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add change bars to SBOL Visual 2.1

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jakebeal
jakebeal committed Mar 30, 2019
1 parent 34d1013 commit 28b0967253743e6528740c7eb3e740182af46233
@@ -83,12 +83,13 @@ \section{Examples}\label{sec:examples}
\label{f:apdx:exa13}
\end{figure}

\twoonezero{
\begin{figure}[h!]
\includegraphics[scale=0.5]{figures/apdx-examples/apdx-exa14.pdf}
\caption{Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form an active transcriptional activator, which then stimulates a promoter.}
\label{f:apdx:exa14}
\end{figure}

}

% Figure black magic: adjust the size here as needed to get the spacing on the last page of the section correct.
%\begin{figure}[h!]
@@ -32,8 +32,10 @@ \subsection{Interaction Glyphs}\label{apdx:sym:interaction}

\input{glyphscript/interactionglyphs.tex}

\twoonezero{
\subsection{Interaction Node Glyphs}\label{apdx:sym:interactionnodes}

These glyphs are placed at the junctions of edges to represent biochemical processes, and include a bounding box (grey dashed box) but are not connected to any nucleic acid backbone. Grey dashed lines provide examples of how edges may connect to the glyph.
}

\input{glyphscript/interactionnodeglyphs.tex}
@@ -25,7 +25,7 @@ \section{SBOL Glyphs}\label{sec:glyphs}

It will also frequently be the case that a diagram element could be represented by more than one glyph (e.g., a glyph for a specific term and a glyph for a more general term).
In such cases, it is RECOMMENDED that the most specific applicable glyph be used.
However, if upward branching in the relevant ontology means two applicable glyphs do not have an ordered parent/child relation, then either MAY be used.
\twoonezero{However, if upward branching in the relevant ontology means two applicable glyphs do not have an ordered parent/child relation, then either MAY be used.}

For example, a protein coding sequence (CDS) is a sequence feature that may be represented either using the CDS glyph (Sequence Ontology term SO:0000316) or the Unspecified glyph (Sequence Ontology term SO:0000001).
Since SO:0000316 is contained by SO:0000001, the preferred glyph is CDS, rather than Unspecified.
@@ -3,8 +3,10 @@
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/assembly-scar.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/blunt-restriction-site.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/cds.pdf}
\twoonezeronopage{
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/chromosomal-locus.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/circular-plasmid.pdf}
}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/cleavage-site.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/composite.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/engineered-region.pdf}
@@ -16,7 +18,9 @@
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/non-coding-rna.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/omitted-detail.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/operator.pdf}
\twoonezeronopage{
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/origin-of-replication.pdf}
}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/origin-of-transfer.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/polyA.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/primer-binding-site.pdf}
@@ -25,6 +29,8 @@
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/signature.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/specific-recombination-site.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/stability-element.pdf}
\twoonezeronopage{
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/stop-site.pdf}
}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/terminator.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/unspecified.pdf}
@@ -1,4 +1,6 @@
% Autogenerated glyph page collection, do not edit by hand
\twoonezeronopage{
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/InteractionNodes/association.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/InteractionNodes/dissociation.pdf}
\includepdf[pagecommand={},pages={1-}]{glyphscript/Glyphs/InteractionNodes/process.pdf}
}
@@ -73,6 +73,7 @@ \subsection{Nucleic Acid Backbone}
\label{exa:1b}
\end{figure}

\twoonezero{
\item As a special case of non-horizontal backbone structure, certain stylized backbone shapes are used as sequence feature glyphs to indicate the genomic context of a sequence.
These glyphs SHOULD be used as a matched pair, indicating the bounds of the context region.
It is further RECOMMENDED that each glyph be concatenated with an Omitted Detail glyph to explicitly indicate that some surrounding context is not being shown.
@@ -86,6 +87,7 @@ \subsection{Nucleic Acid Backbone}
\caption{Examples of RECOMMENDED indication of genomic context.}
\label{exa:1c}
\end{figure}
}

\item A nucleic acid backbone SHOULD have at least one associated feature glyph (else no structural information is being provided).
\end{enumerate}
@@ -224,6 +226,7 @@ \subsection{Interaction}
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}.

\twoonezero{
\item An edge may have multiple heads or multiple tails.
In this case, a split or join in an edge represents either multiple participants with the same role (e.g., a transcription factor repressing two instances of a promoter) or a biochemical process (e.g., association of an inducible protein and a small molecule to form an active complex).
An edge with multiple heads MUST use the same glyph for each head.
@@ -250,9 +253,11 @@ \subsection{Interaction}
\item A biochemical process represented by a glyph at an edge junction SHOULD be represented using a glyph defined in \ref{apdx:sym:interactionnodes}. In this case, the interaction type MUST be contained within at least one of the glyph's associated terms.
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:interactionnodes} MAY be used, but SHOULD be proposed for adoption as described in \ref{sec:extension}.

}

\end{enumerate}

\twoonezero{
\subsection{Modules}

A module within a system MAY be represented by a visual boundary in the form of closed polygon or closed curve.
@@ -329,6 +334,7 @@ \subsection{Modules}
\end{figure}

\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 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.
@@ -1,6 +1,8 @@
\nopagesection{Relation to other BBF RFCs and other Standards}

SBOL Visual 2.1 replaces BBF RFC 115 (SBOL Visual 2.0).
%
Substantive differences between SBOL Visual 2.1 and SBOL Visual 2.0 are marked with change bars identifying the version in which the new material was introduced.

SBOL Visual 2.1 also implicitly supersedes the previously replaced BBF RFC 93 and BBF RFC 16 (prior versions of SBOL Visual).

@@ -6,9 +6,15 @@
\usepackage{todonotes}
\usepackage{subfigure}
\usepackage{longtable}
\usepackage[color]{changebar}
\usepackage{xcolor}
\usepackage{soul}

\usepackage[final]{pdfpages}

% putting versions on changebars
\newcommand{\version}[1]{\marginpar{\hspace*{34pt}\raisebox{-3.0ex}{\color{red}\small #1}}}

%% ============================================================================
%% Description: Documentation for sbmlpkgspec.cls
%% First author: Michael Hucka <mhucka@caltech.edu>
@@ -105,6 +111,51 @@
\newcommand{\todoquery}[1]{\todo[color=yellow, inline]{DECISION NEEDED: #1}}
\newcommand{\todocritical}[1]{\todo[color=red, inline]{CRITICAL ISSUE: #1}}
% -----------------------------------------------------------------------------
% Start of document
% -----------------------------------------------------------------------------
%Commands to highlight SBOL versions
\newcommand{\twoonezero}[1]{%
\cbcolor{red}
\cbstart%
{\color{red}%
\version{2.1.0}%
#1
}
\cbend
}
% version that avoids undesirable page break in glyph collections
\newcommand{\twoonezeronopage}[1]{%
\cbcolor{red}
\cbstart%
{\color{red}%
#1
}
\cbend
}
\newcommand{\twotwozero}[1]{%
\cbcolor{magenta}
\cbstart%
{\color{red}%
\version{2.2.0}%
#1
}
\cbend
}
% version that avoids undesirable page break in glyph collections
\newcommand{\twotwozeronopage}[1]{%
\cbcolor{magenta}
\cbstart%
{\color{red}%
#1
}
\cbend
}
% -----------------------------------------------------------------------------
% Start of document
% -----------------------------------------------------------------------------
@@ -124,7 +175,7 @@
Curtis Madsen & \emph{Boston University, USA}\\
Angel Goni Moreno & \emph{Newcastle University}\\
Zachary Palchick & \emph{Zymergen, USA}\\
Umesh P & \emph{Kerala Technological University}\\
Umesh P & \emph{Kerala Technological University, India}\\
Nicholas Roehner & \emph{Raytheon BBN Technologies, USA}\\
\end{tabular}\\
{\bf Chair:}\hfil\\
@@ -134,7 +185,7 @@
\href{mailto:editors@sbolstandard.org}{\sffamily editors@sbolstandard.org}\\
{\bf Additional authors, by last name:}\\
\begin{tabular}{l>{\hspace*{15pt}}r}
Bryan Bartley & \emph{University of Washington, USA}\\
Bryan Bartley & \emph{Raytheon BBN Technologies, USA}\\
Jacob Beal & \emph{Raytheon BBN Technologies, USA}\\
Swapnil Bhatia & \emph{Boston University, USA}\\
Shyam Bhakta & \emph{Rice University, USA}\\
@@ -57,12 +57,14 @@ \subsection{SBOL Class Names}
\item \emph{\sbol{Interaction}}:
Describes a functional relationship between biological entities, such as regulatory activation or repression, or a biological process such as transcription or translation.

\twoonezero{
\item \emph{\sbol{MapsTo}}:
When a design (\sbol{ComponentDefinition} or \sbol{ModuleDefinition}) includes another design as a sub-design, the parent design might need to refer to a \sbol{ComponentInstance} (either a \sbol{Component} or \sbol{FunctionalComponent}) in the sub-design.
In this case, a \sbol{MapsTo} needs to be added to the instance for the sub-design, and this \sbol{MapsTo} needs to link between the \sbol{ComponentInstance} in the sub-design and a \sbol{ComponentInstance} in the parent design.

\item \emph{\sbol{Module}}:
Pointer class. Incorporates a child \sbol{ModuleDefinition} \textit{by reference} into exactly one parent \sbol{ModuleDefinition}. Represents a specific occurrence or instance of a subsystem within the design of a larger system. Because the same definition in multiple designs or multiple times in a single design, a single \sbol{ModuleDefinition} can have zero or more parent \sbol{ModuleDefinition}s, and each such parent-child link requires its own, distinct \sbol{Module}.
}

\item \emph{\sbol{Participation}}:
Describes the role that a \sbol{FunctionalComponent} plays in an \sbol{Interaction}.

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