment property is OPTIONAL and MAY contain a String. A long comment is an alternative description that is expected to be, well, long.
Since the Unit class is abstract, specific units of measure are represented as instances of its subclasses: SingularUnit, PrefixedUnit, UnitMultiplication, UnitDivision, and UnitExponentiation.
The SingularUnit class is used to describe a unit of measure that is not explicitly represented as a multiplication, division, or exponentiation of two or more units, but could be equivalent to such a representation. For example, joule is considered a SingularUnit, but it is equivalent to the multiplication of a newton and a meter. The 'hasFactor' property of the SingularUnit class is OPTIONAL and MAY contain a xsd:float. The hasUnit property is also OPTIONAL and MAY contain a single URI that refers to another member of the Unit class. These properties can be used in conjunction to specify whether a SingularUnit is defined as another Unit multiplied by some factor. For example, an angstrom is defined as 10-10 meters. If the hasFactor property of a SingularUnit is non-empty, then its hasUnit property SHOULD also be non-empty.
The PrefixedUnit class used to desribe a unit of measure that is explicitly represented as the product of some factor and another Unit. Similar to the SingularUnit class, the PrefixedUnit class includes a hasUnit property, but this property is REQUIRED rather than OPTIONAL. Instead of a hasFactor property, the PrefixedUnit class includes a REQUIRED hasPrefix property that MUST contain a single URI that refers to a member of the Prefix class (a standard factor).
The UnitMultiplication class is used to describe a unit of measure that is the multiplication of two other units of measure. The hasTerm1 and hasTerm2 properties are both REQUIRED and MUST each contain a single URI that refers to a member of the Unit class. Next, the UnitExponentiation class is used to describe a unit of measure that is the exponentiation of one unit of measure by another. The hasBase and hasExponent properties are both REQUIRED and MUST each contain a single URI that refers to a member of the Unit class. Finally, the UnitDivision class is used to describe a unit of measure that is the division of one unit of measure by another. The hasNumerator and hasDenominator properties are both REQUIRED and MUST each contain a single URI that refers to a member of the Unit class.
The purpose of the Prefix class is to describe a standard factor for defining a Unit in terms of a multiplication of said factor and another Unit. For example, a milligram is defined as the multiplication of a gram and the standard factor 10-3 (milli). The hasFactor property is REQUIRED and MUST contain an xsd:float. Much like the Unit class, the Prefix class also has a symbol property that is REQUIRED and MUST contain a String. This String is commonly used to abbreviate the prefix's name. For example, the prefix named "milli" is commonly abbreviated using the String "m". Alternative abbreviations can be specified using the alternativeSymbols property, which is OPTIONAL and MAY contain zero or more Strings. Similarly, alternative common names can be specified using the alternativeLabels property, which is OPTIONAL and MAY contain zero or more Strings. Finally, the longcomment property is OPTIONAL and MAY contain a String.
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.
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."
Figure 2: UML example of a media recipe represented using instances of the Measure and Unit classes from OM.
The best practices in this proposal do not affect backwards compatibility.
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OM - Ontology of Units of Measure. https://github.com/HajoRijgersberg/OM
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SEP 028.
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