Sep028: Measurements/Parameters and Units (#212)

This commit adds incorporates a subset of classes from the Ontology of Units of Measure (OM) to represent measurements/parameters and their associated units. As part of this commit, a new `measure` property has been added to the relevant classes in the data model. As part of this change: * Add new validation rules to ComponentInstance, Module, Interaction, and Participation class * Add uml, text, and validation rules for Measurement class * Add uml, text, and validation rules for Unit class and derived classes * Add uml, text, and validation rules for Prefix class and derived classes Additional changes: * Splits out a complementary standards section
SynBioDex · Apr 3, 2019 · 9833489 · 9833489
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diff --git a/apdx-validation.tex b/apdx-validation.tex
diff --git a/complementary_standards.tex b/complementary_standards.tex
diff --git a/model.tex b/model.tex
@@ -589,6 +589,13 @@ \subsubsection{ComponentInstance}
 
 In some cases, a designer might want to set the \sbol{access} property of a \sbol{ComponentInstance} such that others cannot map to the \sbol{ComponentInstance} when they reuse its parent \sbol{ComponentDefinition}. For example, a designer who is concerned about retroactivity might set the \sbol{access} of the \sbol{ComponentInstance} to ``private'' in order to prevent its mapping to another \sbol{ComponentInstance} that participates in a new \sbol{Interaction} as part of a composite design.
 
+\twothreezero{
+\paragraph{The \sbolheading{measures} property}
+\label{sec:measures:CI}
+
+The \sbolmult{measures:CI}{measures} property is OPTIONAL and MAY contain a set of \sbol{Measure} objects. \ref{sec:Measure} contains a more detailed description of the \sbol{Measure} class.
+}
+
 \paragraph{Serialization}
 
 No serialization is defined for the \sbol{ComponentInstance} class, since this class is only used indirectly through the \sbol{Component} and \sbol{FunctionalComponent} subclasses.
@@ -1272,6 +1279,13 @@ \subsubsection{Module}
 
 \ref{sec:MapsTo} contains a detailed description of the \sbol{MapsTo} class.
 
+\twothreezero{
+\paragraph{The \sbolheading{measures} property}
+\label{sec:measures:M}
+
+The \sbolmult{measures:M}{measures} property is OPTIONAL and MAY contain a set of \sbol{Measure} objects. \ref{sec:Measure} contains a more detailed description of the \sbol{Measure} class.
+}
+
 \paragraph{Serialization}
 The serialization of \sbol{Module}s has the following form.
 \lstsetsbol
@@ -1403,6 +1417,13 @@ \subsubsection{Interaction}
 
 Even though an \sbol{Interaction} generally contains at least one \sbol{Participation}, the case of zero \sbol{Participation} objects is allowed because it is plausible that a designer might want to specify that an \sbol{Interaction} will exist, even if its \sbol{participant}s have not yet been determined.
 
+\twothreezero{
+\paragraph{The \sbolheading{measures} property}
+\label{sec:measures:I}
+
+The \sbolmult{measures:I}{measures} property is OPTIONAL and MAY contain a set of \sbol{Measure} objects. \ref{sec:Measure} contains a more detailed description of the \sbol{Measure} class.
+}
+
 \paragraph{Serialization}
 
 The serialization of an \sbol{Interaction} has the following form.
@@ -1494,6 +1515,12 @@ \subsubsection{Participation}
 
 The \sbol{participant} property MUST specify precisely one \sbol{FunctionalComponent} object that plays the designated role in its parent \sbol{Interaction} object.
 
+\twothreezero{
+\paragraph{The \sbolheading{measures} property}
+\label{sec:measures:P}
+
+The \sbolmult{measures:P}{measures} property is OPTIONAL and MAY contain a set of \sbol{Measure} objects. \ref{sec:Measure} contains a more detailed description of the \sbol{Measure} class.
+}
 
 \paragraph{Serialization}
 

diff --git a/practices.tex b/practices.tex
diff --git a/sbol2.tex b/sbol2.tex
@@ -65,7 +65,10 @@
 \lstdefinelanguage{sbol}
     {morekeywords={xmlns:sbol,xmlns:prov,xmlns:rdf,xmlns:dcterms,xmlns:myapp,rdf:RDF,rdf:resource,rdf:about,sbol:displayId,sbol:persistentIdentity,sbol:version,sbol:timeStamp,sbol:name,sbol:description,sbol:member,sbol:Collection,sbol:type,
         sbol:role, sbol:roleIntegration, sbol:ComponentDefinition, sbol:MapsTo, sbol:sequence,sbol:wasDerivedFrom,sbol:Component,sbol:subComponent,sbol:SequenceAnnotation,sbol:component,sbol:location, sbol:sourceLocation, sbol:sequenceAnnotation, sbol:Range, sbol:start, sbol:end, sbol:orientation,sbol:SequenceConstraint, sbol:restriction, sbol:subject, sbol:object,sbol:Sequence, sbol:elements, sbol:encoding,sbol:Model, sbol:source, sbol:language, sbol:framework,sbol:FunctionalComponent, sbol:Module, sbol:Interaction, sbol:interaction, sbol:module, sbol:model,sbol:Model,sbol:definition, sbol:access, sbol:direction, sbol:mapsTo, sbol:refinement, sbol:local, sbol:remote, sbol:participation, sbol:Participation, sbol:participant,sbol:sequenceConstraint,sbol:at,sbol:Cut,sbol:functionalComponent,sbol:ModuleDefinition,prov:wasDerivedFrom,dcterms:title,dcterms:description,sbol:Implementation,sbol:built,sbol:CombinatorialDerivation,sbol:template,sbol:strategy,sbol:variableComponent,sbol:VariableComponent,sbol:operator,sbol:variable,sbol:variant,sbol:variantCollection,sbol:variantDerivations,sbol:format,sbol:size,sbol:hash,sbol:Attachment,prov:wasGeneratedBy,prov:Activity,prov:startedAtTime,prov:endedAtTime,prov:wasInformedBy,prov:qualifiedUsage,prov:Usage,prov:entity,prov:qualifiedAssociation,prov:Association,prov:hadRole,prov:hadPlan,prov:Plan,prov:agent,prov:Agent,
-sbol:experimentalData,sbol:Experiment,sbol:ExperimentalData,sbol:attachment},
+sbol:experimentalData,sbol:Experiment,sbol:ExperimentalData,sbol:attachment,om:hasNumericalValue,om:symbol,om:alternativeSymbol,om:alternativeLabel,om:longcomment,om:hasFactor,
+om:hasTerm1,om:hasTerm2,om:hasNumerator,om:hasDenominator,om:hasBase,om:hasExponent,om:hasUnit,om:hasPrefix,rdfs:comment,rdfs:label,
+om:Measure,om:Unit,om:SingularUnit,om:CompoundUnit,om:om:UnitMultiplication,om:UnitDivision,om:Exponentiation,om:PrefixedUnit,om:Prefix,om:SIPrefix,
+om:BinaryPrefix,xlmns:om,xlmns:rdfs,xlmns:xsd,xml:lang},
      basicstyle=\fontsize{7}{9}\selectfont\ttfamily,
      backgroundcolor=\color{light-gray},
      keywordstyle=\color{blue},
@@ -269,6 +272,8 @@
 
 \input{practices}
 
+\input{complementary_standards}
+
 \newpage
 \bibliography{sbol}
 

diff --git a/uml/component_instance.pdf b/uml/component_instance.pdf
diff --git a/uml/interaction.pdf b/uml/interaction.pdf
diff --git a/uml/media_example.pdf b/uml/media_example.pdf
diff --git a/uml/module.pdf b/uml/module.pdf
diff --git a/uml/om.pdf b/uml/om.pdf
diff --git a/uml/participation.pdf b/uml/participation.pdf
diff --git a/umlet_source/component_instance_2.3.uxf b/umlet_source/component_instance_2.3.uxf
@@ -0,0 +1,175 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<diagram program="umlet" version="14.2">
+  <zoom_level>10</zoom_level>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>590</x>
+      <y>390</y>
+      <w>180</w>
+      <h>50</h>
+    </coordinates>
+    <panel_attributes>*FunctionalComponent*
+--
+-direction[1] : URI
+
+</panel_attributes>
+    <additional_attributes/>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>390</x>
+      <y>390</y>
+      <w>180</w>
+      <h>70</h>
+    </coordinates>
+    <panel_attributes>*Component*
+--
+-roles[0..*] : URI
+-roleIntegration[0..1] : URI
+
+</panel_attributes>
+    <additional_attributes/>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Relation</type>
+    <coordinates>
+      <x>450</x>
+      <y>310</y>
+      <w>150</w>
+      <h>100</h>
+    </coordinates>
+    <panel_attributes>lt=&lt;&lt;-</panel_attributes>
+    <additional_attributes>130;30;130;60;30;60;30;80</additional_attributes>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Relation</type>
+    <coordinates>
+      <x>570</x>
+      <y>310</y>
+      <w>130</w>
+      <h>100</h>
+    </coordinates>
+    <panel_attributes>lt=&lt;&lt;-</panel_attributes>
+    <additional_attributes>30;30;30;60;110;60;110;80</additional_attributes>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>510</x>
+      <y>250</y>
+      <w>170</w>
+      <h>90</h>
+    </coordinates>
+    <panel_attributes>*/ComponentInstance/*
+--
+-access[1] : URI
+
+
+</panel_attributes>
+    <additional_attributes/>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>540</x>
+      <y>190</y>
+      <w>100</w>
+      <h>30</h>
+    </coordinates>
+    <panel_attributes>/*Identified*/</panel_attributes>
+    <additional_attributes/>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Relation</type>
+    <coordinates>
+      <x>560</x>
+      <y>190</y>
+      <w>50</w>
+      <h>80</h>
+    </coordinates>
+    <panel_attributes>lt=&lt;&lt;-</panel_attributes>
+    <additional_attributes>30;30;30;60</additional_attributes>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>800</x>
+      <y>270</y>
+      <w>90</w>
+      <h>30</h>
+    </coordinates>
+    <panel_attributes>*MapsTo*
+
+
+
+</panel_attributes>
+    <additional_attributes/>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Relation</type>
+    <coordinates>
+      <x>650</x>
+      <y>230</y>
+      <w>170</w>
+      <h>94</h>
+    </coordinates>
+    <panel_attributes>lt=&lt;&lt;&lt;&lt;-&gt;
+mapsTos
+0..*</panel_attributes>
+    <additional_attributes>30;50;150;50</additional_attributes>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Relation</type>
+    <coordinates>
+      <x>310</x>
+      <y>250</y>
+      <w>220</w>
+      <h>110</h>
+    </coordinates>
+    <panel_attributes>lt=&lt;&lt;&lt;-&gt;
+definition
+    1</panel_attributes>
+    <additional_attributes>200;50;60;50;60;90</additional_attributes>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>290</x>
+      <y>340</y>
+      <w>170</w>
+      <h>30</h>
+    </coordinates>
+    <panel_attributes>*ComponentDefinition*</panel_attributes>
+    <additional_attributes/>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Relation</type>
+    <coordinates>
+      <x>650</x>
+      <y>280</y>
+      <w>170</w>
+      <h>94</h>
+    </coordinates>
+    <panel_attributes>lt=&lt;&lt;&lt;&lt;-&gt;
+measures
+0..*</panel_attributes>
+    <additional_attributes>30;50;150;50</additional_attributes>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>800</x>
+      <y>320</y>
+      <w>90</w>
+      <h>30</h>
+    </coordinates>
+    <panel_attributes>*Measure*
+
+
+
+</panel_attributes>
+    <additional_attributes/>
+  </element>
+</diagram>
diff --git a/umlet_source/interaction_2.3.uxf b/umlet_source/interaction_2.3.uxf
@@ -0,0 +1,101 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<diagram program="umlet" version="14.2">
+  <zoom_level>10</zoom_level>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>750</x>
+      <y>420</y>
+      <w>140</w>
+      <h>50</h>
+    </coordinates>
+    <panel_attributes>*Interaction*
+--
+-types[1..*] : URI
+
+</panel_attributes>
+    <additional_attributes/>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Relation</type>
+    <coordinates>
+      <x>860</x>
+      <y>400</y>
+      <w>190</w>
+      <h>94</h>
+    </coordinates>
+    <panel_attributes>lt=&lt;-&gt;&gt;&gt;&gt;
+participations
+0..*
+</panel_attributes>
+    <additional_attributes>170;50;30;50</additional_attributes>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Relation</type>
+    <coordinates>
+      <x>790</x>
+      <y>360</y>
+      <w>50</w>
+      <h>80</h>
+    </coordinates>
+    <panel_attributes>lt=&lt;&lt;-</panel_attributes>
+    <additional_attributes>30;30;30;60</additional_attributes>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>770</x>
+      <y>360</y>
+      <w>100</w>
+      <h>30</h>
+    </coordinates>
+    <panel_attributes>/*Identified*/</panel_attributes>
+    <additional_attributes/>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>1030</x>
+      <y>440</y>
+      <w>120</w>
+      <h>30</h>
+    </coordinates>
+    <panel_attributes>*Participation*
+
+
+
+
+</panel_attributes>
+    <additional_attributes/>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Relation</type>
+    <coordinates>
+      <x>600</x>
+      <y>400</y>
+      <w>170</w>
+      <h>94</h>
+    </coordinates>
+    <panel_attributes>lt=&lt;-&gt;&gt;&gt;&gt;
+measures
+0..*
+</panel_attributes>
+    <additional_attributes>30;50;150;50</additional_attributes>
+  </element>
+  <element>
+    <type>com.baselet.element.old.element.Class</type>
+    <coordinates>
+      <x>540</x>
+      <y>440</y>
+      <w>90</w>
+      <h>30</h>
+    </coordinates>
+    <panel_attributes>*Measure*
+
+
+
+
+</panel_attributes>
+    <additional_attributes/>
+  </element>
+</diagram>