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incorporate Herbert's comments

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jakebeal
jakebeal committed Dec 1, 2017
1 parent c196935 commit 53f7d83958e0e802a299fefb03d88aa98ff31e2a
@@ -37,7 +37,7 @@ \section{Examples}\label{sec:examples}
\begin{figure}[h!]
\includegraphics[scale=0.5]{figures/apdx-examples/apdx-exa6.pdf}
\caption{Promoter stored in a plasmid as in \ref{f:apdx:exa3}, except that there is a ribonuclease sites after the promoter rather than restriction sites flanking it.}
\caption{Promoter stored in a plasmid as in \ref{f:apdx:exa3}, except that there is a ribonuclease site after the promoter rather than restriction sites flanking it.}
\label{f:apdx:exa6}
\end{figure}
@@ -14,14 +14,14 @@ \section{SBOL Visual Glyphs}\label{apdx:symbols}
\subsection{Sequence Feature Glyphs}\label{apdx:sym:feature}
These glyphs represent features of nucleic acid sequences, and include a bounding box and a recommended alignment to the nucleic acid backbone.
These glyphs represent features of nucleic acid sequences, and include a bounding box (grey dashed box) and a recommended alignment to the nucleic acid backbone (grey dashed horizontal line).
\input{glyphscript/glyphs.tex}
\subsection{Molecular Species Glyphs}\label{apdx:sym:species}
These glyphs represent molecular species in a diagram, and include a bounding box but are not connected to any nucleic acid backbone.
These glyphs represent molecular species in a diagram, and include a bounding box (grey dashed box) but are not connected to any nucleic acid backbone.
\input{glyphscript/speciesglyphs.tex}
@@ -4,7 +4,7 @@
%% Variation from BBF RFC 0 specs confirmed in email communication with BBF by Jake Beal, 3/21/15
Copyright (C) The BioBricks Foundation and all authors listed on this BBF RFC. This work is made available under the Creative Commons Attribution 4.0 International Public License. To view a copy of this license visit \href{https://creativecommons.org/licenses/by/4.0/}{https://creativecommons.org/licenses/by/4.0/}.
Copyright \copyright{} The BioBricks Foundation and all authors listed on this BBF RFC. This work is made available under the Creative Commons Attribution 4.0 International Public License. To view a copy of this license visit \href{https://creativecommons.org/licenses/by/4.0/}{https://creativecommons.org/licenses/by/4.0/}.
%In addition to the listed authors, the following people are specifically recognized as additional contributors sharing in the copyright (alphabetically by institution):
%\tododeferred{Any additional authors?}
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@@ -8,15 +8,15 @@ \section{SBOL Glyphs}\label{sec:glyphs}
This section explains how glyphs are specified and how to add new glyphs.
Each SBOL glyph is defined by association with ontology terms, and can be used to represent any diagram element that is well-described by that term.
Currently there are three classes of glyphs, each associated with a different ontology and different class in an SBOL 2 data model:
Currently there are three classes of glyphs, each associated with a different ontology and different class in the SBOL 2 data model:
\begin{itemize}
\item {\bf Sequence Feature Glyphs} describe features of nucleic acid sequences. They are associated with Sequence Ontology terms.
For SBOL 2 data models, this is formally defined as any \sbol{Component} with a compatible term within its associated \sbol{roles},
For the SBOL 2 data model, this is formally defined as any \sbol{Component} with a compatible term within its associated \sbol{roles},
i.e., one that is equal to or a child of at least one term associated with the glyph.
\item {\bf Molecular Species Glyphs} represent any class of molecule whose detailed structure is not being shown using sequence feature glyphs. They are associated with BioPAX terms. For SBOL 2 data models, this is formally defined as any \sbol{FunctionalComponent} with a compatible term within its associated \sbol{types},
\item {\bf Molecular Species Glyphs} represent any class of molecule whose detailed structure is not being shown using sequence feature glyphs. They are associated with BioPAX terms. For the SBOL 2 data model, this is formally defined as any \sbol{FunctionalComponent} with a compatible term within its associated \sbol{types},
i.e., one that is equal to or a child of at least one term associated with the glyph.
\item {\bf Interaction Glyphs} are ``arrows'' indicating functional relationships between sequence features and/or molecular species. They are associated with Systems Biology Ontology terms.
For SBOL 2 data models, this is formally defined as any \sbol{Interaction} with a compatible term within its \sbol{types},
For the SBOL 2 data model, this is formally defined as any \sbol{Interaction} with a compatible term within its \sbol{types},
i.e., one that is equal to or a child of at least one term associated with the glyph,
and with a compatible \sbol{Participation} at the head and tail of the arrow.
\end{itemize}
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@@ -6,9 +6,9 @@ \section{SBOL Visual Diagram Language}
An SBOL Visual diagram represents information about the structure of a nucleic acid design and its associated molecular species and interactions.
%
If desired, an SBOL Visual diagram may also be associated with a machine-interpretable model (e.g., in SBOL, GenBank, or SBML format).
In this document we describe the association for SBOL 2 data models, which provides a formal semantic grounding for all elements of an SBOL Visual diagram, but equivalent associations may be made between diagram elements and other models.
In this document we describe the association for the SBOL 2 data model, which provides a formal semantic grounding for all elements of an SBOL Visual diagram, but equivalent associations may be made between diagram elements and other models.
%
In terms of SBOL 2 data models, the description of a nucleic acid design is formally defined as representation of a \sbol{ComponentDefinition} with a nucleic acid \sbol{type}, the \sbol{Component} and \sbol{SequenceAnnotation} objects describing the features and sub-structure of the design, and \sbol{SequenceConstraint} information on the relative positions of such elements.
In terms of the SBOL 2 data model, the description of a nucleic acid design is formally defined as a representation of a \sbol{ComponentDefinition} with a nucleic acid \sbol{type}, the \sbol{Component} and \sbol{SequenceAnnotation} objects describing the features and sub-structure of the design, and \sbol{SequenceConstraint} information on the relative positions of such elements.
%
The description of interactions between some number of nucleic acid designs and other molecular species is formally defined as a representation of a \sbol{ModuleDefinition}, the \sbol{FunctionalComponent} objects describing the nucleic acid designs and other molecular species, and the \sbol{Interaction} and \sbol{Participation} objects describing their functional relationships.
@@ -41,9 +41,9 @@ \subsection{Nucleic Acid Backbone}
\label{s:lang:backbone}
A diagram for a nucleic acid construct is based around a single or double line, representing the nucleic acid backbone.
Information about features of the construct can then be represented by attaching nucleic acid glyphs to the backbone, as defined below in \ref{s:lang:nacomponent}
Information about features of the construct can then be represented by attaching nucleic acid glyphs to the backbone, as defined below in \ref{s:lang:nacomponent}.
%
In terms of SBOL 2 data models, the backbone represents a \sbol{ComponentDefinition} with a nucleic acid \sbol{type} (e.g., DNA, RNA), and the features represent \sbol{Component} and \sbol{SequenceAnnotation} members of the \sbol{ComponentDefinition}.
In terms of the SBOL 2 data model, the backbone represents a \sbol{ComponentDefinition} with a nucleic acid \sbol{type} (e.g., DNA, RNA), and the features represent \sbol{Component} and \sbol{SequenceAnnotation} members of the \sbol{ComponentDefinition}.
\begin{enumerate}
\item Lines in some cases indicate strand count.
@@ -82,7 +82,7 @@ \subsection{Nucleic Acid Sequence Features}
A glyph in contact with a nucleic acid backbone indicates a feature of the nucleic acid sequence.
%
In terms of SBOL 2 data models, this is either a \sbol{SequenceFeature} or a \sbol{Component} with a nucleic acid \sbol{type} that is contained within the \sbol{ComponentDefinition} associated with that nucleic acid backbone.
In terms of the SBOL 2 data model, this is either a \sbol{SequenceFeature} or a \sbol{Component} with a nucleic acid \sbol{type} that is contained within the \sbol{ComponentDefinition} associated with that nucleic acid backbone.
The \sbol{Component} may be contained either directly, as one of the \sbol{components} of the \sbol{ComponentDefinition}, or recursively through a sequence of such containments.
\begin{enumerate}
@@ -120,7 +120,7 @@ \subsection{Nucleic Acid Sequence Features}
\end{figure}
\item Nucleic acid features in a sequential relationship SHOULD be drawn from 5' left to 3' right on the inline strand and from 5' right to 3' left on the reverse complement strand.
In terms of SBOL 2 data models, this indicates a \sbol{SequenceConstraint} on the relative ordering of two features.
In terms of the SBOL 2 data model, this indicates a \sbol{SequenceConstraint} on the relative ordering of two features.
\item Nucleic acid features that do not overlap in their locations SHOULD NOT have glyphs whose bounding boxes overlap.
An example is provided in~\ref{exa:2d}.
@@ -144,7 +144,7 @@ \subsection{Nucleic Acid Sequence Features}
\end{figure}
\item A nucleic acid feature SHOULD be represented using a glyph defined in \ref{apdx:sym:feature}. In this case, the feature MUST be contained within at least one of the glyph's associated terms.
In terms of SBOL 2 data models, this means the glyph is equal to or a parent of at least one of the \sbol{roles} for the \sbol{Component} or its associated \sbol{ComponentDefinition}.
In terms of the SBOL 2 data model, this means the glyph is equal to or a parent of at least one of the \sbol{roles} for the \sbol{Component} or its associated \sbol{ComponentDefinition}.
Moreover, the glyph used SHOULD be the RECOMMENDED variant of the most specific applicable glyph. Note that novel glyphs not defined in \ref{apdx:sym:feature} MAY be used, but SHOULD be proposed for adoption as described in \ref{sec:extension}.
Examples are provided in~\ref{exa:2f}.
\begin{figure}[h!]
@@ -162,12 +162,12 @@ \subsection{Nucleic Acid Sequence Features}
\subsection{Molecular Species}
A glyph that is not in contact with any backbone represents any class of molecule whose detailed structure is not being shown using sequence feature glyphs.
In other words, either not a nucleic acid (e.g., proteins, small molecules) or else an ``uninteresting'' nucleic acid (e.g., showing a transcribed mRNA, but not the features of its sequence).
In terms of SBOL 2 data models, this is a \sbol{FunctionalComponent} that is contained within a \sbol{ModuleDefinition} implicit in the diagram.
In terms of the SBOL 2 data model, this is a \sbol{FunctionalComponent} that is contained within a \sbol{ModuleDefinition} implicit in the diagram.
\begin{enumerate}
\item A molecular species glyph MUST NOT contact any nucleic acid backbone with any part of its bounding box.
\item A molecular species SHOULD be represented using a glyph defined in \ref{apdx:sym:species}. In this case, the species MUST be contained within at least one of the glyph's associated terms.
In terms of SBOL 2 data models, this means the glyph is equal to or a parent of at least one of the \sbol{types} for the associated \sbol{ComponentDefinition}.
In terms of the SBOL 2 data model, this means the glyph is equal to or a parent of at least one of the \sbol{types} for the associated \sbol{ComponentDefinition}.
Moreover, the glyph used SHOULD be the RECOMMENDED variant of the most specific applicable glyph. Note that novel glyphs not defined in \ref{apdx:sym:species} MAY be used, but SHOULD be proposed for adoption as described in \ref{sec:extension}.
\end{enumerate}
@@ -176,7 +176,7 @@ \subsection{Interaction}
A directed edge ``arrow'' attached to one or more glyphs indicates a functional interaction involving those elements.
The roles of the elements is indicated by their position at the head or tail of the edge.
In terms of SBOL 2 data models, this is an \sbol{Interaction}, with either one or two \sbol{Participation} relationships, their \sbol{role} set by position at the head or tail of the edge.
In terms of the SBOL 2 data model, this is an \sbol{Interaction}, with either one or two \sbol{Participation} relationships, their \sbol{role} set by position at the head or tail of the edge.
An example is provided in~\ref{exa:4}.
\begin{figure}[h!]
@@ -207,13 +207,13 @@ \subsection{Interaction}
\end{figure}
\item An interaction SHOULD be represented using a glyph defined in \ref{apdx:sym:interaction}. In this case, the interaction type MUST be contained within at least one of the glyph's associated terms.
In terms of SBOL 2 data models, this means the glyph is equal to or a parent of at least one of the \sbol{types} for the \sbol{Interaction}, and that each associated \sbol{Participation} object has a \sbol{role} compatible with its position on the head or tail of the edge.
In terms of the SBOL 2 data model, this means the glyph is equal to or a parent of at least one of the \sbol{types} for the \sbol{Interaction}, and that each associated \sbol{Participation} object has a \sbol{role} compatible with its position on the head or tail of the edge.
Moreover, the glyph used SHOULD be the RECOMMENDED variant of the most specific applicable glyph. Note that novel glyphs not defined in \ref{apdx:sym:interaction} MAY be used, but SHOULD be proposed for adoption as described in \ref{sec:extension}.
\end{enumerate}
\subsection{Labels}
The name of any object in a diagram is RECOMMENDED to be displayed as text within, adjacent to, or otherwise clearly visually connected to the object's associated glyph. In terms of SBOL 2 data models, this is the \sbol{name} property, and if no \sbol{name} is supplied then the \sbol{displayId} MAY be used instead.
The name of any object in a diagram is RECOMMENDED to be displayed as text within, adjacent to, or otherwise clearly visually connected to the object's associated glyph. In terms of the SBOL 2 data model, this is the \sbol{name} property, and if no \sbol{name} is supplied then the \sbol{displayId} MAY be used instead.
Examples are provided in~\ref{exa:5}.
\begin{figure}[h!]
@@ -2,7 +2,7 @@
\section{Purpose}
% -----------------------------------------------------------------------------
People who are engineering biological organisms often find it useful to communicate in
People who engineer biological organisms often find it useful to communicate in
diagrams, both about the structure of the nucleic acid sequences that they are engineering
and about the functional relationships between sequence features and other molecular species.
%
@@ -23,8 +23,8 @@ \section{Purpose}
\subsection{Relation to Data Models}
In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics.
In particular, glyphs in SBOL Visual are defined in terms of their relation to the SBOL 2 data model and terms in the Sequence Ontology~\citep{SequenceOntology},
In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with well-defined semantics.
In particular, glyphs in SBOL Visual are defined in terms of their relation to the SBOL 2 data model (as defined in BBF RFC 112) and terms in the Sequence Ontology~\citep{SequenceOntology},
the Systems Biology Ontology~\citep{SBO}, and BioPAX~\citep{BioPAX}.
SBOL Visual is not intended to represent designs at the same level of detail as these data models.

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