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From: <mh...@us...> - 2008-07-17 08:37:46
|
Revision: 405
http://sbgn.svn.sourceforge.net/sbgn/?rev=405&view=rev
Author: mhucka
Date: 2008-07-17 08:37:41 +0000 (Thu, 17 Jul 2008)
Log Message:
-----------
Latest version following today's edits.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2008-07-17 08:35:49
|
Revision: 404
http://sbgn.svn.sourceforge.net/sbgn/?rev=404&view=rev
Author: mhucka
Date: 2008-07-17 08:35:45 +0000 (Thu, 17 Jul 2008)
Log Message:
-----------
Various edits: mostly small typos, some rewording, some layout fixes.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex 2008-07-17 08:33:53 UTC (rev 403)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex 2008-07-17 08:35:45 UTC (rev 404)
@@ -15,7 +15,7 @@
\glyphAux A \glyph{nucleic acid feature} can carry state variables (\sect{stateVariable}) that add information about its precise state. The state of a \glyph{nucleic acid feature} is therefore defined as the vector of all its state variables.
-A \glyph{nucleic acid feature} can also carry one or several \glyph{units of information} (\sect{unitInfo}). These can characterise a \glyph{nucleic acid feature}'s domain, such as a binding site, or an exon. Particular \glyph{units of information} carry the material type (\sect{material-types-cv}) and the conceptual type (\sect{conceptual-types-cv}) of the of the \glyph{nucleic acid feature}.
+A \glyph{nucleic acid feature} can also carry one or several \glyph{units of information} (\sect{unitInfo}). These can characterize a \glyph{nucleic acid feature}'s domain, such as a binding site, or an exon. Particular \glyph{units of information} carry the material type (\sect{material-types-cv}) and the conceptual type (\sect{conceptual-types-cv}) of the of the \glyph{nucleic acid feature}.
A \glyph{nucleic acid feature} may also carry a \glyph{clone marker}
(\sect{cloneMarker}).
@@ -25,8 +25,11 @@
\begin{figure}[H]
\centering
- \includegraphics[scale = 0.3]{images/genetic}
- \caption{The \PD glyph for \glyph{nucleic acid feature} with an additional state variable and a unit of information.}
+ \includegraphics[width = 1.25in]{images/genetic-plain} \hspace*{2em}
+ \raisebox{0.04in}{\includegraphics[width = 1.25in]{images/genetic}}
+ \caption{The \PD glyph for \glyph{nucleic acid feature}, shown plain and
+ unadorned on the left and with with an additional state variable and a
+ unit of information on the right.}
\label{fig:genetic}
\end{figure}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2008-07-17 08:34:07
|
Revision: 403
http://sbgn.svn.sourceforge.net/sbgn/?rev=403&view=rev
Author: mhucka
Date: 2008-07-17 08:33:53 +0000 (Thu, 17 Jul 2008)
Log Message:
-----------
Various edits: mostly small typos, some rewording, some layout fixes.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/CVs.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/and.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/association.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/catalysis.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/compartment.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/complex.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/consumption.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/dissociation.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/equivalenceArc.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/grammar.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/inhibition.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-style.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/logicArc.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/macromolecule.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/modulation.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/not.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/omitted.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/or.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/preface.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/production.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/stateVariable.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/stimulation.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/submap.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/transition.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/trigger.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/truth.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/uncertain.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/unitInformation.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/unspecified.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/CVs.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/CVs.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/CVs.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -5,7 +5,7 @@
Some glyphs in SBGN \PDs can contain particular kinds of textual annotations conveying information relevant to the purpose of the glyph. These annotations are \glyph{units of information} (\sect{unitInfo}) or \glyph{state variable} (\sect{stateVariable}). An example is in the case of multimers, which can have a unit of information conveying the number of monomers composing the multimer. Other cases are described throughout the rest of this chapter.
-The text that appears as the unit of information decorating an Entity Pool Node (EPN) must be prefixed with a controlled vocabulary term indicating the type of information being expressed. The prefixes are mandatory. Without the use of controlled vocabulary prefixes, it would be necessary to have different glyphs to indicate different classes of information; this would lead to an explosion in the number of symbols needed.
+The text that appears as the unit of information decorating an Entity Pool Node (EPN) must in most cases be prefixed with a controlled vocabulary term indicating the type of information being expressed. The prefixes are mandatory except in the case of macromolecule covalent modifications (\sect{covalent-mod-cv}). Without the use of controlled vocabulary prefixes, it would be necessary to have different glyphs to indicate different classes of information; this would lead to an explosion in the number of symbols needed.
In the rest of this section, we describe the controlled vocabularies (CVs) used in \SBGNPDLone. They cover the following categories of information: an EPN's material type, an EPN's conceptual type, covalent modifications on macromolecules, the physical characteristics of compartments, and cardinality (\eg of multimers). In each case, some CV terms are predefined by SBGN, but unless otherwise noted, \emph{they are not the only terms permitted}. Authors may use other CV values not listed here, but in such cases, they should explain the terms' meanings in a figure legend or other text accompanying the diagram.
@@ -13,13 +13,13 @@
\subsection{Entity pool node material types}
\label{sec:material-types-cv}
-The material type of an Entity Pool Node (EPN) indicates its chemical structure. A list of common material types is shown in \tab{material-types-cv}, but others are possible. The values are to be taken from the \sbo (\sbourl), specifically from the branch having identifier \sboid{SBO:0000240} (\emph{material entity} under \emph{participant}$\rightarrow$\emph{physical participant}). The labels are defined by \SBGNPDLone.
+The material type of an EPN indicates its chemical structure. A list of common material types is shown in \tab{material-types-cv}, but others are possible. The values are to be taken from the \sbo (\sbourl), specifically from the branch having identifier \sboid{SBO:0000240} ($\!$\emph{material entity} under \emph{participant}$\rightarrow$\emph{physical participant}). The labels are defined by \SBGNPDLone.
\begin{table}[h]
\centering
- \begin{tabular}{l>{\ttfamily}ll}
+ \begin{tabular}{l>{\ttfamily}l>{\ttfamily}l}
\toprule
- \textbf{Name} & \textbf{\rmfamily Label} & \textbf{SBO term} \\
+ \textbf{Name} & \textbf{\rmfamily Label} & \textbf{\rmfamily SBO term} \\
\midrule
Non-macromolecular ion & mt:ion & SBO:0000327\\
Non-macromolecular radical & mt:rad & SBO:0000328\\
@@ -40,13 +40,13 @@
\subsection{Entity pool node conceptual types}
\label{sec:conceptual-types-cv}
-An EPN's \emph{conceptual type} indicates its function within the context of a given \PD. A list of common conceptual types is shown in \tab{conceptual-types-cv}, but others are possible. The values are to be taken from the \sbo (\sbourl), specifically from the branch having identifier \sboid{SBO:0000241} (\emph{conceptual entity} under \emph{participant}$\rightarrow$\emph{physical participant}). The labels are defined by \SBGNPDLone.
+An EPN's \emph{conceptual type} indicates its function within the context of a given \PD. A list of common conceptual types is shown in \tab{conceptual-types-cv}, but others are possible. The values are to be taken from the \sbo (\sbourl), specifically from the branch having identifier \sboid{SBO:0000241} ($\!$\emph{conceptual entity} under \emph{participant}$\rightarrow$\emph{physical participant}). The labels are defined by \SBGNPDLone.
\begin{table}[h]
\centering
- \begin{tabular}{l>{\ttfamily}ll}
+ \begin{tabular}{l>{\ttfamily}l>{\ttfamily}l}
\toprule
- \textbf{Name} & \textbf{\rmfamily Label} & \textbf{SBO term} \\
+ \textbf{Name} & \textbf{\rmfamily Label} & \textbf{\rmfamily SBO term} \\
\midrule
Gene & ct:gene & SBO:0000243\\
Transcription start site & ct:tss & SBO:0000329\\
@@ -64,15 +64,15 @@
\subsection{Macromolecule covalent modifications}
\label{sec:covalent-mod-cv}
-A common reason for the introduction of state variables on an entity is to allow access to the configuration of possible covalent modification sites on that entity. For instance, a macromolecule may have one or more sites where a phosphate group many be attached; this change in the site's configuration (\ie being either phosphorylated or not) may factor into whether, and how, the entity can participate in different processes. Being able to describe such modifications in a consistent fashion is the motivation for the existence of SBGN's covalent modifications controlled vocabulary.
+A common reason for the introduction of state variables (\sect{stateVariable}) on an entity is to allow access to the configuration of possible covalent modification sites on that entity. For instance, a macromolecule may have one or more sites where a phosphate group many be attached; this change in the site's configuration (\ie being either phosphorylated or not) may factor into whether, and how, the entity can participate in different processes. Being able to describe such modifications in a consistent fashion is the motivation for the existence of SBGN's covalent modifications controlled vocabulary.
-\tab{covalent-mod-cv} lists a number of common types of covalent modifications. The most common values are defined by the \sbo in the branch having identifier \sboid{SBO:0000210} (\emph{addition} under \emph{events}$\rightarrow$\emph{reaction}$\rightarrow$\emph{biochemical reaction}$\rightarrow$\emph{conversion}$\rightarrow$\emph{addition}). The labels shown in \tab{covalent-mod-cv} are defined by \SBGNPDLone; for all other kinds of modifications not listed here, the author of a \PD must create a new label (and should also describe the meaning of the label in a legend or text accompanying the diagram).
+\tab{covalent-mod-cv} lists a number of common types of covalent modifications. The most common values are defined by the \sbo in the branch having identifier \sboid{SBO:0000210} (\emph{addition} under \emph{events}$\rightarrow$\emph{reaction}$\rightarrow$\emph{biochemical reaction}$\rightarrow$\emph{conversion}). The labels shown in \tab{covalent-mod-cv} are defined by \SBGNPDLone; for all other kinds of modifications not listed here, the author of a \PD must create a new label (and should also describe the meaning of the label in a legend or text accompanying the diagram).
\begin{table}[h]
\centering
- \begin{tabular}{l>{\ttfamily}ll}
+ \begin{tabular}{l>{\ttfamily}l>{\ttfamily}l}
\toprule
- \textbf{Name} & \textbf{\rmfamily Label} & \textbf{SBO term} \\
+ \textbf{Name} & \textbf{\rmfamily Label} & \textbf{\rmfamily SBO term} \\
\midrule
Acetylation & Ac & SBO:0000215\\
Glycosylation & G & SBO:0000217\\
@@ -100,9 +100,9 @@
\begin{table}[h]
\centering
- \begin{tabular}{l>{\ttfamily}ll}
+ \begin{tabular}{l>{\ttfamily}l>{\ttfamily}l}
\toprule
- \textbf{Name} & \textbf{\rmfamily Label} & \textbf{SBO term} \\
+ \textbf{Name} & \textbf{\rmfamily Label} & \textbf{\rmfamily SBO term} \\
\midrule
Temperature & pc:T & SBO:0000147\\
Voltage & pc:V & SBO:0000259\\
@@ -122,9 +122,9 @@
\begin{table}[h]
\centering
- \begin{tabular}{l>{\ttfamily}ll}
+ \begin{tabular}{l>{\ttfamily}l>{\ttfamily}l}
\toprule
- \textbf{Name} & \textbf{\rmfamily Label} & \textbf{SBO term} \\
+ \textbf{Name} & \textbf{\rmfamily Label} & \textbf{\rmfamily SBO term} \\
\midrule
cardinality & N:\# & SBO:0000364\\
\bottomrule
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/and.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/and.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/and.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -4,12 +4,12 @@
%\color{blue}
\subsection{Glyph: \glyph{And}}\label{sec:and}
-\begin{description}
- \item[SBO]\mbox{}\\ SBO:0000173 ! and.
- \item[origin]\mbox{}\\ More than one EPN (section~\ref{sec:EPNs}) or logical operator (section~\ref{sec:logic}).
- \item[target]\mbox{}\\ One modulation (section~\ref{sec:modulation}), stimulation (section~\ref{sec:stimulation}), catalysis (section~\ref{sec:catalysis}), inhibition (section~\ref{sec:inhibition}) or trigger (section~\ref{sec:trigger}) arc.
- \item[node]\mbox{}\\ \glyph{And} is represented by a circle carrying the word ``AND''.
- \end{description}
+\begin{glyphDescription}
+ \glyphSboTerm SBO:0000173 ! and.
+ \glyphOrigin More than one EPN (section~\ref{sec:EPNs}) or logical operator (section~\ref{sec:logic}).
+ \glyphTarget One modulation (section~\ref{sec:modulation}), stimulation (section~\ref{sec:stimulation}), catalysis (section~\ref{sec:catalysis}), inhibition (section~\ref{sec:inhibition}) or trigger (section~\ref{sec:trigger}) arc.
+ \glyphNode \glyph{And} is represented by a circle carrying the word ``AND''.
+\end{glyphDescription}
\begin{figure}[H]
\centering
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/association.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/association.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/association.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -1,16 +1,18 @@
+% $HeadURL$
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Association
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%\color{blue}
+
\subsection{Glyph: \glyph{Association}}\label{sec:association}
The association between one or more \glyph{EPNs} represents the non-covalent binding of the biological objects represented by those \glyph{EPNs} into a larger complex.
\begin{glyphDescription}
- \item[SBO]\mbox{}\\ SBO:0000177 ! binding.
- \item[origin]\mbox{}\\ One or more \glyph{consumption} arc (\sect{consumption}).
- \item[target]\mbox{}\\ One \glyph{production} arc (\sect{production}).
- \item[node]\mbox{}\\ An \glyph{association} between several entities is represented by a filled disc.
+ \glyphSboTerm SBO:0000177 ! binding.
+ \glyphOrigin One or more \glyph{consumption} arc (\sect{consumption}).
+ \glyphTarget One \glyph{production} arc (\sect{production}).
+ \glyphNode An \glyph{association} between several entities is represented by a filled disc.
\end{glyphDescription}
\begin{figure}[H]
@@ -20,22 +22,36 @@
\label{fig:association}
\end{figure}
-The following example illustrates the association of cyclin and CDC2 kinase into the Maturation Promoting Factor.
+The example in \fig{assoc-cyclin} illustrates the association of cyclin and CDC2 kinase into the Maturation Promoting Factor.
-\begin{center}
-\scalebox{0.3}{\includegraphics{examples/association-MPF}}
-\end{center}
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.3]{examples/association-MPF}
+ \caption{Association of cyclin and CDC2 kinase into the Maturation Promoting Factor.}
+ \label{fig:assoc-cyclin}
+\end{figure}
-The following example illustrates the association of a pentameric macromolecule (a nicotinic acetylcholine receptor) with a simple chemical (the local anesthetic chlorpromazin) in an unnamed complex
+\fig{assoc-unamed} gives an example illustrating the association of a pentameric macromolecule (a nicotinic acetylcholine receptor) with a simple chemical (the local anesthetic chlorpromazin) in an unnamed complex.
-\begin{center}
-\scalebox{0.3}{\includegraphics{examples/association-unamed}}
-\end{center}
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.3]{examples/association-unamed}
+ \caption{The association of a pentameric macromolecule with a simple chemical in an unnamed complex.}
+ \label{fig:assoc-unamed}
+\end{figure}
-An association does not obligatory results in the formation of a \glyph{complex}, but can also produce a \glyph{multimer}. See the formation of the hemoglobin below.
+An association does not necessarily result in the formation of a \glyph{complex}; it can also produce a \glyph{multimer}. \fig{assoc-multi} gives an example of this, using the formation of hemoglobin.
-\begin{center}
-\scalebox{0.3}{\includegraphics{examples/association-multimerisation}}
-\end{center}
-\normalcolor
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.3]{examples/association-multimerisation}
+ \caption{Formation of hemoglobin.}
+ \label{fig:assoc-multi}
+\end{figure}
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_PD-level1"
+% End:
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/catalysis.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/catalysis.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/catalysis.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -8,10 +8,10 @@
positively the flux of a process represented by the target transition. The positive effect on the transition is due to the lowering of the activation energy of a reaction.
\begin{glyphDescription}
- \item[SBO]\mbox{}\\ SBO:0000172 ! catalysis
- \item[origin]\mbox{}\\ Any \glyph{EPN} (\sect{EPNs}) or any \glyph{logical operator} (\sect{logic}).
- \item[target]\mbox{}\\ Any \glyph{process node} (\sect{PNs}).
- \item[node]\mbox{}\\ The target extremity of a \glyph{catalysis} carries an empty circle.
+ \glyphSboTerm SBO:0000172 ! catalysis.
+ \glyphOrigin Any \glyph{EPN} (\sect{EPNs}) or any \glyph{logical operator} (\sect{logic}).
+ \glyphTarget Any \glyph{process node} (\sect{PNs}).
+ \glyphNode The target extremity of a \glyph{catalysis} carries an empty circle.
\end{glyphDescription}
\begin{figure}[H]
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -3,7 +3,7 @@
\subsection{Glyph: \glyph{Clone marker}}
\label{sec:cloneMarker}
-If an \glyph{EPN} is duplicated on a map, it is necessary to indicate this fact by using the \glyph{clone marker} auxiliary unit. The purpose of this marker is to provide the reader with a visual indication that this node has been cloned, and that at least one other occurrence of the \glyph{EPN} can be found in the map (or in a submap; see \sect{submap}). The clone marker takes two forms, simple and labeled, depending on whether the node being cloned can carry state variables (\ie whether it is a stateful EPN). Note that an \glyph{EPN} belong to a single compartment. If two glyphs labelled ``X'' are located in two different compartments, such as ATP in cytosol and ATP in mitochondiral lumen, they represent different \glyph{EPN}, and therefore do-not need to be marked as cloned.
+If an \glyph{EPN} is duplicated on a map, it is necessary to indicate this fact by using the \glyph{clone marker} auxiliary unit. The purpose of this marker is to provide the reader with a visual indication that this node has been cloned, and that at least one other occurrence of the \glyph{EPN} can be found in the map (or in a submap; see \sect{submap}). The clone marker takes two forms, simple and labeled, depending on whether the node being cloned can carry state variables (\ie whether it is a stateful EPN). Note that an \glyph{EPN} belong to a single compartment. If two glyphs labelled ``X'' are located in two different compartments, such as ATP in cytosol and ATP in mitochondiral lumen, they represent different \glyph{EPN}, and therefore do not need to be marked as cloned.
\subsubsection{Simple clone marker}
@@ -42,7 +42,7 @@
\glyphContainer The labeled \glyph{clone marker} is a portion of the surface of an \glyph{EPN} that has been modified visually through the use of a different shade, texture, or color. The \glyph{clone marker} occupies the lower part of the EPN glyph. The filled area must be significantly smaller than the unfilled one, but the be large enough to have an height larger than the \glyph{clone marker}'s label (cf below). A marker's surface must not exceed 30\% of the \glyph{EPN}'s surface. A value in the range 15 and 25\% is advised. \fig{labeledCloneMarker} illustrates this.
\glyphLabel A \glyph{clone marker} is identified by a label placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container (the portion of the surface
-of the EPN that has been modified visually). The font color of the label and the color of the clone marker should contrast with one another. The label on a labeled \glyph{labeled clone marker} is mandatory.
+of the EPN that has been modified visually). The font color of the label and the color of the clone marker should contrast with one another. The label on a \glyph{labeled clone marker} is mandatory.
\glyphAux A \glyph{clone marker} does not carry any auxiliary items.
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/compartment.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/compartment.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/compartment.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -1,27 +1,23 @@
+% $HeadURL$
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% Compartment
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%\color{blue}
+
\subsection{Glyph: \glyph{Compartment}}\label{sec:compartment}
In order to describe biochemical and cellular events, it is useful to define the notion of pools. A pool is an ensemble of participants that can be considered to be identical for the events in which they are involved. A compartment is a logical or physical structure that contains pools.
\begin{glyphDescription}
+
\glyphSboTerm SBO:0000289 ! functional compartment
-\glyphContainer A compartment is represented by a surface
- enclosed in a continuous border or located between continuous borders. These borders should be noticeably thicker than the borders of the EPNs. A compartment can take \textbf{any} geometry. A compartment must always be entirely enclosed.
-\glyphLabel The identification of the compartment is
- carried by an unbordered box containing a string of characters. The
- characters can be distributed on several lines to improve
- readability, although this is not mandatory. The label box can be
- attached anywhere in the container box. Note that the label can
- spill-over from the container box.
-\glyphAux A \glyph{compartment} can carry a
- certain number of \glyph{units of information}, that will add
- information for instance about the physical environment, such as pH,
- temperature or voltage, see \sect{unitInfo}.
- The center of the bounding box of a \glyph{unit of information} is
- located on the mid-line of the border of the compartment.
+
+\glyphContainer A compartment is represented by a surface enclosed in a continuous border or located between continuous borders. These borders should be noticeably thicker than the borders of the EPNs. A compartment can take \textbf{any} geometry. A compartment must always be entirely enclosed.
+
+\glyphLabel The identification of the compartment is carried by an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box can be attached anywhere in the container box. Note that the label can spill-over from the container box.
+
+\glyphAux A \glyph{compartment} can carry a certain number of \glyph{units of information}, that will add information for instance about the physical environment, such as pH, temperature or voltage, see \sect{unitInfo}. The center of the bounding box of a \glyph{unit of information} is located on the mid-line of the border of the compartment.
+
\end{glyphDescription}
\begin{figure}[H]
@@ -32,33 +28,47 @@
\end{figure}
-It is important to note that a compartment never contains another compartment, but may surround it. Two ``adjacent'' compartments are not separated by one line, but by \textbf{two} lines. The following example represents a cell made up of a nucleus surrounded by the cytoplasm.
+It is important to note that a compartment never contains another compartment, but may surround it. A ket aspect of correctly drawing two ``adjacent'' compartments is that they are not separated by one line, but by \textbf{two} lines. \fig{two-comp} provides an example of this in which a cell is shown made up of a nucleus surrounded by the cytoplasm.
-\begin{center}
-\scalebox{0.3}{\includegraphics{examples/compartment-cell}}
-\end{center}
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.4]{examples/compartment-cell}
+ \caption{Compartments can surround other compartments; in that case, both of the compartment's borders must still be shown, with the result that the separation is drawn as two lines.}
+ \label{fig:two-comp}
+\end{figure}
-The following example represents three adjacent compartments. Two of the compartments carry units of information. Notice the fact that those units of information do not overlap several membrane boundaries.
+The example diagram in \fig{three-comp} represents three adjacent compartments. Two of the compartments carry units of information. Notice that these units of information do not overlap multiple membrane boundaries.
-\begin{center}
-\scalebox{0.3}{\includegraphics{examples/compartment-3comp}}
-\end{center}
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.4]{examples/compartment-3comp}
+ \caption{Illustration of units of information and surrounding compartments.}
+ \label{fig:three-comp}
+\end{figure}
+To allow more aesthetically pleasing and understandable diagrams, compartments are allowed to overlap each other visually, but it must be kept in mind that this does not mean the top compartment contains part of the bottom compartment. \fig{overlap} shows two semantically equivalent placement of compartments:
-To make drawing aesthetically more pleasing and understandable, compartments are
-allowed to overlap each other visually, but this does not mean that the top
-compartment contains part of the bottom compartment. The following
-diagrams represent two semantically equivalent placement of compartments:
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.4]{examples/compartment_overlapping}
+ \caption{Overlapped compartments are permitted, but the overlap does not imply containment.}
+ \label{fig:overlap}
+\end{figure}
-\begin{center}
-\scalebox{0.5}{\includegraphics{examples/compartment_overlapping}}
-\end{center}
+Overlapped (hidden) part of the compartment should not contain any object which could be covered by an overlapping compartment. \fig{overlap-bad} illustrates the problem using an incorrect diagram.
-Overlapped (hidden) part of the compartment should not contain any object,
-which could be covered by overlapping compartment. The next diagram is not
-correct:
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.45]{examples/compartment_overlapping_wrong}
+ \caption{Example of an \textbf{incorrect} diagram. Overlapped compartments must not obscure other objects.}
+ \label{fig:overlap-bad}
+\end{figure}
-\begin{center}
-\scalebox{0.5}{\includegraphics{examples/compartment_overlapping_wrong}}
-\end{center}
+
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_PD-level1"
+% End:
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/complex.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/complex.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/complex.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -1,31 +1,36 @@
+% $HeadURL$
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% Complex
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%\color{blue}
+
\subsection{Glyph: \glyph{Complex}}\label{sec:complex}
-A \glyph{complex} node represents a biochemical entity composed of other biochemical entities, whether macromolecules, simple chemicals, multimers, or themselves complexes.
+A \glyph{complex} node represents a biochemical entity composed of other biochemical entities, whether macromolecules, simple chemicals, multimers, or other complexes. The resulting entity may have its own identity, properties and function in an SBGN diagram.
\begin{glyphDescription}
+
\glyphSboTerm SBO:0000253 ! non-covalent complex
-\glyphContainer A \glyph{complex} possesses its own container box
- surrounding the juxtaposed container boxes of its components. This container box is a rectangle with cut-corners (an octagonal box with sides of two different lengths). The size of the cut-corners are adjusted so that there is no overlap between the container and the components. The container boxes of the components must not overlap.
-\glyphLabel The identification of a \glyph{named complex}
- is carried by an unbordered box containing a string of characters. The
- characters may be distributed on several lines to improve
- readability, although this is not mandatory. The label box has to
- be attached to the midway between the border of the complex's
- container box and the border of the components' container boxes.
-\glyphAux A \glyph{complex} can carry state variables (see \sect{stateVariable}). The state of a complex is defined by the set of the all its state variable and all the state variables of all its components. A \glyph{complex} can also carry one or several \glyph{units
- of information} (see \sect{unitInfo}). Those units of information can characterise a
- domain, such as a binding site. Particular \glyph{units of information} carry the material type and the conceptual type of the macromolecules.
- A \glyph{complex} may carry a \glyph{clone marker} (see \sect{cloneMarker}).
+
+\glyphContainer A \glyph{complex} possesses its own container box surrounding the juxtaposed container boxes of its components. This container box is a rectangle with cut-corners (an octagonal box with sides of two different lengths). The size of the cut-corners are adjusted so that there is no overlap between the container and the components. The container boxes of the components must not overlap.
+
+\glyphLabel The identification of a \glyph{named complex} is carried by an unbordered box containing a string of characters. The characters may be distributed on several lines to improve readability, although this is not mandatory. The label box has to be attached to the midway between the border of the complex's container box and the border of the components' container boxes.
+
+\glyphAux A \glyph{complex} can carry state variables (see \sect{stateVariable}). The state of a complex is defined by the set of the all its state variable and all the state variables of all its components. A \glyph{complex} can also carry one or several \glyph{units of information} (see \sect{unitInfo}). Those units of information can characterize a domain, such as a binding site. Particular \glyph{units of information} carry the material type and the conceptual type of the macromolecules. A \glyph{complex} may carry a \glyph{clone marker} (see \sect{cloneMarker}).
+
\end{glyphDescription}
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/complex}
- \caption{The \PD glyph for \glyph{complex}.}
+ \caption{An example \PD glyph for \glyph{complex}.}
\label{fig:complex}
\end{figure}
+
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_PD-level1"
+% End:
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/consumption.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/consumption.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/consumption.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -1,18 +1,21 @@
+% $HeadURL$
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Consumption
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%\color{blue}
-\subsection{Glyph: \glyph{Consumption} }\label{sec:consumption}
+\subsection{Glyph: \glyph{Consumption}}
+\label{sec:consumption}
+
\glyph{Consumption} is the arc used to represent the fact that an entity affects a process,
but is not affected by the process.
\begin{glyphDescription}
- \item[SBO]\mbox{}\\ To be determined.
- \item[origin]\mbox{}\\ Any \glyph{EPN} (\sect{EPNs}).
- \item[target]\mbox{}\\ Any process node (\sect{PNs}).
- \item[end-points]\mbox{}\\ No particular symbol is used to represent a consumption.
- \end{glyphDescription}
+ \glyphSboTerm To be determined.
+ \glyphOrigin Any \glyph{EPN} (\sect{EPNs}).
+ \glyphTarget Any process node (\sect{PNs}).
+ \glyphEndPoint No particular symbol is used to represent a consumption.
+\end{glyphDescription}
A cardinality label may be associated with \glyph{consumption} (\sect{consumption}) or
@@ -27,16 +30,23 @@
node to avoid misinterpretation.
Omitted cardinality on one edge only should not be treated as cardinality of 1, but
-as unspecified cardinality. In most cases, the exact value could be derived from the
+as an unspecified cardinality. In most cases, the exact value may be derived from the
context, but unless cardinality is explicitly shown, it should be considered as
unspecified. In the case where the stoichiometry of some part of the process is not
-known, or undefined, question mark (?) should be used within the cardinality label
+known, or undefined, a question mark (?) should be used within the cardinality label
of the corresponding arcs.
\begin{figure}[H]
\centering
- \includegraphics[scale = 0.5]{images/consumption}
+ \includegraphics[scale = 0.4]{images/consumption}
\caption{The \PD glyph for \glyph{consumption}.}
\label{fig:consumption}
\end{figure}
+
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_PD-level1"
+% End:
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/dissociation.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/dissociation.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/dissociation.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -7,10 +7,10 @@
The dissociation of an \glyph{EPN} into one or more \glyph{EPNs} represents the rupture of a non-covalent binding between the biological entities represented by those \glyph{EPNs}.
\begin{glyphDescription}
- \item[SBO]\mbox{}\\ SBO:0000180 ! dissociation
- \item[origin]\mbox{}\\ One \glyph{consumption} arc (\sect{consumption}).
- \item[target]\mbox{}\\ One of more \glyph{production} arc (\sect{production}).
- \item[node]\mbox{}\\ A \glyph{dissociation} between several entities is represented by two concentric circles. A simple empty disc could be, in some cases, confused with the \glyph{catalysis} (section \sect{catalysis}). Moreover, the existence of two circles reminds the dissociation, by contrast with the filled disc of the \glyph{association} (\sect{association}).
+ \glyphSboTerm SBO:0000180 ! dissociation.
+ \glyphOrigin One \glyph{consumption} arc (\sect{consumption}).
+ \glyphTarget One of more \glyph{production} arc (\sect{production}).
+ \glyphNode A \glyph{dissociation} between several entities is represented by two concentric circles. A simple empty disc could be, in some cases, confused with the \glyph{catalysis} (section \sect{catalysis}). Moreover, the existence of two circles reminds the dissociation, by contrast with the filled disc of the \glyph{association} (\sect{association}).
\end{glyphDescription}
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/equivalenceArc.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/equivalenceArc.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/equivalenceArc.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -7,16 +7,16 @@
\glyph{Equivalence Arc} is the arc used to represent the fact that all entities
marked by a \glyph{tag} are equivalent.
-\begin{description}
- \item[SBO]\mbox{}\\ To be determined.
- \item[origin]\mbox{}\\ Any \glyph{EPN} (\sect{EPNs}).
- \item[target]\mbox{}\\ \glyph{Tag} (\sect{tag}).
- \item[end-points]\mbox{}\\ No particular symbol is used to represent an \glyph{equivalence arc}.
- \end{description}
+\begin{glyphDescription}
+ \glyphSboTerm To be determined.
+ \glyphOrigin Any \glyph{EPN} (\sect{EPNs}).
+ \glyphTarget \glyph{Tag} (\sect{tag}).
+ \glyphEndPoint No particular symbol is used to represent an \glyph{equivalence arc}.
+ \end{glyphDescription}
\begin{figure}[H]
\centering
- \includegraphics[scale = 0.5]{images/equivalence}
+ \includegraphics[scale = 0.4]{images/equivalence}
\caption{The \PD glyph for \glyph{Equivalence arc}.}
\label{fig:equivalence}
\end{figure}
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -52,7 +52,7 @@
\section{Container nodes}\label{sec:CNs}
-\glyph{Containers} are SBGN constructions that contain one or several other SBGN constructs.
+\glyph{Containers} are SBGN constructions that contain one or several other SBGN constructs. There are three container nodes in \SBGNPDLone: \glyph{complex}, \glyph{compartment}, and \glyph{submap}.
\input{sources/complex.tex}
\input{sources/compartment.tex}
@@ -67,7 +67,7 @@
\section{Process nodes}\label{sec:PNs}
-Process nodes represent processes that transform one or several EPNs into one or several different EPNs. In \SBGNPDLone a generic transition is defined (\sect{transition}), as well as four more specific ones, the omitted transition (\sect{omitted}), the uncertain transition (\sect{uncertain}), the association (\sect{association}) and the dissociation (\sect{dissociation}). In future levels, more transitions might be defined. One could even envision to develop a controlled vocabulary of transitions, as we do for \glyph{EPNs} (\sect{CVs}).
+Process nodes represent processes that transform one or several EPNs into one or several different EPNs. \SBGNPDLone defines a generic \glyph{transition} (\sect{transition}), as well as four more specific ones: the \glyph{omitted process} (\sect{omitted}), the \glyph{uncertain process} (\sect{uncertain}), the \glyph{association} (\sect{association}) and the \glyph{dissociation} (\sect{dissociation}). In future levels of the SBGN Process Diagram notation, more transitions may be defined. (One can even envision the development of a controlled vocabulary of transitions, as is done now for \glyph{EPNs}; see \sect{CVs}.)
\input{sources/transition.tex}
\input{sources/omitted.tex}
@@ -84,7 +84,7 @@
\section{Connecting arcs}\label{sec:arcs}
-Connecting arcs are lines that link \glyph{EPNs} and \glyph{PNs} together. The symbols attached to their extremities precise their semantics.
+Connecting arcs are lines that link \glyph{EPNs} and \glyph{PNs} together. The symbols attached to their extremities indicate their semantics.
\input{sources/consumption.tex}
\input{sources/production.tex}
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/grammar.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/grammar.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/grammar.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -73,7 +73,7 @@
\section{The conceptual model}
-In order to formalise the conceptual representation described above
+In order to formalize the conceptual representation described above
and the semantic rules that we will describe later, we have developed a UML
Domain Object Model of SBGN\@. This defines what would otherwise be
vaguely defined in the SBGN specification, and enables us to define
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/inhibition.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/inhibition.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/inhibition.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -5,13 +5,13 @@
\subsection{Glyph: \glyph{Inhibition}}\label{sec:inhibition}
%\color{blue}
-An inhibition affects \textbf{negatively} the flux of a process represented by the target transition. This inhibition can be for instance a competitive inhibition or an allosteric inhibition.
+An inhibition \textbf{negatively} affects the flux of a process represented by the target transition. This inhibition can be for instance a competitive inhibition or an allosteric inhibition.
\begin{glyphDescription}
- \item[SBO]\mbox{}\\ SBO:0000169 ! inhibition
- \item[origin]\mbox{}\\ Any \glyph{EPN} (\sect{EPNs}) or any \glyph{logical operator} (\sect{logic}).
- \item[target]\mbox{}\\ Any \glyph{process node} (\sect{PNs}).
- \item[node]\mbox{}\\ The target extremity of an \glyph{inhibition} carries a bar perpendicular to the arc.
+ \glyphSboTerm SBO:0000169 ! inhibition.
+ \glyphOrigin Any \glyph{EPN} (\sect{EPNs}) or any \glyph{logical operator} (\sect{logic}).
+ \glyphTarget Any \glyph{process node} (\sect{PNs}).
+ \glyphNode The target extremity of an \glyph{inhibition} carries a bar perpendicular to the arc.
\end{glyphDescription}
\begin{figure}[H]
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -32,7 +32,7 @@
Kitano originated the idea of having multiple views of the \emph{same} model. This addresses two problems: no single view can satisfy the needs of all users, and a given view can only represent a subset of the semantics necessary to express biological knowledge. Kitano proposed the development of process diagrams, entity-relationship diagrams, timing charts (to describe temporal changes in a system), and abstract flow charts~\cite{Kitano:2003}. The \PD notation was the first to be fully defined using a well-delineated set of symbols and syntax~\cite{Kitano:2005}. It lead to a desire to establish a unified standard for graphical representation of biochemical entities, and from this arose the current SBGN effort. Separately and roughly concurrently, other groups designed similar notations, for example the Edinburgh Pathway Notation~\cite{Moodie:2006}. All of these efforts began to attract attention as more emphasis in biological research was placed on networks of interactions and not just characterization of individual entities.
-In 2005, thanks to funding from the Japanese agency \emph{The New Energy and Industrial Technology Development Organization} (NEDO, \url{http://www.nedo.go.jp/}), Kitano initiated the Systems Biology Markup Language project as a community effort. The first SBGN workshop was held in February 2006 in Tokyo, with over 30 participants from major organizations interested in this effort. From the in-depth discussions held during that meeting emerged a set of decisions that are the basis of the current SBGN specification. These decisions are:
+In 2005, thanks to funding from the Japanese agency \emph{The New Energy and Industrial Technology Development Organization} (NEDO, \url{http://www.nedo.go.jp/}), Kitano initiated the Systems Biology Graphical Notation (SBGN) project as a community effort. The first SBGN workshop was held in February 2006 in Tokyo, with over 30 participants from major organizations interested in this effort. From the in-depth discussions held during that meeting emerged a set of decisions that are the basis of the current SBGN specification. These decisions are:
\begin{itemize}
@@ -42,7 +42,7 @@
\end{itemize}
-The second SBGN workshop was held in October, 2006, in Yokohama, Japan. This meeting featured the first technical discussions about which symbols to include in SBGN Level~1, as well as discussions about the syntax, semantics, and layout of graphs. A follow-up technical meeting was held in March, 2007, in Heidelberg, Germany; the participants of that meeting fleshed out most of the design of SBGN. The third SBGN workshop, held in Long Beach in October of 2007, was dedicated to reaching agreement on the final outstanding issues of notation and syntax. The participants of that meeting collectively realized that a third language would be necessary: the \AF diagrams. The specification for the \PD language was finalized and largely completed during a follow-up technical meeting held in Okinawa, Japan, in January of 2008. At this last meeting, attendees also held the first in-depth discussions about the syntax of the \ER language.
+The second SBGN workshop was held in October, 2006, in Yokohama, Japan. This meeting featured the first technical discussions about which symbols to include in SBGN Level~1, as well as discussions about the syntax, semantics, and layout of graphs. A follow-up technical meeting was held in March, 2007, in Heidelberg, Germany; the participants of that meeting fleshed out most of the design of SBGN. The third SBGN workshop, held in Long Beach in October, 2007, was dedicated to reaching agreement on the final outstanding issues of notation and syntax. The participants of that meeting collectively realized that a third language would be necessary: the \AF diagrams. The specification for the \PD language was finalized and largely completed during a follow-up technical meeting held in Okinawa, Japan, in January, 2008. At this last meeting, attendees also held the first in-depth discussions about the syntax of the \ER language.
SBGN workshops are an opportunity for public discussions about SBGN, allowing interested persons to learn more about SBGN and help identify needs and issues. More meetings are expected to be held in the future, long after this specification document has been issued.
@@ -76,7 +76,7 @@
\section{SBGN levels}
\label{sec:sbgn-levels}
-It was clear at the outset of SBGN development that it would be impossible to design a perfect and complete notation right from the beginning. Apart from the prescience this would require (which, sadly, none of the authors possess), it also would likely require a vast language that most newcomers would shun as being too complex. Thus, the SBGN community followed an idea used in SBML development~\cite{Hucka:2003}: stratify language development into levels.
+It was clear at the outset of SBGN development that it would be impossible to design a perfect and complete notation right from the beginning. Apart from the prescience this would require (which, sadly, none of the authors possess), it also would likely require a vast language that most newcomers would shun as being too complex. Thus, the SBGN community followed an idea used in the development of the Systems Biology Markup Language (SBML; \cite{Hucka:2003}): stratify language development into levels.
A \emph{level} of SBGN represents a set of features deemed to fit together cohesively, constituting a usable set of functionality that the user community agrees is sufficient for a reasonable set of tasks and goals. Capabilities and features that cannot be agreed upon and are judged insufficiently critical to require inclusion in a given level, are postponed to a higher level. In this way, SBGN development is envisioned to proceed in stages, with each higher SBGN level adding richness compared to the levels below it.
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-style.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-style.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-style.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -310,6 +310,10 @@
\newcommand{\glyphContainer}{\item[Container:]\mbox{}\newline}
\newcommand{\glyphLabel}{\item[Label:]\mbox{}\newline}
\newcommand{\glyphAux}{\item[Auxiliary items:]\mbox{}\newline}
+\newcommand{\glyphOrigin}{\item[Origin:]\mbox{}\newline}
+\newcommand{\glyphTarget}{\item[Target:]\mbox{}\newline}
+\newcommand{\glyphNode}{\item[Node:]\mbox{}\newline}
+\newcommand{\glyphEndPoint}{\item[End point:]\mbox{}\newline}
%% ----------------------------------------------------------------------------
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/logicArc.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/logicArc.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/logicArc.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -8,15 +8,15 @@
the outcome of a logic operator.
\begin{glyphDescription}
- \item[SBO]\mbox{}\\ To be determined.
- \item[origin]\mbox{}\\ Any \glyph{EPN} (\sect{EPNs}) or \glyph{logical operator} (\sect{logic}).
- \item[target]\mbox{}\\ Any \glyph{logical operator} (\sect{logic}).
- \item[end-points]\mbox{}\\ No particular symbol is used to represent a logic arc.
+ \glyphSboTerm To be determined.
+ \glyphOrigin Any \glyph{EPN} (\sect{EPNs}) or \glyph{logical operator} (\sect{logic}).
+ \glyphTarget Any \glyph{logical operator} (\sect{logic}).
+ \glyphEndPoint No particular symbol is used to represent a logic arc.
\end{glyphDescription}
\begin{figure}[H]
\centering
- \includegraphics[scale = 0.5]{images/logicArc}
+ \includegraphics[scale = 0.4]{images/logicArc}
\caption{The \PD glyph for \glyph{logic arc}.}
\label{fig:logicArc}
\end{figure}
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/macromolecule.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/macromolecule.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/macromolecule.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -15,7 +15,7 @@
\glyphAux A \glyph{macromolecule} can carry state variables that can add information about its state (\sect{stateVariable}). The state of a macromolecule is therefore defined as the vector of all its state variables.
-A \glyph{macromolecule} can also carry one or several \glyph{units of information} (\sect{unitInfo}). The units of information can characterise a domain, such as a binding site. Particular \glyph{units of information} are available for describing the material type (\sect{material-types-cv}) and the conceptual type (\sect{conceptual-types-cv}) of a macromolecule.
+A \glyph{macromolecule} can also carry one or several \glyph{units of information} (\sect{unitInfo}). The units of information can characterize a domain, such as a binding site. Particular \glyph{units of information} are available for describing the material type (\sect{material-types-cv}) and the conceptual type (\sect{conceptual-types-cv}) of a macromolecule.
A \glyph{macromolecule} may also carry a \glyph{clone marker} (see \sect{cloneMarker})
@@ -23,8 +23,11 @@
\begin{figure}[H]
\centering
- \includegraphics[scale = 0.3]{images/macromolecule}
- \caption{The \PD glyph for \glyph{macromolecule} with an additional state variable and a unit of information.}
+ \includegraphics[width = 1.25in]{images/macromolecule-plain} \hspace*{2em}
+ \raisebox{0.04in}{\includegraphics[width = 1.25in]{images/macromolecule}}
+ \caption{The \PD glyph for \glyph{macromolecule}, shown plain and
+ unadorned on the left, and with with an additional state variable and a
+ unit of information on the right.}
\label{fig:macromolecule}
\end{figure}
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/modulation.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/modulation.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/modulation.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -11,10 +11,10 @@
participants. A \glyph{modulation} can also be used when one does not know the precise direction of the effect.
\begin{glyphDescription}
- \item[SBO]\mbox{}\\ SBO:0000168 ! control
- \item[origin]\mbox{}\\ Any \glyph{EPN} (\sect{EPNs}) or any \glyph{logical operator} (\sect{logic}).
- \item[target]\mbox{}\\ Any \glyph{process node} (\sect{PNs}).
- \item[end-points]\mbox{}\\ The target extremity of a \glyph{modulation} carries an empty diamond.
+ \glyphSboTerm SBO:0000168 ! control.
+ \glyphOrigin Any \glyph{EPN} (\sect{EPNs}) or any \glyph{logical operator} (\sect{logic}).
+ \glyphTarget Any \glyph{process node} (\sect{PNs}).
+ \glyphEndPoint The target extremity of a \glyph{modulation} carries an empty diamond.
\end{glyphDescription}
\begin{figure}[H]
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/not.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/not.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/not.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -4,12 +4,12 @@
%\color{blue}
\subsection{Glyph: \glyph{Not}}\label{sec:not}
-\begin{description}
- \item[SBO]\mbox{}\\ SBO:0000238 ! not.
- \item[origin]\mbox{}\\ One EPN (section~\ref{sec:EPNs}) or logical operator (section~\ref{sec:logic}).
- \item[target]\mbox{}\\ One modulation (section~\ref{sec:modulation}), stimulation (section~\ref{sec:stimulation}), catalysis (section~\ref{sec:catalysis}), inhibition (section~\ref{sec:inhibition}) or trigger (section~\ref{sec:trigger}) arc.
- \item[node]\mbox{}\\ \glyph{Not} is represented by a circle carrying the word ``NOT''.
- \end{description}
+\begin{glyphDescription}
+ \glyphSboTerm SBO:0000238 ! not.
+ \glyphOrigin One EPN (section~\ref{sec:EPNs}) or logical operator (section~\ref{sec:logic}).
+ \glyphTarget One modulation (section~\ref{sec:modulation}), stimulation (section~\ref{sec:stimulation}), catalysis (section~\ref{sec:catalysis}), inhibition (section~\ref{sec:inhibition}) or trigger (section~\ref{sec:trigger}) arc.
+ \glyphNode \glyph{Not} is represented by a circle carrying the word ``NOT''.
+ \end{glyphDescription}
\begin{figure}[H]
\centering
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/omitted.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/omitted.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/omitted.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -7,10 +7,11 @@
Omitted processes are processes that are known to exist, but are omitted from the diagram for the sake of clarity or parsimony. A single \glyph{omitted process} can represent any number of actual processes. The omitted process is different from a \glyph{submap}.
\begin{glyphDescription}
- \item[SBO]\mbox{}\\ To be determined
- \item[origin]\mbox{}\\ One or several \glyph{consumption} arcs (\sect{consumption}) or one or several \glyph{production} arcs (\sect{production}).
- \item[target]\mbox{}\\ One or several \glyph{production} arcs (\sect{production}).
- \item[node]\mbox{}\\ Omitted processes are represented as a transition which square box contains a double slanted NW-SE line separated by an empty space.
+ \glyphSboTerm To be determined.
+ \glyphOrigin One or several \glyph{consumption} arcs (\sect{consumption}) or one or several \glyph{production} arcs (\sect{production}).
+ \glyphTarget One or several \glyph{production} arcs (\sect{production}).
+
+ \glyphNode Omitted processes are represented as a transition in which the square box contains a two parallel slanted lines oriented northwest-to-southeast and separated by an empty space.
\end{glyphDescription}
\begin{figure}[H]
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/or.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/or.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/or.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -4,12 +4,12 @@
%\color{blue}
\subsection{Glyph: \glyph{Or}}\label{sec:or}
-\begin{description}
- \item[SBO]\mbox{}\\ SBO:0000174 ! or.
- \item[origin]\mbox{}\\ More than one EPN (section~\ref{sec:EPNs}) or logical operator (section~\ref{sec:logic}).
- \item[target]\mbox{}\\ One modulation (section~\ref{sec:modulation}), stimulation (section~\ref{sec:stimulation}), catalysis (section~\ref{sec:catalysis}), inhibition (section~\ref{sec:inhibition}) or trigger (section~\ref{sec:trigger}) arc.
- \item[node]\mbox{}\\ \glyph{Or} is represented by a circle carrying the word ``OR''.
- \end{description}
+\begin{glyphDescription}
+ \glyphSboTerm SBO:0000174 ! or.
+ \glyphOrigin More than one EPN (section~\ref{sec:EPNs}) or logical operator (section~\ref{sec:logic}).
+ \glyphTarget One modulation (section~\ref{sec:modulation}), stimulation (section~\ref{sec:stimulation}), catalysis (section~\ref{sec:catalysis}), inhibition (section~\ref{sec:inhibition}) or trigger (section~\ref{sec:trigger}) arc.
+ \glyphNode \glyph{Or} is represented by a circle carrying the word ``OR''.
+ \end{glyphDescription}
\begin{figure}[H]
\centering
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex 2008-07-17 08:30:30 UTC (rev 402)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex 2008-07-17 08:33:53 UTC (rev 403)
@@ -2,9 +2,10 @@
To set the stage for what follows in this chapter, we first give a brief overview of some of the concepts in the \PD notation with the help of an example shown in \fig{eg1}.
-\begin{figure}[htb]
+\begin{figure}[H]
\centering
- \includegraphics{examples/MAPK-only}
+ \vspace*{-0.5em}
+ \includegraphics[scale=0.8]{examples/MAPK-only}
\caption{This example of a \PD uses two kinds of entity pool nodes: one
for pools of different macromolecules (\sect{macromolecule}) and
another for pools of simple chemicals (\sect{simpleChemical}). Most
@@ -20,7 +21,7 @@
The diagram in \fig{eg1} is a simple diagram for part of...
[truncated message content] |
|
From: <mh...@us...> - 2008-07-17 08:30:39
|
Revision: 402
http://sbgn.svn.sourceforge.net/sbgn/?rev=402&view=rev
Author: mhucka
Date: 2008-07-17 08:30:30 +0000 (Thu, 17 Jul 2008)
Log Message:
-----------
New diagrams for further illustrations.
Added Paths:
-----------
trunk/documents/specifications/ProcessDiagram/Level1/images/genetic-plain.eps
trunk/documents/specifications/ProcessDiagram/Level1/images/genetic-plain.graffle
trunk/documents/specifications/ProcessDiagram/Level1/images/genetic-plain.pdf
trunk/documents/specifications/ProcessDiagram/Level1/images/genetic-plain.svg
trunk/documents/specifications/ProcessDiagram/Level1/images/macromolecule-plain.eps
trunk/documents/specifications/ProcessDiagram/Level1/images/macromolecule-plain.graffle
trunk/documents/specifications/ProcessDiagram/Level1/images/macromolecule-plain.pdf
trunk/documents/specifications/ProcessDiagram/Level1/images/macromolecule-plain.svg
Added: trunk/documents/specifications/ProcessDiagram/Level1/images/genetic-plain.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/images/genetic-plain.eps (rev 0)
+++ trunk/documents/specifications/ProcessDiagram/Level1/images/genetic-plain.eps 2008-07-17 08:30:30 UTC (rev 402)
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Property changes on: trunk/documents/specifications/ProcessDiagram/Level1/images/genetic-plain.graffle
___________________________________________________________________
Added: svn:mime-type
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|
From: <le...@us...> - 2008-07-15 16:41:13
|
Revision: 401
http://sbgn.svn.sourceforge.net/sbgn/?rev=401&view=rev
Author: lenov
Date: 2008-07-15 09:41:11 -0700 (Tue, 15 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
trunk/documents/specifications/ProcessDiagram/Level1/sources/working.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/working.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/working.tex 2008-07-14 14:35:51 UTC (rev 400)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/working.tex 2008-07-15 16:41:11 UTC (rev 401)
@@ -18,6 +18,10 @@
The current specification cannot represent combinations of events and entities. For instance a variable ''voltage'' cannot be controlled by a difference of concentration between different entities, such as a given ion in both sides of a membrane.
-\section{}
+\section{Generics}
-\section{}
+\SBGNPDLone does not provide mechanisms to sub-class \glyph{EPNs}. There is no specific means of specifying that \glyph{macromolecules} or \glyph{nucleic acid features} X1, X2 and X2 are subclasses of X. Therefore, any process that applies to all the subtypes of X has to be triplicated. That situation can easily generate combinatorial explosions of the number of \glyph{EPNs} or \glyph{PNs}.
+
+\section{State and transformation of compartments}
+
+In \SBGNPDLone a \glyph{compartment} is a stateless entity. It cannot carry \glyph{state variables}, and cannot be subjected to process modifying a state. As a recult, a \glyph{compartment} cannot be transformed, moved, split or merged with another. If one want to represent the transformation of a compartment, one has to create the start and end compartments, and represent the transport of all the \glyph{EPNs} from one to the other. This is not satisfactory, and should be addressed in the future.
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-07-14 14:35:52
|
Revision: 400
http://sbgn.svn.sourceforge.net/sbgn/?rev=400&view=rev
Author: lenov
Date: 2008-07-14 07:35:51 -0700 (Mon, 14 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
trunk/documents/specifications/ProcessDiagram/Level1/sources/syntax.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/syntax.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/syntax.tex 2008-07-14 14:33:08 UTC (rev 399)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/syntax.tex 2008-07-14 14:35:51 UTC (rev 400)
@@ -10,7 +10,7 @@
\hline
\raisebox{20pt}{$Arc \backslash SN$} &\vglyph{macromolecule} & \vglyph{simple chemical} &
\vglyph{unspecified entity} & \vglyph{tag} & \vglyph{source/sink} & \vglyph{perturbation} &
-\vglyph{observable} & \vglyph{multimer} & \vglyph{complex} & \vglyph{nucleic acid feature}&
+\vglyph{observable} & \vglyph{multimer} & \vglyph{complex} & \vglyph{nucleic acid feature} &
\vglyph{submap}\\ \hline
\glyph{consumption} & I & I & I & & I & & & I & I & I & \\ \hline
\glyph{production} & O & O & O & & O & & & O & O & O & \\ \hline
@@ -47,7 +47,7 @@
\glyph{submap}. Next table describes the relationships between \SBGNPDLone glyphs and these three containers. A ``+'' sign means that the element is able to be
contained within the container. A ``-'' means that this containment is not allowed.
-\begin{tabular}{||c|c|c||}
+\begin{tabular}{||c|c|c|c||}
\hline
$EPN \backslash Containers$ & \glyph{complex} & \glyph{compartment} & \glyph{submap} \\ \hline
\glyph{unspecified entity} & + & + & + \\ \hline
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-07-14 14:33:10
|
Revision: 399
http://sbgn.svn.sourceforge.net/sbgn/?rev=399&view=rev
Author: lenov
Date: 2008-07-14 07:33:08 -0700 (Mon, 14 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/syntax.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex 2008-07-14 14:04:02 UTC (rev 398)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex 2008-07-14 14:33:08 UTC (rev 399)
@@ -51,7 +51,7 @@
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/labeledCloneMarker}
- \caption{The \PD glyph for \glyph{labeled clone marker} applied to a \glyph{macromolecule}, a \glyph{genetic entity} and a \glyph{multimer} of \glyph{macromolecules}.}
+ \caption{The \PD glyph for \glyph{labeled clone marker} applied to a \glyph{macromolecule}, a \glyph{nucleic acid feature} and a \glyph{multimer} of \glyph{macromolecules}.}
\label{fig:labeledCloneMarker}
\end{figure}
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex 2008-07-14 14:04:02 UTC (rev 398)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex 2008-07-14 14:33:08 UTC (rev 399)
@@ -15,7 +15,7 @@
\glyphAux A \glyph{nucleic acid feature} can carry state variables (\sect{stateVariable}) that add information about its precise state. The state of a \glyph{nucleic acid feature} is therefore defined as the vector of all its state variables.
-A \glyph{nucleic acid feature} can also carry one or several \glyph{units of information} (\sect{unitInfo}). These can characterise a \glyph{nucleic acid feature}'s domain, such as a binding site, or an exon. Particular \glyph{units of information} carry the material type (\sect{material-types-cv}) and the conceptual type (\sect{conceptual-types-cv}) of the of the genetic entity.
+A \glyph{nucleic acid feature} can also carry one or several \glyph{units of information} (\sect{unitInfo}). These can characterise a \glyph{nucleic acid feature}'s domain, such as a binding site, or an exon. Particular \glyph{units of information} carry the material type (\sect{material-types-cv}) and the conceptual type (\sect{conceptual-types-cv}) of the of the \glyph{nucleic acid feature}.
A \glyph{nucleic acid feature} may also carry a \glyph{clone marker}
(\sect{cloneMarker}).
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex 2008-07-14 14:04:02 UTC (rev 398)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex 2008-07-14 14:33:08 UTC (rev 399)
@@ -24,7 +24,7 @@
An entity pool is a population of entities that cannot be distinguished from each other, when it comes to the \SBGNPDLone map. For instance all the molecular entities that fulfill the same role in a given process form an entity pool. As a result, and entity pool can represent different granularity levels, such as all the proteins, all the instances of a given protein, only certain forms of a given protein. To belong to a compartment is sufficient to belong to different entity pools. Calcium ions in the endoplasmic reticulum and calcium ions in the cytosol belong to different entity pools whent it comes to representing calcium release from the endoplasmic reticulum.
-\SBGNPDLone{} contains five glyphs representing classes of material entities: \glyph{unspecified entity}, \glyph{simple chemical}, \glyph{macromolecule}, \glyph{genetic entity}, and \glyph{multimer}. (Specific types of macromolecules, such as protein, RNA, DNA, polysaccharide, and specific simple chemicals are not defined by \SBGNPDLone but may be part of future levels of SBGN.) In addition to the material entities, \SBGNPDLone{} represents four conceptual entities: \glyph{source/sink}, \glyph{perturbation}, \glyph{observable}, and \glyph{tag}. Material and conceptual entities can optionally carry auxiliary units such as \glyph{units of information}, \glyph{state variables} and \glyph{clone markers}.
+\SBGNPDLone{} contains five glyphs representing classes of material entities: \glyph{unspecified entity}, \glyph{simple chemical}, \glyph{macromolecule}, \glyph{nucleic acid feature}, and \glyph{multimer}. (Specific types of macromolecules, such as protein, RNA, DNA, polysaccharide, and specific simple chemicals are not defined by \SBGNPDLone but may be part of future levels of SBGN.) In addition to the material entities, \SBGNPDLone{} represents four conceptual entities: \glyph{source/sink}, \glyph{perturbation}, \glyph{observable}, and \glyph{tag}. Material and conceptual entities can optionally carry auxiliary units such as \glyph{units of information}, \glyph{state variables} and \glyph{clone markers}.
\input{sources/unspecified.tex}
\input{sources/simpleChemical.tex}
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/syntax.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/syntax.tex 2008-07-14 14:04:02 UTC (rev 398)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/syntax.tex 2008-07-14 14:33:08 UTC (rev 399)
@@ -10,7 +10,7 @@
\hline
\raisebox{20pt}{$Arc \backslash SN$} &\vglyph{macromolecule} & \vglyph{simple chemical} &
\vglyph{unspecified entity} & \vglyph{tag} & \vglyph{source/sink} & \vglyph{perturbation} &
-\vglyph{observable} & \vglyph{multimer} & \vglyph{complex} & \vglyph{genetic entity}&
+\vglyph{observable} & \vglyph{multimer} & \vglyph{complex} & \vglyph{nucleic acid feature}&
\vglyph{submap}\\ \hline
\glyph{consumption} & I & I & I & & I & & & I & I & I & \\ \hline
\glyph{production} & O & O & O & & O & & & O & O & O & \\ \hline
@@ -43,34 +43,42 @@
\end{tabular}
\subsection{Containment definition}
-There are two EPN types which allows containment in SBGN: \glyph{compartment} and
-\glyph{complex}. Next table describe relationship between EPN elements of SBGN
-and these two containers. Plus sign means that the element is able to be
-contained within container. Empty cell means containment is not allowed.
+There are three EPN types which allow containment in SBGN: \glyph{complex}, \glyph{compartment} and
+\glyph{submap}. Next table describes the relationships between \SBGNPDLone glyphs and these three containers. A ``+'' sign means that the element is able to be
+contained within the container. A ``-'' means that this containment is not allowed.
-
\begin{tabular}{||c|c|c||}
\hline
-$EPN \backslash Containers$ &
-\glyph{compartment}& \glyph{complex} \\ \hline
-\glyph{compartment} & + & +\\ \hline
-\glyph{complex} & & + \\ \hline
-\glyph{macromolecule} & + & + \\ \hline
-\glyph{simple chemical} & + & + \\ \hline
-\glyph{multimer} & + & + \\ \hline
-\glyph{complex} & + & + \\ \hline
-\glyph{unspecified entity} & + & \\ \hline
-\glyph{source/sink} & & \\ \hline
-\glyph{transition} & + & \\ \hline
-\glyph{omitted process} & + & \\ \hline
-\glyph{uncertain process} & + & \\ \hline
-\glyph{module} & + & \\ \hline
-\glyph{association} & + & \\ \hline
-\glyph{dissociation} & + & \\ \hline
-\glyph{and} & + & \\ \hline
-\glyph{or} & + & \\ \hline
-\glyph{xor} & + & \\ \hline
-\glyph{not} & + & \\ \hline
+$EPN \backslash Containers$ & \glyph{complex} & \glyph{compartment} & \glyph{submap} \\ \hline
+\glyph{unspecified entity} & + & + & + \\ \hline
+\glyph{simple chemical} & + & + & + \\ \hline
+\glyph{macromolecule} & + & + & + \\ \hline
+\glyph{nucleic acid feature} & + & + & + \\ \hline
+\glyph{multimer} & + & + & + \\ \hline
+\glyph{source/sink} & - & + & + \\ \hline
+\glyph{perturbation} & - & + & + \\ \hline
+\glyph{observable} & - & + & + \\ \hline
+\glyph{tag} & - & + & + \\ \hline
+\glyph{complex} & + & + & + \\ \hline
+\glyph{compartment} & - & - & + \\ \hline
+\glyph{submap} & - & + & + \\ \hline
+\glyph{transition} & - & + & + \\ \hline
+\glyph{omitted process} & - & + & + \\ \hline
+\glyph{uncertain process} & - & + & + \\ \hline
+\glyph{association} & - & + & + \\ \hline
+\glyph{dissociation} & - & + & + \\ \hline
+\glyph{consumption} & - & + & + \\ \hline
+\glyph{production} & - & + & + \\ \hline
+\glyph{modulation} & - & + & + \\ \hline
+\glyph{stimulation} & - & + & + \\ \hline
+\glyph{catalysis} & - & + & + \\ \hline
+\glyph{inhibition} & - & + & + \\ \hline
+\glyph{trigger} & - & + & + \\ \hline
+\glyph{logic arc} & - & + & + \\ \hline
+\glyph{equivalence arc} & - & + & + \\ \hline
+\glyph{and} & - & + & + \\ \hline
+\glyph{or} & - & + & + \\ \hline
+\glyph{not} & - & + & + \\ \hline
\end{tabular}
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From: <le...@us...> - 2008-07-14 14:04:07
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Revision: 398
http://sbgn.svn.sourceforge.net/sbgn/?rev=398&view=rev
Author: lenov
Date: 2008-07-14 07:04:02 -0700 (Mon, 14 Jul 2008)
Log Message:
-----------
Modified Paths:
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trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex 2008-07-14 04:54:20 UTC (rev 397)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex 2008-07-14 14:04:02 UTC (rev 398)
@@ -1,23 +1,23 @@
% $HeadURL$
-\subsection{Glyph: \glyph{Genetic entity}}
+\subsection{Glyph: \glyph{Nucleic acid feature}}
\label{sec:genetic}
-The \emph{genetic entity} construct in SBGN is meant to represent a fragment of a macromolecule carrying genetic information. A common use for this construct is to represent a gene or transcript. The label of this EPN and its \emph{units of information} are often important for making the purpose clear to the reader of a diagram.
+The \emph{Nucleic acid feature} construct in SBGN is meant to represent a fragment of a macromolecule carrying genetic information. A common use for this construct is to represent a gene or transcript. The label of this EPN and its \emph{units of information} are often important for making the purpose clear to the reader of a diagram.
\begin{glyphDescription}
\glyphSboTerm SBO:0000354 ! genetic entity
-\glyphContainer A \glyph{genetic entity} is represented by a rectangular container whose bottom half has rounded corners, as shown in \fig{genetic}. This design reminds that we are fundamentally dealing with a unit of information, but this information is carried by a macromolecule.
+\glyphContainer A \glyph{nucleic acid feature} is represented by a rectangular container whose bottom half has rounded corners, as shown in \fig{genetic}. This design reminds that we are fundamentally dealing with a unit of information, but this information is carried by a macromolecule.
-\glyphLabel The identity of a particular \glyph{genetic entity} is established by a label placed in an unordered box containing a string of characters. The characters may be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
+\glyphLabel The identity of a particular \glyph{Nucleic acid feature} is established by a label placed in an unordered box containing a string of characters. The characters may be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
-\glyphAux A \glyph{genetic entity} can carry state variables (\sect{stateVariable}) that add information about its precise state. The state of a genetic entity is therefore defined as the vector of all its state variables.
+\glyphAux A \glyph{nucleic acid feature} can carry state variables (\sect{stateVariable}) that add information about its precise state. The state of a \glyph{nucleic acid feature} is therefore defined as the vector of all its state variables.
-A \glyph{genetic information} can also carry one or several \glyph{units of information} (\sect{unitInfo}). These can characterise a \glyph{genetic entity}'s domain, such as a binding site, or an exon. Particular \glyph{units of information} carry the material type (\sect{material-types-cv}) and the conceptual type (\sect{conceptual-types-cv}) of the of the genetic entity.
+A \glyph{nucleic acid feature} can also carry one or several \glyph{units of information} (\sect{unitInfo}). These can characterise a \glyph{nucleic acid feature}'s domain, such as a binding site, or an exon. Particular \glyph{units of information} carry the material type (\sect{material-types-cv}) and the conceptual type (\sect{conceptual-types-cv}) of the of the genetic entity.
-A \glyph{genetic entity} may also carry a \glyph{clone marker}
+A \glyph{nucleic acid feature} may also carry a \glyph{clone marker}
(\sect{cloneMarker}).
\end{glyphDescription}
@@ -26,13 +26,10 @@
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/genetic}
- \caption{The \PD glyph for \glyph{genetic entity} with an additional state variable and a unit of information.}
+ \caption{The \PD glyph for \glyph{nucleic acid feature} with an additional state variable and a unit of information.}
\label{fig:genetic}
\end{figure}
-
-
-
% The following is for [X]Emacs users. Please leave in place.
% Local Variables:
% TeX-master: "../sbgn_PD-level1"
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From: <mh...@us...> - 2008-07-14 04:54:21
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Revision: 397
http://sbgn.svn.sourceforge.net/sbgn/?rev=397&view=rev
Author: mhucka
Date: 2008-07-13 21:54:20 -0700 (Sun, 13 Jul 2008)
Log Message:
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Avoid a possible garden path sentence.
Modified Paths:
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trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex 2008-07-14 04:33:24 UTC (rev 396)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex 2008-07-14 04:54:20 UTC (rev 397)
@@ -20,7 +20,7 @@
The diagram in \fig{eg1} is a simple diagram for part of a mitogen-activated protein kinase (MAPK) cascade. The larger nodes in the figure (some of which are in the shape of rounded rectangles and others in the shape of circles) represent biological materials---things like macromolecules and simple chemicals. The biological materials are altered via processes, which are indicated in SBGN by lines with arrows and other decorations. In this particular diagram, all of the processes happen to be the same: transitions catalyzed by biochemical entities. The directions of the arrows indicate the direction of the transitions; for example, unphosphorylated RAF kinase transitions to phosphorylated RAF kinase via a process catalyzed by RAS. ATP and ADP are also involved in the same process, but the focus of the diagram is on what happens to RAF, so ATP and ADP are shown as incidental to the main transition. The small circles on the nodes for RAF and other entity pools represent units of information (in this case, phosphorylation sites), while the other small circles touching small squares indicate a specific kind of process. The details of this and other aspects of \PD notation are explained in the rest of this chapter.
-The essence of the \PD is \emph{change}: it shows how different entities in the system transition from one form to another. The entities themselves can be many different things. In the example of \fig{eg1}, they are either pools of macromolecules or pools of simple chemicals, but as will become clear later in this chapter, they can be other material and conceptual constructs as well. Note also that we speak of \emph{entity pools} rather than individuals; this is because in biochemical network models, one does not focus on single molecules, but rather collections of molecules of the same kind. The molecules in a given pool are considered indistinguishable from each other. The way in which a type of entity is transformed into another is conveyed by \emph{process nodes}, and links between entity pool nodes and process nodes indicate an influence by the entities on the processes. In the case of \fig{eg1}, they happen all to be catalysis, \sect{catalysis}, but others are possible. Finally, nodes in \PDs are usually not repeated; if they do need to be repeated, they are marked with \emph{clone markers}---specific modifications to the appearance of the node (\sect{cloneMarker}).
+The essence of the \PD is \emph{change}: it shows how different entities in the system transition from one form to another. The entities themselves can be many different things. In the example of \fig{eg1}, they are either pools of macromolecules or pools of simple chemicals, but as will become clear later in this chapter, they can be other conceptual and material constructs as well. Note also that we speak of \emph{entity pools} rather than individuals; this is because in biochemical network models, one does not focus on single molecules, but rather collections of molecules of the same kind. The molecules in a given pool are considered indistinguishable from each other. The way in which a type of entity is transformed into another is conveyed by \emph{process nodes}, and links between entity pool nodes and process nodes indicate an influence by the entities on the processes. In the case of \fig{eg1}, they happen all to be catalysis, \sect{catalysis}, but others are possible. Finally, nodes in \PDs are usually not repeated; if they do need to be repeated, they are marked with \emph{clone markers}---specific modifications to the appearance of the node (\sect{cloneMarker}).
\tab{component-summary} summarizes the different SBGN abstractions described in this chapter.
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From: <mh...@us...> - 2008-07-14 04:33:26
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Revision: 396
http://sbgn.svn.sourceforge.net/sbgn/?rev=396&view=rev
Author: mhucka
Date: 2008-07-13 21:33:24 -0700 (Sun, 13 Jul 2008)
Log Message:
-----------
Fixed inconsistent font of the TOC page numbers.
Modified Paths:
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trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-style.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-style.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-style.tex 2008-07-14 04:17:27 UTC (rev 395)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-style.tex 2008-07-14 04:33:24 UTC (rev 396)
@@ -206,6 +206,27 @@
\if@restonecol\twocolumn\fi
}
+% There seems to be no way to redefine the font used by the table of contents
+% line printing command except to modify the source from latex.ltx.
+
+\def\@dottedtocline#1#2#3#4#5{%
+ \ifnum #1>\c@tocdepth \else
+ \vskip \z@ \@plus.2\p@
+ {\leftskip #2\relax \rightskip \@tocrmarg \parfillskip -\rightskip
+ \parindent #2\relax\@afterindenttrue
+ \interlinepenalty\@M
+ \leavevmode
+ \@tempdima #3\relax
+ \advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
+ {#4}\nobreak
+ \leaders\hbox{$\m@th
+ \mkern \@dotsep mu\hbox{.}\mkern \@dotsep
+ mu$}\hfill
+ \nobreak
+ \hb@xt@\@pnumwidth{\hfil\normalfont\sffamily \normalcolor #5}%
+ \par}%
+ \fi}
+
% The following was ripped out of caption.sty, version 1.4b.
% Copyright (C) 1994-95 Harald Axel Sommerfeldt
% The first few lines set up the parameters for the layout created
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From: <mh...@us...> - 2008-07-14 04:17:28
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Revision: 395
http://sbgn.svn.sourceforge.net/sbgn/?rev=395&view=rev
Author: mhucka
Date: 2008-07-13 21:17:27 -0700 (Sun, 13 Jul 2008)
Log Message:
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Ignore .dvi files.
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trunk/documents/specifications/ProcessDiagram/Level1/.svnignore
Modified: trunk/documents/specifications/ProcessDiagram/Level1/.svnignore
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/.svnignore 2008-07-14 04:16:51 UTC (rev 394)
+++ trunk/documents/specifications/ProcessDiagram/Level1/.svnignore 2008-07-14 04:17:27 UTC (rev 395)
@@ -6,3 +6,4 @@
*.aux
*.out
*.mp
+*.dvi
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From: <mh...@us...> - 2008-07-14 04:16:54
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Revision: 394
http://sbgn.svn.sourceforge.net/sbgn/?rev=394&view=rev
Author: mhucka
Date: 2008-07-13 21:16:51 -0700 (Sun, 13 Jul 2008)
Log Message:
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Added the 'auto' directory created by Emacs AuCTeX.
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trunk/documents/specifications/ProcessDiagram/Level1/sources/.svnignore
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/.svnignore
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/.svnignore 2008-07-14 04:16:29 UTC (rev 393)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/.svnignore 2008-07-14 04:16:51 UTC (rev 394)
@@ -1,2 +1,3 @@
+auto
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*.log
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From: <mh...@us...> - 2008-07-14 04:16:30
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Revision: 393
http://sbgn.svn.sourceforge.net/sbgn/?rev=393&view=rev
Author: mhucka
Date: 2008-07-13 21:16:29 -0700 (Sun, 13 Jul 2008)
Log Message:
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Updated list of ignored files.
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trunk/documents/specifications/ProcessDiagram/Level1/sources/
Property changes on: trunk/documents/specifications/ProcessDiagram/Level1/sources
___________________________________________________________________
Name: svn:ignore
- *.aux
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From: <mh...@us...> - 2008-07-14 04:16:08
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Revision: 392
http://sbgn.svn.sourceforge.net/sbgn/?rev=392&view=rev
Author: mhucka
Date: 2008-07-13 21:16:06 -0700 (Sun, 13 Jul 2008)
Log Message:
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Updated list of ignored files.
Property Changed:
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trunk/documents/specifications/ProcessDiagram/Level1/
Property changes on: trunk/documents/specifications/ProcessDiagram/Level1
___________________________________________________________________
Name: svn:ignore
- auto
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*.toc
*.bbl
*.blg
*.aux
*.out
*.mp
+ auto
*.log
*.toc
*.bbl
*.blg
*.aux
*.out
*.mp
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From: <mh...@us...> - 2008-07-14 04:15:32
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Revision: 391
http://sbgn.svn.sourceforge.net/sbgn/?rev=391&view=rev
Author: mhucka
Date: 2008-07-13 21:15:31 -0700 (Sun, 13 Jul 2008)
Log Message:
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Using home-grown .svnignore file to help manage ignored files.
Added Paths:
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trunk/documents/specifications/ProcessDiagram/Level1/.svnignore
trunk/documents/specifications/ProcessDiagram/Level1/sources/.svnignore
Added: trunk/documents/specifications/ProcessDiagram/Level1/.svnignore
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/.svnignore (rev 0)
+++ trunk/documents/specifications/ProcessDiagram/Level1/.svnignore 2008-07-14 04:15:31 UTC (rev 391)
@@ -0,0 +1,8 @@
+auto
+*.log
+*.toc
+*.bbl
+*.blg
+*.aux
+*.out
+*.mp
Added: trunk/documents/specifications/ProcessDiagram/Level1/sources/.svnignore
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/.svnignore (rev 0)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/.svnignore 2008-07-14 04:15:31 UTC (rev 391)
@@ -0,0 +1,2 @@
+*.aux
+*.log
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From: <mh...@us...> - 2008-07-14 04:14:22
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Revision: 390
http://sbgn.svn.sourceforge.net/sbgn/?rev=390&view=rev
Author: mhucka
Date: 2008-07-13 21:14:21 -0700 (Sun, 13 Jul 2008)
Log Message:
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trunk/documents/specifications/ProcessDiagram/Level1/
trunk/documents/specifications/ProcessDiagram/Level1/Makefile
trunk/documents/specifications/ProcessDiagram/Level1/README.txt
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.bib
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/CVs.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/and.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/association.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/catalysis.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/compartment.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/complex-epn-eg.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/complex.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/consumption.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/dissociation.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/equivalenceArc.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/examples.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/grammar.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/inhibition.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-macros.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-style.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/logicArc.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/macromolecule.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/modulation.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/multimer.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/not.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/observable.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/omitted.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/or.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/perturbation.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/preface.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/production.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/refcard.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/semantics.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/simpleChemical.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/sourceSink.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/stateVariable.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/stimulation.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/submap.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/syntax.tex
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trunk/documents/specifications/ProcessDiagram/Level1/sources/toc.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/transition.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/trigger.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/truth.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/uncertain.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/unitInformation.tex
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trunk/documents/specifications/ProcessDiagram/Level1/sources/working.tex
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From: <mh...@us...> - 2008-07-14 04:12:55
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Revision: 389
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <le...@us...> - 2008-07-09 22:10:02
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[truncated message content] |
|
From: <le...@us...> - 2008-07-09 10:01:58
|
Revision: 387
http://sbgn.svn.sourceforge.net/sbgn/?rev=387&view=rev
Author: lenov
Date: 2008-07-09 03:01:57 -0700 (Wed, 09 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex 2008-07-08 16:03:06 UTC (rev 386)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex 2008-07-09 10:01:57 UTC (rev 387)
@@ -3,7 +3,7 @@
\subsection{Glyph: \glyph{Clone marker}}
\label{sec:cloneMarker}
-If an \glyph{EPN} is duplicated on a map, it is necessary to indicate this fact by using the \glyph{clone marker} auxiliary unit. The purpose of this marker is to provide the reader with a visual indication that this node has been cloned, and that at least one other occurrence of the \glyph{EPN} can be found in the map (or in a submap; see \sect{submap}). The clone marker takes two forms, simple and labeled, depending on whether the node being cloned can carry state variables (\ie whether it is a stateful EPN).
+If an \glyph{EPN} is duplicated on a map, it is necessary to indicate this fact by using the \glyph{clone marker} auxiliary unit. The purpose of this marker is to provide the reader with a visual indication that this node has been cloned, and that at least one other occurrence of the \glyph{EPN} can be found in the map (or in a submap; see \sect{submap}). The clone marker takes two forms, simple and labeled, depending on whether the node being cloned can carry state variables (\ie whether it is a stateful EPN). Note that an \glyph{EPN} belong to a single compartment. If two glyphs labelled ``X'' are located in two different compartments, such as ATP in cytosol and ATP in mitochondiral lumen, they represent different \glyph{EPN}, and therefore do-not need to be marked as cloned.
\subsubsection{Simple clone marker}
@@ -15,7 +15,7 @@
\glyphSboTerm Not applicable.
-\glyphContainer The simple (unlabeled) \glyph{clone marker} is a portion of the surface of an \glyph{EPN} that has been modified visually through the use of a different shade, texture, or color. \fig{simpleCloneMarker} illustrates this. The \glyph{clone marker} occupies the lower part of the \glyph{EPN} and the marker's surface must not exceed 30\% of the \glyph{EPN}'s surface.
+\glyphContainer The simple (unlabeled) \glyph{clone marker} is a portion of the surface of an \glyph{EPN} that has been modified visually through the use of a different shade, texture, or color. \fig{simpleCloneMarker} illustrates this. The \glyph{clone marker} occupies the lower part of the \glyph{EPN}. The filled area must be significantly smaller than the unfilled one. A marker's surface must not exceed 30\% of the \glyph{EPN}'s surface. A value in the range 15 and 25\% is advised.
\glyphLabel Not applicable.
@@ -39,7 +39,7 @@
\glyphSboTerm Not applicable.
-\glyphContainer The labeled \glyph{clone marker} is a portion of the surface of an \glyph{EPN} that has been modified visually through the use of a different shade, texture, or color. The \glyph{clone marker} occupies the lower part of the EPN glyph the marker's surface must not exceed 30\% of the \glyph{EPN}'s surface. \fig{labeledCloneMarker} illustrates this.
+\glyphContainer The labeled \glyph{clone marker} is a portion of the surface of an \glyph{EPN} that has been modified visually through the use of a different shade, texture, or color. The \glyph{clone marker} occupies the lower part of the EPN glyph. The filled area must be significantly smaller than the unfilled one, but the be large enough to have an height larger than the \glyph{clone marker}'s label (cf below). A marker's surface must not exceed 30\% of the \glyph{EPN}'s surface. A value in the range 15 and 25\% is advised. \fig{labeledCloneMarker} illustrates this.
\glyphLabel A \glyph{clone marker} is identified by a label placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container (the portion of the surface
of the EPN that has been modified visually). The font color of the label and the color of the clone marker should contrast with one another. The label on a labeled \glyph{labeled clone marker} is mandatory.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-07-08 16:03:14
|
Revision: 386
http://sbgn.svn.sourceforge.net/sbgn/?rev=386&view=rev
Author: lenov
Date: 2008-07-08 09:03:06 -0700 (Tue, 08 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/preface.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/preface.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/preface.tex 2008-07-07 14:31:48 UTC (rev 385)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/preface.tex 2008-07-08 16:03:06 UTC (rev 386)
@@ -8,7 +8,7 @@
% Thanks to Steven Watterson for thoroughly proof-reading the final draft
-The development of SBGN was mainly supported by a grant from the Japanese \emph{New Energy and Industrial Technology Development Organization} (NEDO, \url{http://www.nedo.go.jp/}) and also benefited from the help of a Japan Partnering Award of the British \emph{Biotechnology and Biological Sciences Research Council} (BBSRC, \url{http://www.bbsrc.ac.uk/})
+The development of SBGN was mainly supported by a grant from the Japanese \emph{New Energy and Industrial Technology Development Organization} (NEDO, \url{http://www.nedo.go.jp/}). The \emph{Okinawa Institute of Science and Technology} (OIST, \url{http://www.oist.jp/}) and the British \emph{Biotechnology and Biological Sciences Research Council} (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award supported workshops. The \emph{Japan Science and Technology Agency} (JST, \url{http://www.jst.go.jp/}) and the \emph{Genome Network Project} of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT) also suppoprted the gene regulation network aspect of SBGN.
\section*{Notes on typographical conventions}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-07-07 14:33:09
|
Revision: 385
http://sbgn.svn.sourceforge.net/sbgn/?rev=385&view=rev
Author: lenov
Date: 2008-07-07 07:31:48 -0700 (Mon, 07 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/images/refcard.eps
trunk/documents/specifications/ProcessDiagram/Level1/images/refcard.pdf
trunk/documents/specifications/ProcessDiagram/Level1/images/refcard.png
trunk/documents/specifications/ProcessDiagram/Level1/images/refcard.svg
Modified: trunk/documents/specifications/ProcessDiagram/Level1/images/refcard.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/images/refcard.eps 2008-07-07 12:16:02 UTC (rev 384)
+++ trunk/documents/specifications/ProcessDiagram/Level1/images/refcard.eps 2008-07-07 14:31:48 UTC (rev 385)
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[truncated message content] |
|
From: <le...@us...> - 2008-07-07 12:16:04
|
Revision: 384
http://sbgn.svn.sourceforge.net/sbgn/?rev=384&view=rev
Author: lenov
Date: 2008-07-07 05:16:02 -0700 (Mon, 07 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
trunk/documents/specifications/ProcessDiagram/Level1/sources/examples.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/examples.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/examples.tex 2008-07-07 10:37:54 UTC (rev 383)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/examples.tex 2008-07-07 12:16:02 UTC (rev 384)
@@ -29,7 +29,7 @@
\end{center}
\end{figure}
-\fig{muscle} introduces an SBGN \PD that spans several compartments. It exemplifies the use of of the \glyph{PN} \glyph{omitted} and \glyph{dissociation}, and the \glyph{connecting arc} \glyph{trigger}. Note that the compartment ``synaptic vesicle'' is not \textbf{contained} in the compartment ``synaptic button'' but \textbf{surrounded} by it. The situation is simular for the compartments ``ER'' and ``muscle cytosol''.
+\fig{muscle} introduces an SBGN \PD that spans several compartments. Note that the compartment ``synaptic vesicle'' is not \textbf{contained} in the compartment ``synaptic button'' but \textbf{overlap} it. The \glyph{simple chemical} ``ACh'' of the ''synaptic vesicle`` is not the same \glyph{EPN} than the ``ACh'' of the ``synaptic button'' and of ``synaptic cleft''. The situation is simular with the compartments ``ER'' and ``muscle cytosol''. The diagram exemplifies the use of of the \glyph{PN} \glyph{omitted} and \glyph{dissociation}, and the \glyph{connecting arc} \glyph{trigger}.
\begin{figure}[htb]
\begin{center}
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex 2008-07-07 10:37:54 UTC (rev 383)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex 2008-07-07 12:16:02 UTC (rev 384)
@@ -22,6 +22,8 @@
\section{Entity pool nodes}\label{sec:EPNs}
+An entity pool is a population of entities that cannot be distinguished from each other, when it comes to the \SBGNPDLone map. For instance all the molecular entities that fulfill the same role in a given process form an entity pool. As a result, and entity pool can represent different granularity levels, such as all the proteins, all the instances of a given protein, only certain forms of a given protein. To belong to a compartment is sufficient to belong to different entity pools. Calcium ions in the endoplasmic reticulum and calcium ions in the cytosol belong to different entity pools whent it comes to representing calcium release from the endoplasmic reticulum.
+
\SBGNPDLone{} contains five glyphs representing classes of material entities: \glyph{unspecified entity}, \glyph{simple chemical}, \glyph{macromolecule}, \glyph{genetic entity}, and \glyph{multimer}. (Specific types of macromolecules, such as protein, RNA, DNA, polysaccharide, and specific simple chemicals are not defined by \SBGNPDLone but may be part of future levels of SBGN.) In addition to the material entities, \SBGNPDLone{} represents four conceptual entities: \glyph{source/sink}, \glyph{perturbation}, \glyph{observable}, and \glyph{tag}. Material and conceptual entities can optionally carry auxiliary units such as \glyph{units of information}, \glyph{state variables} and \glyph{clone markers}.
\input{sources/unspecified.tex}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-07-07 10:37:55
|
Revision: 383
http://sbgn.svn.sourceforge.net/sbgn/?rev=383&view=rev
Author: lenov
Date: 2008-07-07 03:37:54 -0700 (Mon, 07 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.bib
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
trunk/documents/specifications/ProcessDiagram/Level1/sources/stateVariable.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.bib
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.bib 2008-07-07 09:58:21 UTC (rev 382)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.bib 2008-07-07 10:37:54 UTC (rev 383)
@@ -71,7 +71,7 @@
@Article{Kohn:1999,
author = {Kurt W. Kohn},
- title = {Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems},
+ title = {Molecular Interaction Map of the Mammalian Cell Cycle Control and {DNA} Repair Systems},
journal = {Molecular Biology of the Cell},
year = {1999},
volume = {10},
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/stateVariable.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/stateVariable.tex 2008-07-07 09:58:21 UTC (rev 382)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/stateVariable.tex 2008-07-07 10:37:54 UTC (rev 383)
@@ -27,7 +27,8 @@
\glyphLabel The identification of an instance of a \glyph{state variable}
is carried by one or two unbordered boxes, each containing a string of
characters. The characters cannot be distributed on several lines. One
- box is mandatory, and contains the value of the \glyph{state variable}.
+ box is mandatory, and contains the value of the \glyph{state variable}. it should be noted the value can be
+empty (empty string), e.g. non-phosphorylated phosporylation site.
The second box is optional and carries the identification of the
\glyph{state variable}. This identification should be present if
confusion is possible between several state varibles (\eg several
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-07-07 09:58:24
|
Revision: 382
http://sbgn.svn.sourceforge.net/sbgn/?rev=382&view=rev
Author: lenov
Date: 2008-07-07 02:58:21 -0700 (Mon, 07 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.eps
trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.pdf
trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.png
trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.svg
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
trunk/documents/specifications/ProcessDiagram/Level1/sources/examples.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.eps 2008-07-07 09:45:43 UTC (rev 381)
+++ trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.eps 2008-07-07 09:58:21 UTC (rev 382)
@@ -4486,51 +4486,138 @@
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.pdf
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.png
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.svg
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.svg 2008-07-07 09:45:43 UTC (rev 381)
+++ trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.svg 2008-07-07 09:58:21 UTC (rev 382)
@@ -33,8 +33,8 @@
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
inkscape:zoom="3.0479999"
- inkscape:cx="395.92691"
- inkscape:cy="233.1915"
+ inkscape:cx="264.40812"
+ inkscape:cy="355.0445"
inkscape:document-units="px"
inkscape:current-layer="layer1"
width="1052.3622px"
@@ -868,7 +868,7 @@
y="391.62012"
x="196.66531"
id="tspan9244"
- sodipodi:role="line">muscle cell</tspan></text>
+ sodipodi:role="line">muscle cytosol</tspan></text>
<path
sodipodi:type="arc"
style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:6.44922256;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
@@ -1324,7 +1324,7 @@
id="tspan10461"
x="193.34001"
y="65.740532"
- style="font-size:13.41586399px">neuronal cell</tspan></text>
+ style="font-size:13.41586399px">synaptic button</tspan></text>
<text
id="text10463"
y="116.00229"
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/examples.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/examples.tex 2008-07-07 09:45:43 UTC (rev 381)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/examples.tex 2008-07-07 09:58:21 UTC (rev 382)
@@ -29,7 +29,7 @@
\end{center}
\end{figure}
-\fig{muscle} introduces an SBGB \PD that spans several compartments. It exemplifies the use of of the \glyph{PN} \glyph{omitted} and the \glyph{connecting arc} \glyph{trigger}.
+\fig{muscle} introduces an SBGN \PD that spans several compartments. It exemplifies the use of of the \glyph{PN} \glyph{omitted} and \glyph{dissociation}, and the \glyph{connecting arc} \glyph{trigger}. Note that the compartment ``synaptic vesicle'' is not \textbf{contained} in the compartment ``synaptic button'' but \textbf{surrounded} by it. The situation is simular for the compartments ``ER'' and ``muscle cytosol''.
\begin{figure}[htb]
\begin{center}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-07-07 09:45:46
|
Revision: 381
http://sbgn.svn.sourceforge.net/sbgn/?rev=381&view=rev
Author: lenov
Date: 2008-07-07 02:45:43 -0700 (Mon, 07 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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