Fixed typos

Author: cjmyers

apdx-validation.tex

@@ -169,7 +169,8 @@ \subsubsection*{Rules for the \class{Sequence} class}
 \setcounter{sbolCtr}{10401}
 
 \twozeroone{
-\printValid{A \sbol{Sequence} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations}, \sbol{elements}, and \sbol{encoding}.\\ Reference: \sec{sec:Sequence}}
+\printValid{A \sbol{Sequence} MUST NOT have properties other than the following: \sbol{identity},\\ \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\
+\sbol{annotations}, \sbol{elements}, and \sbol{encoding}.\\ Reference: \sec{sec:Sequence}}
 % A \sbol{Sequence} MUST inherit all properties of the \sbol{TopLevel} class.
 }
 
@@ -193,7 +194,9 @@ \subsubsection*{Rules for the \class{ComponentDefinition} class}
 \setcounter{sbolCtr}{10501}
 
 \twozeroone{
-\printValid{A \sbol{ComponentDefinition} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations}, \sbolmult{types:CD}{types}, \sbolmult{types:CD}{roles}, \sbol{components}, \sbol{sequences}, \sbol{sequenceAnnotations}, and \sbol{sequenceConstraints}.\\ Reference: \sec{sec:ComponentDefinition}}
+\printValid{A \sbol{ComponentDefinition} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\
+\sbol{annotations}, \sbolmult{types:CD}{types}, \sbolmult{types:CD}{roles}, \sbol{components}, \sbol{sequences}, \sbol{sequenceAnnotations}, and\\
+\sbol{sequenceConstraints}.\\ Reference: \sec{sec:ComponentDefinition}}
 %A \sbol{ComponentDefinition} MUST inherit all properties of the \sbol{TopLevel} class.}
 }
 
@@ -327,7 +330,8 @@ \subsubsection*{Rules for the \class{Component} class}
 \setcounter{sbolCtr}{10701}
 
 \twoonezero{
-\printValid{A \sbol{Component} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations}, \sbol{access}, \sbolmult{definition:CI}{definition}, \sbolmult{mapsTos:CI}{mapsTos}, \sbolmult{roles:C}{roles}, and \sbolmult{roleIntegration:C}{roleIntegration}.\\ Reference: \sec{sec:Component}}
+\printValid{A \sbol{Component} MUST NOT have properties other than the following: \sbol{identity},\\ \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\
+\sbol{annotations}, \sbol{access}, \sbolmult{definition:CI}{definition}, \sbolmult{mapsTos:CI}{mapsTos}, \sbolmult{roles:C}{roles}, and \sbolmult{roleIntegration:C}{roleIntegration}.\\ Reference: \sec{sec:Component}}
 % A \sbol{Component} MUST inherit all properties of the \sbol{ComponentInstance} class.
 }
 
@@ -406,7 +410,8 @@ \subsubsection*{Rules for the \class{SequenceAnnotation} class}
 \setcounter{sbolCtr}{10901}
 
 \twoonezero{
-\printValid{A \sbol{SequenceAnnotation} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations}, \sbol{component}, \sbol{locations}, and \sbolmult{roles:SA}{roles}.\\ Reference: \sec{sec:SequenceAnnotation}}
+\printValid{A \sbol{SequenceAnnotation} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\
+\sbol{annotations}, \sbol{component}, \sbol{locations}, and \sbolmult{roles:SA}{roles}.\\ Reference: \sec{sec:SequenceAnnotation}}
 %A \sbol{SequenceAnnotation} MUST inherit all properties of the \sbol{Identified} class.
 }
 
@@ -474,7 +479,10 @@ \subsubsection*{Rules for the \class{GenericLocation} class}
 \setcounter{sbolCtr}{11301}
 
 \twozeroone{
-\printValid{A \sbol{GenericLocation} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations}, and \sbol{orientation}.\\
+\printValid{A \sbol{GenericLocation} MUST NOT have properties other than the following: 
+\sbol{identity},\\
+\sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\
+\sbol{annotations}, and \sbol{orientation}.\\
 Reference: \sec{sec:GenericLocation}}
 %A \sbol{GenericLocation} MUST inherit all properties of the \sbol{Location} class.
 }
@@ -483,7 +491,8 @@ \subsubsection*{Rules for the \class{SequenceConstraint} class}
 \setcounter{sbolCtr}{11401}
 
 \twozeroone{
-\printValid{A \sbol{SequenceConstraint} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations}, \sbol{restriction}, \sbol{subject}, and \sbol{object}.\\ Reference: \sec{sec:SequenceConstraint}}
+\printValid{A \sbol{SequenceConstraint} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\
+\sbol{annotations}, \sbol{restriction}, \sbol{subject}, and \sbol{object}.\\ Reference: \sec{sec:SequenceConstraint}}
 %A \sbol{SequenceConstraint} MUST inherit all properties of the \sbol{Identified} class.
 }
 
@@ -549,7 +558,8 @@ \subsubsection*{Rules for the \class{ModuleDefinition} class}
 \setcounter{sbolCtr}{11601}
 
 \twozeroone{
-\printValid{A \sbol{ModuleDefinition} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations}, \sbolmult{roles:MD}{roles}, \sbol{modules}, \sbol{interactions}, \sbol{functionalComponents}, and \sbol{models}.\\ Reference: \sec{sec:ModuleDefinition}}
+\printValid{A \sbol{ModuleDefinition} MUST NOT have properties other than the following: \sbol{identity},\\ \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\
+\sbol{annotations}, \sbolmult{roles:MD}{roles}, \sbol{modules}, \sbol{interactions}, \sbol{functionalComponents}, and \sbol{models}.\\ Reference: \sec{sec:ModuleDefinition}}
 % A \sbol{ModuleDefinition} MUST inherit all properties of the \sbol{TopLevel} class.
 }
 
@@ -561,7 +571,7 @@ \subsubsection*{Rules for the \class{ModuleDefinition} class}
 
 \printValid{The \sbol{interactions} property is OPTIONAL and MAY contain a set of \sbol{Interaction} objects.\\ Reference: \sec{sec:ModuleDefinition}}
 
-\printValid{The \sbol{functionalComponents} property is OPTIONAL and MAY contain a set of \sbol{FunctionalComponent} objects.\\ Reference: \sec{sec:ModuleDefinition}}
+\printValid{The \sbol{functionalComponents} property is OPTIONAL and MAY contain a set of\\ \sbol{FunctionalComponent} objects.\\ Reference: \sec{sec:ModuleDefinition}}
 
 \printValid{The \sbol{models} property is OPTIONAL and MAY contain a set of \sbol{URI}s.  \\ Reference: \sec{sec:ModuleDefinition}}
 
@@ -583,7 +593,7 @@ \subsubsection*{Rules for the \class{Module} class}
 \printComplete{The \sbol{URI} contained by the \sbolmult{definition:M}{definition} property of \sbol{Module} MUST refer to a \sbol{ModuleDefinition}.\\ Reference: \sec{sec:Module}}
 }
 
-\printValid{The \sbolmult{definition:CI}{definition} property of a \sbol{Module} MUST NOT contain a \sbol{URI} reference to the \sbol{ModuleDefinition} that contains the \sbol{Module}.\\ Reference: \sec{sec:Module}}
+\printValid{The \sbolmult{definition:CI}{definition} property of a \sbol{Module} MUST NOT contain a \sbol{URI} reference to the\\ \sbol{ModuleDefinition} that contains the \sbol{Module}.\\ Reference: \sec{sec:Module}}
 
 \twozeroone{
 \printComplete{\sbol{Module} objects MUST NOT form circular reference chains via their \sbolmult{definition:CI}{definition} properties and parent \sbol{ModuleDefinition} objects.\\ Reference: \sec{sec:Module}}
@@ -595,7 +605,7 @@ \subsubsection*{Rules for the \class{FunctionalComponent} class}
 \setcounter{sbolCtr}{11801}
 
 \twozeroone{
-\printValid{A \sbol{FunctionalComponent} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations},\sbol{access}, \sbolmult{definition:M}{definition}, and \sbolmult{mapsTos:M}{mapsTos}, and \sbol{direction}.\\ Reference: \sec{sec:ComponentInstance}}
+\printValid{A \sbol{FunctionalComponent} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\ \sbol{annotations}, \sbol{access}, \sbolmult{definition:M}{definition}, and \sbolmult{mapsTos:M}{mapsTos}, and \sbol{direction}.\\ Reference: \sec{sec:ComponentInstance}}
 %A \sbol{FunctionalComponent} MUST inherit all properties of the \sbol{ComponentInstance} class.
 }
 
@@ -606,7 +616,8 @@ \subsubsection*{Rules for the \class{Interaction} class}
 \setcounter{sbolCtr}{11901}
 
 \twozeroone{
-\printValid{An \sbol{Interaction} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations}, \sbolmult{types:I}{types}, and \sbol{participations}.\\ Reference: \sec{sec:Interaction}}
+\printValid{An \sbol{Interaction} MUST NOT have properties other than the following: \sbol{identity},\\ \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\
+\sbol{annotations}, \sbolmult{types:I}{types}, and \sbol{participations}.\\ Reference: \sec{sec:Interaction}}
 %An \sbol{Interaction} MUST inherit all properties of the \sbol{Identified} class.
 }
 
@@ -631,7 +642,7 @@ \subsubsection*{Rules for the \class{Participation} class}
 \setcounter{sbolCtr}{12001}
 
 \twozeroone{
-\printValid{A \sbol{Participation} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations}, \sbolmult{roles:P}{roles}, and \sbol{participant}.\\ Reference: \sec{sec:Participation}}
+\printValid{A \sbol{Participation} MUST NOT have properties other than the following: \sbol{identity},\\ \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\ \sbol{annotations}, \sbolmult{roles:P}{roles}, and \sbol{participant}.\\ Reference: \sec{sec:Participation}}
 % A \sbol{Participation} MUST inherit all properties of the \sbol{Identified} class.
 }
 
@@ -655,7 +666,7 @@ \subsubsection*{Rules for the \class{Collection} class}
 \setcounter{sbolCtr}{12101}
 
 \twozeroone{
-\printValid{A \sbol{Collection} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, \sbol{annotations}, and \sbol{members}.\\Reference: \sec{sec:Collection}}
+\printValid{A \sbol{Collection} MUST NOT have properties other than the following: \sbol{identity},\\ \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description},\\ \sbol{annotations}, and \sbol{members}.\\Reference: \sec{sec:Collection}}
 }
 
 \printValid{The \sbol{members} property of a \sbol{Collection} is OPTIONAL and MAY contain a set of \sbol{URI}s.\\ Reference: \sec{sec:Collection}}
@@ -687,7 +698,7 @@ \subsubsection*{Rules for the \class{GenericTopLevel} class}
 \setcounter{sbolCtr}{12301}
 
 \twozeroone{
-\printValid{A \sbol{GenericTopLevel} MUST NOT have properties other than the following: \sbol{identity}, \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, and \sbol{annotations}.\\Reference: \sec{sec:GenericTopLevel}}
+\printValid{A \sbol{GenericTopLevel} MUST NOT have properties other than the following: \sbol{identity},\\ \sbol{persistentIdentity}, \sbol{displayId}, \sbol{version}, \sbol{wasDerivedFrom}, \sbol{name}, \sbol{description}, and\\ \sbol{annotations}.\\Reference: \sec{sec:GenericTopLevel}}
 }
 
 \printValid{The \sbol{rdfType} property of a \sbol{GenericTopLevel} object is REQUIRED and MUST contain a \sbol{QName}.\\ Reference: \sec{sec:GenericTopLevel}}

model.tex

@@ -788,7 +788,7 @@ \subsubsection{SequenceAnnotation}
 
 The \sbolmult{roles:SA}{roles} property comprises an OPTIONAL set of zero or more \sbol{URI}s describing the specified sequence feature being annotated.  If provided, these \sbolmult{roles:SA}{role} \sbol{URI}s MUST identify terms from appropriate ontologies. Roles are not restricted to describing biological function; they may annotate \sbol{Sequence}s' function in any domain for which an ontology exists.
 
-It is RECOMMENDED that these \sbolmult{roles:SA}{role} \sbol{URI}s identify terms that are compatible with the \sbolmult{types:CD}{type} properties of this \sbol{SequenceAnnotation}'s' parent \sbol{ComponentDefinition}. For example, a \sbolmult{roles:SA}{role} of a \sbol{SequenceAnnotation} which belongs to a \sbol{ComponentDefinition} of type DNA might refer to terms from the Sequence Ontology. A table of recommended ontology terms for \sbolmult{roles:SA}{roles} is given in \ref{tbl:componentdefinition_roles}.
+It is RECOMMENDED that these \sbolmult{roles:SA}{role} \sbol{URI}s identify terms that are compatible with the \sbolmult{types:CD}{type} properties of this \sbol{SequenceAnnotation}'s parent \sbol{ComponentDefinition}. For example, a \sbolmult{roles:SA}{role} of a \sbol{SequenceAnnotation} which belongs to a \sbol{ComponentDefinition} of type DNA might refer to terms from the Sequence Ontology. A table of recommended ontology terms for \sbolmult{roles:SA}{roles} is given in \ref{tbl:componentdefinition_roles}.
 }
 
 \paragraph{Serialization}

practices.tex

@@ -181,7 +181,7 @@ \subsubsection{Association}
 An \sbol{Association} is linked to an \sbol{Agent} through the \sbol{agent} relationship. The \sbol{Association} includes the \texttt{hadRole} property to qualify the role of the \sbol{Agent} in the \sbol{Activity}.
 
 \paragraph{The \sbolheading{agent} property}\label{sec:agent}
-The \sbol{agent} property is REQUIRED and MUST contain a \sbol{URI}s that refers to an \sbol{Agent} object.
+The \sbol{agent} property is REQUIRED and MUST contain a \sbol{URI} that refers to an \sbol{Agent} object.
 
 \paragraph{The \sbolheading{hadRole} property}\label{sec:hadRole}
 The \sbol{hadRole} property is REQUIRED and MUST contain a \sbol{URI} that refers to a particular term describing the usage of the agent.