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From: <le...@us...> - 2008-07-07 09:44:22
|
Revision: 380
http://sbgn.svn.sourceforge.net/sbgn/?rev=380&view=rev
Author: lenov
Date: 2008-07-07 02:44:20 -0700 (Mon, 07 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.eps
trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.pdf
trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.png
trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.svg
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/sources/examples.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.eps 2008-07-04 22:43:12 UTC (rev 379)
+++ trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.eps 2008-07-07 09:44:20 UTC (rev 380)
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.pdf
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.png
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.svg
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.svg 2008-07-04 22:43:12 UTC (rev 379)
+++ trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK.svg 2008-07-07 09:44:20 UTC (rev 380)
@@ -31,7 +31,7 @@
inkscape:pageshadow="2"
inkscape:zoom="1.7640121"
inkscape:cx="160.98736"
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+ inkscape:cy="487.94723"
inkscape:document-units="px"
inkscape:current-layer="layer1"
width="744.09448px"
@@ -697,7 +697,7 @@
x="81.897087"
y="656.33911"
style="font-size:12px;font-weight:normal;text-align:center;text-anchor:middle"
- id="tspan3802">MAPK</tspan></text>
+ id="tspan3802">ERK</tspan></text>
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.eps 2008-07-04 22:43:12 UTC (rev 379)
+++ trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.eps 2008-07-07 09:44:20 UTC (rev 380)
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[truncated message content] |
|
From: <le...@us...> - 2008-07-04 22:43:14
|
Revision: 379
http://sbgn.svn.sourceforge.net/sbgn/?rev=379&view=rev
Author: lenov
Date: 2008-07-04 15:43:12 -0700 (Fri, 04 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex 2008-07-04 22:05:05 UTC (rev 378)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex 2008-07-04 22:43:12 UTC (rev 379)
@@ -22,7 +22,7 @@
\end{enumerate}
-This document defines the \emph{\PD{}} visual language of SBGN. As explained more fully in Section~\vref{sec:languages}, \PDs are one of three views of a model offered by SBGN. It is the product of many hours of discussion and development by many individuals and groups. In the following sections, we describe the background, motivations, and context of \PDs.
+This document defines the \emph{\PD{}} visual language of SBGN. As explained more fully in~\sect{languages}, \PDs are one of three views of a model offered by SBGN. It is the product of many hours of discussion and development by many individuals and groups. In the following sections, we describe the background, motivations, and context of \PDs.
\section{History of SBGN development}
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex 2008-07-04 22:05:05 UTC (rev 378)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex 2008-07-04 22:43:12 UTC (rev 379)
@@ -48,95 +48,91 @@
\subsection{Requirements}
-Requirements are rules which must be fulfilled by a layout to
-produce a valid SBGN diagram.
+Requirements are rules which \textbf{must} be fulfilled by a layout to
+produce a valid \SBGNPDLone graph.
\subsubsection{Node-node overlaps}
Nodes are only allowed to overlap in two cases:
\begin{enumerate}
\item the overlapping nodes define a glyph (e.\,g.~a \glyph{multimer}
- composed by stacking of two containers representing the monomers)
+ composed by stacking of two containers representing the monomers).
\item nodes overlapping compartments
(e.\,g.~a complex placed on the compartment border).
\end{enumerate}
-Otherwise nodes are not allowed to overlap. This includes the
+Otherwise, nodes are not allowed to overlap (\fig{layout1}). This includes the
touching of nodes. Touching is not allowed apart from the case where
it has a specific meaning, e.\,g.~two macromolecules touching each
-other within a complex because they form the complex. Compartment
-borders are not allowed to overlap and are only allowed to touch
-each other if this is meaningful, e.\,g.~ER and ER membrane. Modules
-are not allowed to overlap. Compartments and modules can contain
-other nodes including compartments and/or modules.
+other within a complex because they form the complex. Submaps
+are not allowed to overlap.
\begin{figure}[h!]
\centering
\includegraphics[scale=0.3]{images/layout-node-node}
- \caption{Nodes must not overlap.}\label{layout1}
+ \caption{Nodes must not overlap.}\label{fig:layout1}
\end{figure}
\subsubsection{Node-edge crossing}\label{crosEdNoRe}
In case of node-edge crossing the edge must be drawn on the top of
-the node. See also recommendation \ref{crosEdNo} (crossing between
+the node (\fig{layout2}). See also recommendation \ref{crosEdNo} (crossing between
edges and nodes should be avoided).
\begin{figure}[h!]
\centering
\includegraphics[scale=0.3]{images/layout-node-edge}
\caption{If an edge crosses a node, the edge must be drawn on top
- of the node.}\label{layout2}
+ of the node.}\label{fig:layout2}
\end{figure}
\subsubsection{Node border-edge overlaps}
-Edges are not allowed to overlap the border lines of nodes.
+Edges are not allowed to overlap the border lines of nodes (\fig{layout3}).
\begin{figure}[h!]
\centering
\includegraphics[scale=0.3]{images/layout-node-border-edge}
- \caption{Edges must not overlap node borders.}\label{layout3}
+ \caption{Edges must not overlap node borders.}\label{fig:layout3}
\end{figure}
\subsubsection{Edge-edge overlaps}
-Edges are not allowed to overlap. This include touching of edges.
+Edges are not allowed to overlap (\fig{layout4}). This include touching of edges.
Furthermore, an edge is neither allowed to cross itself nor to cross
-a boundary of nodes or other edges more than once.
+a boundary of node more than twice or other edges more than once.
\begin{figure}[h!]
\centering
\includegraphics[scale=0.3]{images/layout-edge-edge}
- \caption{Edges must not overlap.}\label{layout4}
+ \caption{Edges must not overlap.}\label{fig:layout4}
\end{figure}
\subsubsection{Node orientation}
Nodes have to be drawn horizontally or vertically, any other
-rotation of elements is not allowed.
+rotation of elements is not allowed (\fig{layout5}).
\begin{figure}[h!]
\centering
\includegraphics[scale=0.3]{images/layout-orientation}
\caption{The node orientation must be horizontally or
- vertically.}\label{layout5}
+ vertically.}\label{fig:layout5}
\end{figure}
\subsubsection{Node-edge connection}
-The arcs linking the square box of a transition to the state/entity
-nodes are attached to the center of opposite sides. The modulatory
-arcs point are attached to the other two sides, but not necessarily
-all to the center as several modifiers can touch the same transition
-node. A transition connected to glyph-production arcs on opposite
+The arcs linking the square glyph of a \glyph{transition} to the \glyph{consumption} and \glyph{production arcs}
+ are attached to the center of opposite sides (\fig{layout6}). The modulatory
+arcs are attached to the other two sides, but not necessarily
+all to the center, as several modifiers can affect the same \glyph{transition
+node}. A \glyph{transition} connected to \glyph{production arcs} on opposite
sides is a reversible transition.
\begin{figure}[h!]
\centering
\includegraphics[scale=0.3]{images/layout-connecting-arcs}
- \caption{Arcs between a transition and the state/entity
- nodes must be attached to the center of opposite sides, modulatory
- arcs must be attached to the other two sides.}\label{layout6}
+ \caption{Arcs between a \glyph{transition} and the \glyph{consumption} and \glyph{production arcs} must be attached to the center of opposite sides, modulatory
+ arcs must be attached to the other two sides.}\label{fig:layout6}
\end{figure}
\subsubsection{Node labels}
@@ -198,13 +194,13 @@
\subsubsection{Units of information}
Units of information should not hide the structure of the
-corresponding node.
+corresponding node (\fig{layout7}).
\begin{figure}[h!]
\centering
\includegraphics[scale=0.5]{images/layout-unit-information}
\caption{Units of information should not overlap with any
- other element.}\label{layout7}
+ other element.}\label{fig:layout7}
\end{figure}
\newpage
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-07-04 22:05:11
|
Revision: 378
http://sbgn.svn.sourceforge.net/sbgn/?rev=378&view=rev
Author: lenov
Date: 2008-07-04 15:05:05 -0700 (Fri, 04 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.eps
trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.pdf
trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.svg
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.bib
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
trunk/documents/specifications/ProcessDiagram/Level1/sources/and.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/grammar.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/not.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/or.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.eps 2008-07-02 14:02:03 UTC (rev 377)
+++ trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.eps 2008-07-04 22:05:05 UTC (rev 378)
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.pdf
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.pdf 2008-07-02 14:02:03 UTC (rev 377)
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From: <le...@us...> - 2008-07-02 14:02:11
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Revision: 377
http://sbgn.svn.sourceforge.net/sbgn/?rev=377&view=rev
Author: lenov
Date: 2008-07-02 07:02:03 -0700 (Wed, 02 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.eps
trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.pdf
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.eps
===================================================================
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.pdf
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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...> - 2008-07-02 09:07:29
|
Revision: 376
http://sbgn.svn.sourceforge.net/sbgn/?rev=376&view=rev
Author: lenov
Date: 2008-07-02 02:07:14 -0700 (Wed, 02 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
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
Modified: trunk/documents/specifications/ProcessDiagram/Level1/images/refcard.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/images/refcard.eps 2008-07-02 09:05:33 UTC (rev 375)
+++ trunk/documents/specifications/ProcessDiagram/Level1/images/refcard.eps 2008-07-02 09:07:14 UTC (rev 376)
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From: <le...@us...> - 2008-07-02 09:05:49
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Revision: 375
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Author: lenov
Date: 2008-07-02 02:05:33 -0700 (Wed, 02 Jul 2008)
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From: <le...@us...> - 2008-07-02 08:55:39
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Revision: 374
http://sbgn.svn.sourceforge.net/sbgn/?rev=374&view=rev
Author: lenov
Date: 2008-07-02 01:55:38 -0700 (Wed, 02 Jul 2008)
Log Message:
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Modified Paths:
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/muscle.png
===================================================================
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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...> - 2008-07-02 08:49:16
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Revision: 373
http://sbgn.svn.sourceforge.net/sbgn/?rev=373&view=rev
Author: lenov
Date: 2008-07-02 01:49:12 -0700 (Wed, 02 Jul 2008)
Log Message:
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[truncated message content] |
|
From: <le...@us...> - 2008-07-01 10:58:10
|
Revision: 372
http://sbgn.svn.sourceforge.net/sbgn/?rev=372&view=rev
Author: lenov
Date: 2008-07-01 03:58:05 -0700 (Tue, 01 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
===================================================================
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From: <le...@us...> - 2008-07-01 10:55:13
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Revision: 371
http://sbgn.svn.sourceforge.net/sbgn/?rev=371&view=rev
Author: lenov
Date: 2008-07-01 03:55:09 -0700 (Tue, 01 Jul 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/examples/insulin.eps
trunk/documents/specifications/ProcessDiagram/Level1/examples/insulin.pdf
trunk/documents/specifications/ProcessDiagram/Level1/examples/insulin.png
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/insulin.eps
===================================================================
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[truncated message content] |
|
From: <le...@us...> - 2008-06-30 08:42:57
|
Revision: 370
http://sbgn.svn.sourceforge.net/sbgn/?rev=370&view=rev
Author: lenov
Date: 2008-06-30 01:42:54 -0700 (Mon, 30 Jun 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.
|
|
From: <le...@us...> - 2008-06-30 07:56:01
|
Revision: 369
http://sbgn.svn.sourceforge.net/sbgn/?rev=369&view=rev
Author: lenov
Date: 2008-06-30 00:55:59 -0700 (Mon, 30 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
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trunk/documents/specifications/ProcessDiagram/Level1/images/and.pdf
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===================================================================
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===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/images/not.eps 2008-06-30 00:14:33 UTC (rev 368)
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/images/not.png
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/images/not.svg
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--- trunk/documents/specifications/ProcessDiagram/Level1/images/not.svg 2008-06-30 00:14:33 UTC (rev 368)
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===================================================================
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-06-30 00:14:36
|
Revision: 368
http://sbgn.svn.sourceforge.net/sbgn/?rev=368&view=rev
Author: lenov
Date: 2008-06-29 17:14:33 -0700 (Sun, 29 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.eps
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.eps
===================================================================
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[truncated message content] |
|
From: <le...@us...> - 2008-06-28 22:08:23
|
Revision: 367
http://sbgn.svn.sourceforge.net/sbgn/?rev=367&view=rev
Author: lenov
Date: 2008-06-28 15:08:22 -0700 (Sat, 28 Jun 2008)
Log Message:
-----------
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 2008-06-28 22:05:31 UTC (rev 366)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/genetic.tex 2008-06-28 22:08:22 UTC (rev 367)
@@ -9,7 +9,7 @@
\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}.
+\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.
\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.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-06-28 22:05:33
|
Revision: 366
http://sbgn.svn.sourceforge.net/sbgn/?rev=366&view=rev
Author: lenov
Date: 2008-06-28 15:05:31 -0700 (Sat, 28 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/images/labeledCloneMarker.eps
trunk/documents/specifications/ProcessDiagram/Level1/images/labeledCloneMarker.pdf
trunk/documents/specifications/ProcessDiagram/Level1/images/labeledCloneMarker.svg
trunk/documents/specifications/ProcessDiagram/Level1/images/multimer.eps
trunk/documents/specifications/ProcessDiagram/Level1/images/multimer.pdf
trunk/documents/specifications/ProcessDiagram/Level1/images/multimer.png
trunk/documents/specifications/ProcessDiagram/Level1/images/multimer.svg
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
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.pdf
trunk/documents/specifications/ProcessDiagram/Level1/sources/cloneMarker.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/images/labeledCloneMarker.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/images/labeledCloneMarker.eps 2008-06-27 22:31:40 UTC (rev 365)
+++ trunk/documents/specifications/ProcessDiagram/Level1/images/labeledCloneMarker.eps 2008-06-28 22:05:31 UTC (rev 366)
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/images/labeledCloneMarker.pdf
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From: <le...@us...> - 2008-06-27 22:31:41
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Revision: 365
http://sbgn.svn.sourceforge.net/sbgn/?rev=365&view=rev
Author: lenov
Date: 2008-06-27 15:31:40 -0700 (Fri, 27 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
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[truncated message content] |
|
From: <le...@us...> - 2008-06-27 17:46:10
|
Revision: 364
http://sbgn.svn.sourceforge.net/sbgn/?rev=364&view=rev
Author: lenov
Date: 2008-06-27 10:46:03 -0700 (Fri, 27 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
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trunk/documents/specifications/ProcessDiagram/Level1/sources/compartment.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/complex.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/introduction.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/macromolecule.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/multimer.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/preface.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/semantics.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/stateVariable.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/submap.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/syntax.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/unitInformation.tex
trunk/documents/specifications/ProcessDiagram/Level1/sources/working.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK-only.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK-only.eps 2008-06-25 22:26:20 UTC (rev 363)
+++ trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK-only.eps 2008-06-27 17:46:03 UTC (rev 364)
@@ -1,11676 +1,3060 @@
@@ Diff output truncated at 100000 characters. @@
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-06-25 22:26:22
|
Revision: 363
http://sbgn.svn.sourceforge.net/sbgn/?rev=363&view=rev
Author: lenov
Date: 2008-06-25 15:26:20 -0700 (Wed, 25 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/EntityRelationship/Level1/sbgn_ER-level1.pdf
Modified: trunk/documents/specifications/EntityRelationship/Level1/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-06-25 22:25:55
|
Revision: 362
http://sbgn.svn.sourceforge.net/sbgn/?rev=362&view=rev
Author: lenov
Date: 2008-06-25 15:25:53 -0700 (Wed, 25 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex
Modified: trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex
===================================================================
--- trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex 2008-06-25 21:17:32 UTC (rev 361)
+++ trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex 2008-06-25 22:25:53 UTC (rev 362)
@@ -28,18 +28,16 @@
\input{sources/unspecified.tex}
\input{sources/simpleChemical.tex}
\input{sources/macromolecule.tex}
-% \input{sources/genetic.tex}
-% \input{sources/multimer.tex}
-%
-% \input{sources/sourceSink.tex}
+\input{sources/genetic.tex}
+
+\input{sources/sourceSink.tex}
% \input{sources/perturbation.tex}
% \input{sources/observable.tex}
% \input{sources/tag.tex}
%
% \input{sources/unitInformation.tex}
% \input{sources/stateVariable.tex}
-% \input{sources/cloneMarker.tex}
-%
+%
% \input{sources/complex-epn-eg.tex}
%
%
@@ -53,8 +51,6 @@
%
% \glyph{Containers} are SBGN constructions that contain one or several other SBGN constructs.
%
-% \input{sources/complex.tex}
-% \input{sources/compartment.tex}
% \input{sources/submap.tex}
%
%
@@ -71,10 +67,9 @@
% \input{sources/transition.tex}
% \input{sources/omitted.tex}
% \input{sources/uncertain.tex}
-% \input{sources/association.tex}
-% \input{sources/dissociation.tex}
+%
+% Outcome
%
-%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%% Arcs
@@ -96,6 +91,9 @@
% \input{sources/logicArc.tex}
% \input{sources/equivalenceArc.tex}
%
+% Assignment
+% Interaction
+% Self
%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-06-25 21:17:36
|
Revision: 361
http://sbgn.svn.sourceforge.net/sbgn/?rev=361&view=rev
Author: lenov
Date: 2008-06-25 14:17:32 -0700 (Wed, 25 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex
Added Paths:
-----------
trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.eps
trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.pdf
trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.png
trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.svg
trunk/documents/specifications/EntityRelationship/Level1/sources/macromolecule.tex
Added: trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.eps
===================================================================
--- trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.eps (rev 0)
+++ trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.eps 2008-06-25 21:17:32 UTC (rev 361)
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Added: trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.png
===================================================================
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Property changes on: trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.png
___________________________________________________________________
Name: svn:mime-type
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Added: trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.svg
===================================================================
--- trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.svg (rev 0)
+++ trunk/documents/specifications/EntityRelationship/Level1/images/macromolecule.svg 2008-06-25 21:17:32 UTC (rev 361)
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Modified: trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex
===================================================================
--- trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex 2008-06-24 22:32:06 UTC (rev 360)
+++ trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex 2008-06-25 21:17:32 UTC (rev 361)
@@ -27,7 +27,7 @@
\input{sources/unspecified.tex}
\input{sources/simpleChemical.tex}
-% \input{sources/macromolecule.tex}
+\input{sources/macromolecule.tex}
% \input{sources/genetic.tex}
% \input{sources/multimer.tex}
%
Added: trunk/documents/specifications/EntityRelationship/Level1/sources/macromolecule.tex
===================================================================
--- trunk/documents/specifications/EntityRelationship/Level1/sources/macromolecule.tex (rev 0)
+++ trunk/documents/specifications/EntityRelationship/Level1/sources/macromolecule.tex 2008-06-25 21:17:32 UTC (rev 361)
@@ -0,0 +1,33 @@
+% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/trunk/documents/specifications/EntityRelationship/Level1/sources/macromolecule.tex $
+
+\subsection{Glyph: \glyph{Macromolecule}}
+\label{sec:macromolecule}
+
+Many biological processes involve macromolecules: biochemical substances that are built up from the covalent linking of pseudo-identical units. Examples of macromolecules include proteins, nucleic acids (RNA, DNA), and polysaccharides (glycogen, cellulose, starch, etc.). Attempting to define a separate glyph for all of these different molecules would lead to an explosion of symbols in SBGN, so instead, \SBGNERLone defines only one glyph for all macromolecules. The same glyph is to be used for a protein, a nucleic acid, a complex sugar, and so on. The exact nature of a particular macromolecule in a diagram is then clarified using its label and decorations, as will become clear below. (Future levels of SBGN may subclass the macromolecule and introduce different glyphs to differentiate macromolecules.)
+
+\begin{glyphDescription}
+
+\glyphSboTerm SBO:0000245 ! macromolecule
+
+\glyphContainer A macromolecule is represented by a rectangular container with rounded corners, as illustrated in \fig{macromolecule}.
+
+\glyphLabel A \glyph{macromolecule} 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.
+
+\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 variable values. A state variable is represented by an ellipsoid container, with the long axis of the ellipsoid placed on the border of the \glyph{macromolecule}'s container as illustrated in \fig{macromolecule}. The label of the state variable (which can precise the type of characteristic represented by the state variable, residue type, residue number etc.) is written within the state variable's container.
+
+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. The center of the bounding box of a \glyph{unit of information} is located on the mid-line of the border of the macromolecule.
+
+\end{glyphDescription}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.3]{images/macromolecule}
+ \caption{The \PD glyph for \glyph{macromolecule}.}
+ \label{fig:macromolecule}
+\end{figure}
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_ER-level1"
+% End:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-06-24 22:32:11
|
Revision: 360
http://sbgn.svn.sourceforge.net/sbgn/?rev=360&view=rev
Author: lenov
Date: 2008-06-24 15:32:06 -0700 (Tue, 24 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/EntityRelationship/Level1/sbgn_ER-level1.pdf
trunk/documents/specifications/EntityRelationship/Level1/sbgn_ER-level1.tex
trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex
trunk/documents/specifications/EntityRelationship/Level1/sources/latex-macros.tex
Added Paths:
-----------
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trunk/documents/specifications/EntityRelationship/Level1/images/simpleChemical.eps
trunk/documents/specifications/EntityRelationship/Level1/images/simpleChemical.pdf
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trunk/documents/specifications/EntityRelationship/Level1/sources/CVs.tex
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trunk/documents/specifications/EntityRelationship/Level1/sources/simpleChemical.tex
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|
From: <le...@us...> - 2008-06-24 16:31:03
|
Revision: 359
http://sbgn.svn.sourceforge.net/sbgn/?rev=359&view=rev
Author: lenov
Date: 2008-06-24 09:31:01 -0700 (Tue, 24 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.eps
trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.pdf
trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.svg
Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.eps 2008-06-24 16:14:32 UTC (rev 358)
+++ trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.eps 2008-06-24 16:31:01 UTC (rev 359)
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Modified: trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.pdf
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.pdf 2008-06-24 16:14:32 UTC (rev 358)
+++ trunk/documents/specifications/ProcessDiagram/Level1/examples/IFNGeneRef.pdf 2008-06-24 16:31:01 UTC (rev 359)
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Revision: 358
http://sbgn.svn.sourceforge.net/sbgn/?rev=358&view=rev
Author: lenov
Date: 2008-06-24 09:14:32 -0700 (Tue, 24 Jun 2008)
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|
From: <le...@us...> - 2008-06-24 15:49:36
|
Revision: 357
http://sbgn.svn.sourceforge.net/sbgn/?rev=357&view=rev
Author: lenov
Date: 2008-06-24 08:49:35 -0700 (Tue, 24 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/CVs.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/CVs.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/CVs.tex 2008-06-24 11:43:40 UTC (rev 356)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/CVs.tex 2008-06-24 15:49:35 UTC (rev 357)
@@ -3,7 +3,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\color{blue}
-Some glyphs in SBGN \PDs can contain particular kinds of textual annotations conveying information relevant to the purpose of the glyph. These annotations are \emph{units of information} (\sect{unitInfo}). 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.
+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.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2008-06-24 11:43:42
|
Revision: 356
http://sbgn.svn.sourceforge.net/sbgn/?rev=356&view=rev
Author: lenov
Date: 2008-06-24 04:43:40 -0700 (Tue, 24 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/documents/specifications/EntityRelationship/Level1/sbgn_ER-level1.pdf
trunk/documents/specifications/EntityRelationship/Level1/sbgn_ER-level1.tex
trunk/documents/specifications/EntityRelationship/Level1/sources/preface.tex
Added Paths:
-----------
trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex
trunk/documents/specifications/EntityRelationship/Level1/sources/toc.tex
Modified: trunk/documents/specifications/EntityRelationship/Level1/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: trunk/documents/specifications/EntityRelationship/Level1/sbgn_ER-level1.tex
===================================================================
--- trunk/documents/specifications/EntityRelationship/Level1/sbgn_ER-level1.tex 2008-06-24 10:53:26 UTC (rev 355)
+++ trunk/documents/specifications/EntityRelationship/Level1/sbgn_ER-level1.tex 2008-06-24 11:43:40 UTC (rev 356)
@@ -22,11 +22,11 @@
\input{sources/front-page}
\input{sources/preface}
-%\input{sources/toc}
+\input{sources/toc}
\mainmatter
-%\include{sources/introduction}
+\include{sources/introduction}
%\include{sources/glyphs}
%\include{sources/grammar}
%\include{sources/layout}
Added: trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex
===================================================================
--- trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex (rev 0)
+++ trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex 2008-06-24 11:43:40 UTC (rev 356)
@@ -0,0 +1,117 @@
+% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/trunk/documents/specifications/EntityRelationship/Level1/sources/glyphs.tex $
+
+\chapter{Entity Relationship Glyphs}
+
+%[Note on the color code: \textcolor{blue}{The glyphs that have been thorougly discussed, and are considered frozen, are represented in blue}. \textcolor{green}{The glyphs that have been thorougly discussed, but are still posing problems are represented in green}. \textcolor{red}{The glyphs that have been proposed but for which in-depth discussion is yet to come are represented in red}.]
+
+This chapter provides a catalog of the graphical symbols available for representing entities in \ER diagramss. There are different classes of glyphs corresponding to different classes of material or conceptual entities, containers, processes, connecting arcs, and logical operators. In \chap{grammar} beginning on page~\pageref{chp:grammar}, we describe the rules for combining these glyphs into a legal SBGN \ER, and in \chap{layout} beginning on page~\pageref{chp:layout}, we describe requirements and guidelines for the way that diagrams are visually organized.
+
+% \section{Overview}
+%
+% \input{sources/pd-overview.tex}
+%
+% \section{Controlled vocabularies used in \SBGNPDLone}\label{sec:CVs}
+%
+% \input{sources/CVs.tex}
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%% State nodes
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% \section{Entity pool nodes}\label{sec:EPNs}
+%
+% \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}
+% \input{sources/simpleChemical.tex}
+% \input{sources/macromolecule.tex}
+% \input{sources/genetic.tex}
+% \input{sources/multimer.tex}
+%
+% \input{sources/sourceSink.tex}
+% \input{sources/perturbation.tex}
+% \input{sources/observable.tex}
+% \input{sources/tag.tex}
+%
+% \input{sources/unitInformation.tex}
+% \input{sources/stateVariable.tex}
+% \input{sources/cloneMarker.tex}
+%
+% \input{sources/complex-epn-eg.tex}
+%
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%% Container nodes
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% \section{Container nodes}\label{sec:CNs}
+%
+% \glyph{Containers} are SBGN constructions that contain one or several other SBGN constructs.
+%
+% \input{sources/complex.tex}
+% \input{sources/compartment.tex}
+% \input{sources/submap.tex}
+%
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%% Transition nodes
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% \section{Process nodes}\label{sec:PNs}
+%
+% Process nodes represent processes that transform one or several EPNs into one or several different EPNs.
+%
+% \input{sources/transition.tex}
+% \input{sources/omitted.tex}
+% \input{sources/uncertain.tex}
+% \input{sources/association.tex}
+% \input{sources/dissociation.tex}
+%
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%% Arcs
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% \section{Connecting arcs}\label{sec:arcs}
+%
+% Connecting arcs are lines that link EPNs and PNs together. The symbols attached to their extremities precise their semantics.
+%
+% \input{sources/consumption.tex}
+% \input{sources/production.tex}
+% %\input{sources/truth.tex}
+% \input{sources/modulation.tex}
+% \input{sources/stimulation.tex}
+% \input{sources/catalysis.tex}
+% \input{sources/inhibition.tex}
+% \input{sources/trigger.tex}
+% \input{sources/logicArc.tex}
+% \input{sources/equivalenceArc.tex}
+%
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%% Logical operators
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% \section{Logical operators}\label{sec:logic}
+%
+% \input{sources/and.tex}
+% \input{sources/or.tex}
+% \input{sources/not.tex}
+
+
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_ER-level1"
+% End:
Modified: trunk/documents/specifications/EntityRelationship/Level1/sources/preface.tex
===================================================================
--- trunk/documents/specifications/EntityRelationship/Level1/sources/preface.tex 2008-06-24 10:53:26 UTC (rev 355)
+++ trunk/documents/specifications/EntityRelationship/Level1/sources/preface.tex 2008-06-24 11:43:40 UTC (rev 356)
@@ -1,4 +1,4 @@
-% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/trunk/documents/specifications/EntityRelationshi/Level1/sources/preface.tex $
+% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/trunk/documents/specifications/EntityRelationship/Level1/sources/preface.tex $
\chapter{Preface}
@@ -18,5 +18,5 @@
% The following is for [X]Emacs users. Please leave in place.
% Local Variables:
-% TeX-master: "../sbgn_PD-level1"
+% TeX-master: "../sbgn_ER-level1"
% End:
Added: trunk/documents/specifications/EntityRelationship/Level1/sources/toc.tex
===================================================================
--- trunk/documents/specifications/EntityRelationship/Level1/sources/toc.tex (rev 0)
+++ trunk/documents/specifications/EntityRelationship/Level1/sources/toc.tex 2008-06-24 11:43:40 UTC (rev 356)
@@ -0,0 +1,20 @@
+% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/sources/toc.tex $
+
+\clearpage
+\chapter*{Contents}
+
+\begingroup
+\sffamily
+\small
+\setlength{\columnsep}{12pt}%
+\begin{multicols}{2}
+ \tableofcontents
+\end{multicols}
+\endgroup
+
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_PD-level1"
+% End:
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