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From: <le...@us...> - 2012-07-14 22:10:20
|
Revision: 833
http://sbgn.svn.sourceforge.net/sbgn/?rev=833&view=rev
Author: lenov
Date: 2012-07-14 22:10:11 +0000 (Sat, 14 Jul 2012)
Log Message:
-----------
Added Paths:
-----------
ProcessDiagram/trunk/UserManual/images/MAPK-NoVar.eps
ProcessDiagram/trunk/UserManual/images/MAPK-NoVar.pdf
ProcessDiagram/trunk/UserManual/images/MAPK-NoVar.png
ProcessDiagram/trunk/UserManual/images/MAPK-NoVar.svg
ProcessDiagram/trunk/UserManual/images/MAPK-OneVar.eps
ProcessDiagram/trunk/UserManual/images/MAPK-OneVar.pdf
ProcessDiagram/trunk/UserManual/images/MAPK-OneVar.png
ProcessDiagram/trunk/UserManual/images/MAPK-OneVar.svg
ProcessDiagram/trunk/UserManual/images/MAPK-TwoVar.eps
ProcessDiagram/trunk/UserManual/images/MAPK-TwoVar.pdf
ProcessDiagram/trunk/UserManual/images/MAPK-TwoVar.png
ProcessDiagram/trunk/UserManual/images/MAPK-TwoVar.svg
Added: ProcessDiagram/trunk/UserManual/images/MAPK-NoVar.eps
===================================================================
--- ProcessDiagram/trunk/UserManual/images/MAPK-NoVar.eps (rev 0)
+++ ProcessDiagram/trunk/UserManual/images/MAPK-NoVar.eps 2012-07-14 22:10:11 UTC (rev 833)
@@ -0,0 +1,365 @@
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[truncated message content] |
|
From: <le...@us...> - 2012-07-13 23:12:01
|
Revision: 832
http://sbgn.svn.sourceforge.net/sbgn/?rev=832&view=rev
Author: lenov
Date: 2012-07-13 23:11:52 +0000 (Fri, 13 Jul 2012)
Log Message:
-----------
Modified Paths:
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[truncated message content] |
|
From: <le...@us...> - 2012-07-13 18:07:48
|
Revision: 831
http://sbgn.svn.sourceforge.net/sbgn/?rev=831&view=rev
Author: lenov
Date: 2012-07-13 18:07:38 +0000 (Fri, 13 Jul 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/images/MAPK-only.eps
ProcessDiagram/trunk/UserManual/images/MAPK-only.pdf
ProcessDiagram/trunk/UserManual/images/MAPK-only.png
ProcessDiagram/trunk/UserManual/images/MAPK-only.svg
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bbl
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
ProcessDiagram/trunk/UserManual/sources/introduction.tex
ProcessDiagram/trunk/UserManual/sources/introduction.tex~
Modified: ProcessDiagram/trunk/UserManual/images/MAPK-only.eps
===================================================================
--- ProcessDiagram/trunk/UserManual/images/MAPK-only.eps 2012-07-13 17:49:29 UTC (rev 830)
+++ ProcessDiagram/trunk/UserManual/images/MAPK-only.eps 2012-07-13 18:07:38 UTC (rev 831)
@@ -1,2924 +1,1418 @@
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[truncated message content] |
|
From: <le...@us...> - 2012-07-13 17:49:39
|
Revision: 830
http://sbgn.svn.sourceforge.net/sbgn/?rev=830&view=rev
Author: lenov
Date: 2012-07-13 17:49:29 +0000 (Fri, 13 Jul 2012)
Log Message:
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ProcessDiagram/trunk/UserManual/images/dissociation-ribosome_small.png
Added: ProcessDiagram/trunk/UserManual/images/association-MPF.eps
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From: <le...@us...> - 2012-07-13 15:19:36
|
Revision: 829
http://sbgn.svn.sourceforge.net/sbgn/?rev=829&view=rev
Author: lenov
Date: 2012-07-13 15:19:24 +0000 (Fri, 13 Jul 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/images/process-dimerisation.eps
ProcessDiagram/trunk/UserManual/images/process-dimerisation.pdf
ProcessDiagram/trunk/UserManual/images/process-dimerisation.png
ProcessDiagram/trunk/UserManual/images/process-dimerisation.svg
ProcessDiagram/trunk/UserManual/images/process-phosphorylation.eps
ProcessDiagram/trunk/UserManual/images/process-phosphorylation.pdf
ProcessDiagram/trunk/UserManual/images/process-phosphorylation.png
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ProcessDiagram/trunk/UserManual/images/process-reaction.eps
ProcessDiagram/trunk/UserManual/images/process-reaction.pdf
ProcessDiagram/trunk/UserManual/images/process-reaction.png
ProcessDiagram/trunk/UserManual/images/process-reaction.svg
ProcessDiagram/trunk/UserManual/images/process-translocation.eps
ProcessDiagram/trunk/UserManual/images/process-translocation.pdf
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ProcessDiagram/trunk/UserManual/images/process.eps
ProcessDiagram/trunk/UserManual/images/process.pdf
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ProcessDiagram/trunk/UserManual/images/process.svg
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
ProcessDiagram/trunk/UserManual/sources/process.tex
ProcessDiagram/trunk/UserManual/sources/process.tex.backup
ProcessDiagram/trunk/UserManual/sources/symbols.aux
Modified: ProcessDiagram/trunk/UserManual/images/process-dimerisation.eps
===================================================================
--- ProcessDiagram/trunk/UserManual/images/process-dimerisation.eps 2012-07-13 13:55:58 UTC (rev 828)
+++ ProcessDiagram/trunk/UserManual/images/process-dimerisation.eps 2012-07-13 15:19:24 UTC (rev 829)
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[truncated message content] |
|
From: <le...@us...> - 2012-07-13 13:56:05
|
Revision: 828
http://sbgn.svn.sourceforge.net/sbgn/?rev=828&view=rev
Author: lenov
Date: 2012-07-13 13:55:58 +0000 (Fri, 13 Jul 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
ProcessDiagram/trunk/UserManual/sources/build.aux
ProcessDiagram/trunk/UserManual/sources/interpret.aux
ProcessDiagram/trunk/UserManual/sources/process.tex
ProcessDiagram/trunk/UserManual/sources/process.tex~
ProcessDiagram/trunk/UserManual/sources/refcard.aux
ProcessDiagram/trunk/UserManual/sources/symbols.aux
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-07-13 13:43:12 UTC (rev 827)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-07-13 13:55:58 UTC (rev 828)
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2012.5.4) 13 JUL 2012 14:38
+This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2012.5.4) 13 JUL 2012 14:55
entering extended mode
%&-line parsing enabled.
**sbgn_PD-level1-user.tex
@@ -1239,75 +1239,98 @@
) [11] (./sources/process.tex
<images/process.pdf, id=157, 244.915pt x 84.315pt>
File: images/process.pdf Graphic file (type pdf)
- <use images/process.pdf>)
-(./sources/omitted.tex <images/omitted.pdf, id=158, 244.915pt x 84.315pt>
+ <use images/process.pdf>
+<images/process-phosphorylation.pdf, id=158, 422.57875pt x 110.4125pt>
+File: images/process-phosphorylation.pdf Graphic file (type pdf)
+
+<use images/process-phosphorylation.pdf>
+<images/process-reaction.pdf, id=159, 380.42125pt x 304.13625pt>
+File: images/process-reaction.pdf Graphic file (type pdf)
+
+<use images/process-reaction.pdf>
+Underfull \hbox (badness 5548) in paragraph at lines 31--31
+ []\T1/phv/b/n/10 Figure 2.15: \T1/futs/m/it/10 Re-ac-tion be-tween ATP and fru
+ctose-6-phosphate to pro-duce fructose-1,6-
+ []
+
+[12 <./images/process.pdf> <./images/process-phosphorylation.pdf>]
+<images/process-translocation.pdf, id=176, 489.83pt x 269.005pt>
+File: images/process-translocation.pdf Graphic file (type pdf)
+
+<use images/process-translocation.pdf>
+<images/process-dimerisation.pdf, id=177, 365.365pt x 97.36375pt>
+File: images/process-dimerisation.pdf Graphic file (type pdf)
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+<use images/process-dimerisation.pdf>) (./sources/omitted.tex
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File: images/omitted.pdf Graphic file (type pdf)
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+ <use images/omitted.pdf>)
+(./sources/uncertain.tex [13 <./images/process-reaction.pdf> <./images/process-
+translocation.pdf> <./images/process-dimerisation.pdf> <./images/omitted.pdf>]
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<use images/uncertain.pdf>) (./sources/association.tex
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File: images/association.pdf Graphic file (type pdf)
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+<images/dissociation.pdf, id=206, 179.67125pt x 84.315pt>
File: images/dissociation.pdf Graphic file (type pdf)
<use images/dissociation.pdf>) (./sources/phenotype.tex
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File: images/phenotype.pdf Graphic file (type pdf)
-<use images/phenotype.pdf> [13 <./images/uncertain.pdf> <./images/association.p
+<use images/phenotype.pdf> [14 <./images/uncertain.pdf> <./images/association.p
df> <./images/dissociation.pdf>]) (./sources/consumption.tex
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File: images/consumption.pdf Graphic file (type pdf)
<use images/consumption.pdf>) (./sources/production.tex
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File: images/production.pdf Graphic file (type pdf)
<use images/production.pdf>) (./sources/modulation.tex
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+<images/modulation.pdf, id=223, 199.74625pt x 60.225pt>
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+<use images/modulation.pdf>) (./sources/stimulation.tex [15 <./images/phenotype
.pdf> <./images/consumption.pdf> <./images/production.pdf>]
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+<use images/necessary_stim.pdf>) (./sources/logicArc.tex [16 <./images/modulati
on.pdf> <./images/stimulation.pdf> <./images/catalysis.pdf> <./images/inhibitio
-n.pdf>] <images/logicArc.pdf, id=248, 395.4775pt x 81.30376pt>
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File: images/or.pdf Graphic file (type pdf)
<use images/or.pdf>) (./sources/not.tex
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+<images/not.pdf, id=288, 158.5925pt x 69.25874pt>
File: images/not.pdf Graphic file (type pdf)
- <use images/not.pdf> [16 <./images/necessary_stim.pdf> <./images/logicArc.pdf>
+ <use images/not.pdf> [17 <./images/necessary_stim.pdf> <./images/logicArc.pdf>
<./images/equivalence.pdf> <./images/and.pdf> <./images/or.pdf>]) (./sources/c
ompartment.tex
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LaTeX Font Info: Font shape `T1/phv/b/sl' will be
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<use images/compartment.pdf>) (./sources/submap.tex
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+<images/submap.pdf, id=323, 798.985pt x 515.9275pt>
File: images/submap.pdf Graphic file (type pdf)
<use images/submap.pdf>
-[17 <./images/not.pdf> <./images/compartment.pdf>]
+[18 <./images/not.pdf> <./images/compartment.pdf>]
Overfull \hbox (6.09357pt too wide) in paragraph at lines 16--17
-[]\T1/futs/m/n/10.95 The left part of Fig-ure 2.33[] rep-re-sents a \T1/futs/m/
+[]\T1/futs/m/n/10.95 The left part of Fig-ure 2.37[] rep-re-sents a \T1/futs/m/
it/10.95 submap \T1/futs/m/n/10.95 that trans-forms glu-cose into fructose-6-ph
osphate.
[]
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olded.pdf> <./images/submap-unfolded.pdf>]
\openout2 = `sources/build.aux'.
(./sources/build.tex
Chapter 3.
-) [19
+) [20
@@ -1353,7 +1376,7 @@
(./sources/interpret.tex
Chapter 4.
-) [20
+) [21
@@ -1361,17 +1384,17 @@
\openout2 = `sources/refcard.aux'.
(./sources/refcard.tex
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+<images/refcard.pdf, id=368, 798.985pt x 575.14874pt>
File: images/refcard.pdf Graphic file (type pdf)
<use images/refcard.pdf>)
Overfull \hbox (7.15172pt too wide) in paragraph at lines 1--27
[]
[]
-[21
+[22
- <./images/refcard.pdf>] (./sbgn_PD-level1-user.bbl) [22
+ <./images/refcard.pdf>] (./sbgn_PD-level1-user.bbl) [23
@@ -1380,10 +1403,10 @@
(./sbgn_PD-level1-user.aux (./sources/introduction.aux) (./sources/symbols.aux)
(./sources/build.aux) (./sources/interpret.aux) (./sources/refcard.aux)) )
Here is how much of TeX's memory you used:
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+ 5497 strings out of 493848
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></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvbo8a.pfb>
-Output written on sbgn_PD-level1-user.pdf (23 pages, 1685255 bytes).
+Output written on sbgn_PD-level1-user.pdf (24 pages, 1704013 bytes).
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+ 206 words of extra memory for PDF output out of 10000 (max. 10000000)
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/UserManual/sources/build.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/build.aux 2012-07-13 13:43:12 UTC (rev 827)
+++ ProcessDiagram/trunk/UserManual/sources/build.aux 2012-07-13 13:55:58 UTC (rev 828)
@@ -1,9 +1,9 @@
\relax
-\@writefile{toc}{\contentsline {chapter}{\numberline {3}How to build a SBGN Process Description map\xspace ?}{19}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {3}How to build a SBGN Process Description map\xspace ?}{20}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\@setckpt{sources/build}{
-\setcounter{page}{20}
+\setcounter{page}{21}
\setcounter{equation}{0}
\setcounter{enumi}{0}
\setcounter{enumii}{0}
Modified: ProcessDiagram/trunk/UserManual/sources/interpret.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/interpret.aux 2012-07-13 13:43:12 UTC (rev 827)
+++ ProcessDiagram/trunk/UserManual/sources/interpret.aux 2012-07-13 13:55:58 UTC (rev 828)
@@ -1,9 +1,9 @@
\relax
-\@writefile{toc}{\contentsline {chapter}{\numberline {4}How to interpret an SBGN Process Description map\xspace ?}{20}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {4}How to interpret an SBGN Process Description map\xspace ?}{21}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\@setckpt{sources/interpret}{
-\setcounter{page}{21}
+\setcounter{page}{22}
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Modified: ProcessDiagram/trunk/UserManual/sources/process.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/process.tex 2012-07-13 13:43:12 UTC (rev 827)
+++ ProcessDiagram/trunk/UserManual/sources/process.tex 2012-07-13 13:55:58 UTC (rev 828)
@@ -14,3 +14,39 @@
\label{fig:process}
\end{figure}
+The example in \fig{trans-phos} illustrates the use of a \glyph{process} node to represent the phosphorylation of a protein in a \PD.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.3]{images/process-phosphorylation}
+ \caption{Phosphorylation of the protein MAP kinase.}
+ \label{fig:trans-phos}
+\end{figure}
+
+The example in \fig{trans-react} illustrates the use of a \glyph{process} node to represent a reaction between two reactants that generates three products.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.3]{images/process-reaction}
+ \caption{Reaction between ATP and fructose-6-phosphate to produce fructose-1,6-biphosphate, ADP and a proton.}
+ \label{fig:trans-react}
+\end{figure}
+
+The example in \fig{trans-trans} illustrates the use of a \glyph{process} node to represent a translocation. The large round-cornered rectangle represents a compartment border (see \sect{compartment}).
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.3]{images/process-translocation}
+ \caption{Translocation of calcium ion out of the endoplasmic reticulum. Note that the \glyph{process} does not have to be located on the boundary of the \glyph{compartment}. A \glyph{process} is not attached to any \glyph{compartment}.}
+ \label{fig:trans-trans}
+\end{figure}
+
+The example in \fig{trans-dim} presents the conversion of two galactoses into a lactose. Galactoses are represented by only one \glyph{simple chemical}, the cardinality being carried by the \glyph{consumption} arc.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.3]{images/process-dimerisation}
+ \caption{Conversion of two galactoses into a lactose.}
+ \label{fig:trans-dim}
+\end{figure}
+
Modified: ProcessDiagram/trunk/UserManual/sources/process.tex~
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/process.tex~ 2012-07-13 13:43:12 UTC (rev 827)
+++ ProcessDiagram/trunk/UserManual/sources/process.tex~ 2012-07-13 13:55:58 UTC (rev 828)
@@ -5,7 +5,7 @@
\subsection{Glyph: \glyph{Process}}
\label{sec:process}
-A process is the basic process node in SBGN. It describes a process that transforms a given set of biochemical entities---macromolecules, simple chemicals or unspecified entities---into another set of biochemical entities. Such a transformation might imply modification of covalent bonds (conversion), modification of the relative position of constituents (conformational process) or movement from one compartment to another (translocation). A process transforms a set of entity pools (represented by \glyph{EPNs} in \SBGNPDLone) into another set of entity pools. Typically, a process node represents a biochemical reaction, or a transport between compartments. A \glyph{process} is represented by a square box linked to two connectors, small arcs attached to the centers of opposite sides. The consumption (\sect{consumption}) and production (\sect{production}) arcs are linked to the extremities of those connectors. The modulatory arcs (\sect{arcs}) point to the other two sides of the box. A \glyph{process} connected to \glyph{production} arcs on opposite sides is a reversible process.
+A process is the basic process node in SBGN. It describes a process that transforms a given set of biochemical entities---macromolecules, simple chemicals or unspecified entities---into another set of biochemical entities. Such a transformation might imply modification of covalent bonds (conversion), modification of the relative position of constituents (conformational process) or movement from one compartment to another (translocation). A process transforms a set of entity pools (represented by \glyph{EPNs} in \SBGNPDLone) into another set of entity pools. A \glyph{process} is represented by a square box linked to two connectors, small arcs attached to the centers of opposite sides. The consumption (\sect{consumption}) and production (\sect{production}) arcs are linked to the extremities of those connectors. The modulatory arcs (\sect{arcs}) point to the other two sides of the box. A \glyph{process} connected to \glyph{production} arcs on opposite sides is a reversible process.
\begin{figure}[H]
\centering
@@ -14,17 +14,11 @@
\label{fig:process}
\end{figure}
-A process is the basic process node in SBGN. It describes a process that transforms a given set of biochemical entities---macromolecules, simple chemicals or unspecified entities---into another set of biochemical entities. Such a transformation might imply modification of covalent bonds (conversion), modification of the relative position of constituents (conformational process) or movement from one compartment to another (translocation).
-
-A cardinality label may be associated with \glyph{consumption} (\sect{consumption}) or \glyph{production} (\sect{production}) arcs to indicate the stoichiometry of the process. This label becomes a requirement when the exact composition of the number of copies of the inputs or outputs to a reaction are ambiguous in the map.
-
-A process is regarded as reversible if both `sides' of the process are connected to \glyph{production} arcs (see section \ref{sec: semantics reversible procs}).
-
The example in \fig{trans-phos} illustrates the use of a \glyph{process} node to represent the phosphorylation of a protein in a \PD.
\begin{figure}[H]
\centering
- \includegraphics[scale = 0.3]{examples/process-phosphorylation}
+ \includegraphics[scale = 0.3]{images/process-phosphorylation}
\caption{Phosphorylation of the protein MAP kinase.}
\label{fig:trans-phos}
\end{figure}
@@ -33,7 +27,7 @@
\begin{figure}[H]
\centering
- \includegraphics[scale = 0.3]{examples/process-reaction}
+ \includegraphics[scale = 0.3]{images/process-reaction}
\caption{Reaction between ATP and fructose-6-phosphate to produce fructose-1,6-biphosphate, ADP and a proton.}
\label{fig:trans-react}
\end{figure}
@@ -42,42 +36,17 @@
\begin{figure}[H]
\centering
- \includegraphics[scale = 0.3]{examples/process-translocation}
+ \includegraphics[scale = 0.3]{images/process-translocation}
\caption{Translocation of calcium ion out of the endoplasmic reticulum. Note that the \glyph{process} does not have to be located on the boundary of the \glyph{compartment}. A \glyph{process} is not attached to any \glyph{compartment}.}
\label{fig:trans-trans}
\end{figure}
-The example in \fig{trans-reverse} illustrates the use of a \glyph{process} node to represent the reversible opening and closing of an ionic channel in a \PD.
-
-\begin{figure}[H]
- \centering
- \includegraphics[scale = 0.3]{examples/process-reversible}
- \caption{Reversible opening and closing of an ionic channel.}
- \label{fig:trans-reverse}
-\end{figure}
-
-When such a reversible process is asymmetrically modulated, it must be represented by two different processes in a \PD. \fig{trans-mod} illustrates the use of two \glyph{process} nodes to represent the reversible activation of a G-protein coupled receptor. In the absence of any effector, an equilibrium exists between the inactive and active forms. The agonist stabilises the active form, while the inverse agonist stabilises the inactive form.
-
-\begin{figure}[H]
- \centering
- \includegraphics[scale = 0.3]{examples/process-modulated}
- \caption{The reversible activation of a G-protein coupled receptor.}
- \label{fig:trans-mod}
-\end{figure}
-
The example in \fig{trans-dim} presents the conversion of two galactoses into a lactose. Galactoses are represented by only one \glyph{simple chemical}, the cardinality being carried by the \glyph{consumption} arc.
\begin{figure}[H]
\centering
- \includegraphics[scale = 0.3]{examples/process-dimerisation}
+ \includegraphics[scale = 0.3]{images/process-dimerisation}
\caption{Conversion of two galactoses into a lactose.}
\label{fig:trans-dim}
\end{figure}
-
-
-
-% The following is for [X]Emacs users. Please leave in place.
-% Local Variables:
-% TeX-master: "../sbgn_PD-level1"
-% End:
Modified: ProcessDiagram/trunk/UserManual/sources/refcard.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/refcard.aux 2012-07-13 13:43:12 UTC (rev 827)
+++ ProcessDiagram/trunk/UserManual/sources/refcard.aux 2012-07-13 13:55:58 UTC (rev 828)
@@ -1,6 +1,6 @@
\relax
\@setckpt{sources/refcard}{
-\setcounter{page}{22}
+\setcounter{page}{23}
\setcounter{equation}{0}
\setcounter{enumi}{0}
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Modified: ProcessDiagram/trunk/UserManual/sources/symbols.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.aux 2012-07-13 13:43:12 UTC (rev 827)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.aux 2012-07-13 13:55:58 UTC (rev 828)
@@ -81,90 +81,98 @@
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-\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces The Process Description\xspace glyph for \emph {omitted process}.}}{12}}
-\newlabel{fig:omitted}{{2.14}{12}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.3}Glyph: \emph {Uncertain process}}{13}}
-\newlabel{sec:uncertain}{{2.3.3}{13}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces The Process Description\xspace glyph for an \emph {uncertain process}.}}{13}}
-\newlabel{fig:uncertain}{{2.15}{13}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.4}Glyph: \emph {Association}}{13}}
-\newlabel{sec:association}{{2.3.4}{13}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces The Process Description\xspace glyph for \emph {association}.}}{13}}
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-\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.5}Glyph: \emph {Dissociation}}{13}}
-\newlabel{sec:dissociation}{{2.3.5}{13}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.17}{\ignorespaces The Process Description\xspace glyph for \emph {dissociation}.}}{13}}
-\newlabel{fig:dissociation}{{2.17}{13}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.6}Glyph: \emph {Phenotype}}{13}}
-\newlabel{sec:phenotype}{{2.3.6}{13}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\ignorespaces The Process Description\xspace glyph for \emph {phenotype}.}}{14}}
-\newlabel{fig:phenotype}{{2.18}{14}}
-\@writefile{toc}{\contentsline {section}{\numberline {2.4}Arcs}{14}}
-\newlabel{sec:arcs}{{2.4}{14}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.1}Glyph: \emph {Consumption}}{14}}
-\newlabel{sec:consumption}{{2.4.1}{14}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\ignorespaces The Process Description\xspace glyph for \emph {consumption}.}}{14}}
-\newlabel{fig:consumption}{{2.19}{14}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.2}Glyph: \emph {Production}}{14}}
-\newlabel{sec:production}{{2.4.2}{14}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.20}{\ignorespaces The Process Description\xspace glyph for \emph {production}.}}{14}}
-\newlabel{fig:production}{{2.20}{14}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.3}Glyph: \emph {Modulation}}{14}}
-\newlabel{sec:modulation}{{2.4.3}{14}}
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-\newlabel{fig:modulation}{{2.21}{15}}
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-\newlabel{fig:stimulation}{{2.22}{15}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.5}Glyph: \emph {Catalysis}}{15}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {2.23}{\ignorespaces The Process Description\xspace glyph for \emph {catalysis}.}}{15}}
-\newlabel{fig:catalysis}{{2.23}{15}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.6}Glyph: \emph {Inhibition}}{15}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {2.24}{\ignorespaces The Process Description\xspace glyph for \emph {inhibition}.}}{15}}
-\newlabel{fig:inhibition}{{2.24}{15}}
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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...> - 2012-07-13 13:43:25
|
Revision: 827
http://sbgn.svn.sourceforge.net/sbgn/?rev=827&view=rev
Author: lenov
Date: 2012-07-13 13:43:12 +0000 (Fri, 13 Jul 2012)
Log Message:
-----------
Modified Paths:
--------------
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ProcessDiagram/trunk/UserManual/images/complex.pdf
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Modified: ProcessDiagram/trunk/UserManual/images/complex.eps
===================================================================
--- ProcessDiagram/trunk/UserManual/images/complex.eps 2012-05-24 15:43:40 UTC (rev 826)
+++ ProcessDiagram/trunk/UserManual/images/complex.eps 2012-07-13 13:43:12 UTC (rev 827)
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[truncated message content] |
|
From: <lp...@us...> - 2012-05-24 15:43:50
|
Revision: 826
http://sbgn.svn.sourceforge.net/sbgn/?rev=826&view=rev
Author: lptolik
Date: 2012-05-24 15:43:40 +0000 (Thu, 24 May 2012)
Log Message:
-----------
typo fixes and beginning of rule extraction
Modified Paths:
--------------
ProcessDiagram/trunk/sbgn_PD-level1.pdf
ProcessDiagram/trunk/sbgn_PD-level1.tex
ProcessDiagram/trunk/sources/glyphs.tex
Added Paths:
-----------
ProcessDiagram/trunk/sources/validation.tex
ProcessDiagram/trunk/validation-rules/
ProcessDiagram/trunk/validation-rules/000001.tex
ProcessDiagram/trunk/validation-rules/000002.tex
ProcessDiagram/trunk/validation-rules/000003.tex
ProcessDiagram/trunk/validation-rules/000004.tex
ProcessDiagram/trunk/validation-rules/000005.tex
ProcessDiagram/trunk/validation-rules/000006.tex
ProcessDiagram/trunk/validation-rules/000007.tex
ProcessDiagram/trunk/validation-rules/000008.tex
ProcessDiagram/trunk/validation-rules/000009.tex
ProcessDiagram/trunk/validation-rules/000010.tex
ProcessDiagram/trunk/validation-rules/000011.tex
ProcessDiagram/trunk/validation-rules/000012.tex
ProcessDiagram/trunk/validation-rules/000013.tex
ProcessDiagram/trunk/validation-rules/000014.tex
ProcessDiagram/trunk/validation-rules/000015.tex
Modified: ProcessDiagram/trunk/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/sbgn_PD-level1.tex
===================================================================
--- ProcessDiagram/trunk/sbgn_PD-level1.tex 2012-05-23 13:37:17 UTC (rev 825)
+++ ProcessDiagram/trunk/sbgn_PD-level1.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -31,15 +31,16 @@
\include{sources/introduction}
\include{sources/concepts}
\include{sources/glyphs}
-%\include{sources/grammar}
\include{sources/layout}
+
\include{sources/acknowledgments}
\appendix
\include{sources/examples}
\include{sources/refcard}
+\include{sources/validation}
\include{sources/working}
\include{sources/revision_history}
Modified: ProcessDiagram/trunk/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/sources/glyphs.tex 2012-05-23 13:37:17 UTC (rev 825)
+++ ProcessDiagram/trunk/sources/glyphs.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -513,12 +513,12 @@
has been there implicitly in previous versions and comes up in
discussions. This class aims to formalise that concept and the rules
associated with it and enable us to formalise rules associated with
-EPNs.} is one of the code concepts in the \PDl. It
+EPNs.} is one of the core concepts in the \PDl. It
defines the type of entity that is instantiated by one or more
entity pools in a \PDm. The \sbgnclass{EntityType} has associated
state variable definitions (see figure \ref{fig:entitytypeuml}) and
this enforces one of the core rules in the \PDl that once a state is
-associated with an entity type is must be used by all entity pools of
+associated with an entity type it must be used by all entity pools of
that type.
@@ -530,7 +530,7 @@
\begin{attributes}
\attitem{name}{string}{R} The name that identifies the entity in the
- \PDm. EPNs with the same label should be from the same entity. the
+ \PDm. EPNs with the same label should be from the same entity. The
string cannot be empty and must start and end with a non-space
character. Any Unicode character is acceptable\query{Not discussed
or defined anywhere, but would make sense to define this explicitly.}.
@@ -575,6 +575,7 @@
and the associated rules did exist in the language.
\subsection{StateVariableDefinition}
+\label{defn:StateVariableDefinition}
The \sbgnclass{StateVariableDefinition}\query{As with EntityType this
is new and aims to formalise the concept that an entity pool must
@@ -3840,7 +3841,7 @@
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{entity}).
+\sboid{SBO:0000240} ($\!$\emph{material entity} under \emph{physical entity representation}).
The labels are defined by \SBGNPDLone.
\begin{table}[h]
@@ -3865,7 +3866,7 @@
The material types are in contrast to the \emph{conceptual types} (see
below). The distinction is that material types are about physical
composition, while conceptual types are about roles. For example, a
-strand of RNA is a physical artifact, but its use as messenger RNA is
+strand of RNA is a physical artefact, but its use as messenger RNA is
a role.
@@ -3876,8 +3877,8 @@
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{entity}). The labels are defined by \SBGNPDLone.
+identifier \sboid{SBO:0000241} ($\!$\emph{functional entity} under
+\emph{physical entity representation}). The labels are defined by \SBGNPDLone.
\begin{table}[h]
\centering
Added: ProcessDiagram/trunk/sources/validation.tex
===================================================================
--- ProcessDiagram/trunk/sources/validation.tex (rev 0)
+++ ProcessDiagram/trunk/sources/validation.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,16 @@
+\chapter{Validation and consistency rules}
+
+\newcommand{\validationRule} [1]{\item[#1.~]\input{validation-rules/#1.tex}}
+
+This section describes criteria that must be met by the diagram (or SBGN-ML diagram description) to conform
+\SBGNPDLone specification.
+
+All criteria has unique and perennial numbering. In the case when modification of the specification makes a rule
+irrelevant it will be deleted but the number of the rule will not be taken, so there will be gaps in rule numbering.
+
+\section{EPN rules}
+\begin{enumerate}
+\validationRule{000001}
+\validationRule{000002}
+\validationRule{000003}
+\end{enumerate}
Added: ProcessDiagram/trunk/validation-rules/000001.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000001.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000001.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1 @@
+Elements that do not comply \SBGNPDLone specification are not allowed on \SBGNPDLone map.
Added: ProcessDiagram/trunk/validation-rules/000002.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000002.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000002.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,2 @@
+All instances of \classref{SBGNGlyph} must be unique (see
+ section \ref{sec:uniquenessdefinition}).
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000003.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000003.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000003.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,4 @@
+The set of \sbgnclass{SBGNNode}s linked to this node via a
+ \sbgnclass{SBGNArc} (its adjacent nodes) must be all belong to
+ different entity pools (as defined by \sbgnclass{EntityPoolNode})
+ and cannot include more than one clone of the same entity pool.
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000004.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000004.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000004.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,4 @@
+The name identifies the entity in the
+ \PDm and is required. EPNs with the same label should be from the same entity. The name
+ string cannot be empty and must start and end with a non-space
+ character. Any Unicode character is acceptable.
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000005.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000005.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000005.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,4 @@
+The nature of the entity pool node as defined
+ by a controlled vocabulary. Zero, one or more values may be set, but
+ each one must belong to a different controlled vocabulary.
+ (References: \ref{defn:EntityType})
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000006.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000006.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000006.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,4 @@
+Once a state is
+associated with an entity type it must be used by all entity pools of
+that type.
+(References: \ref{defn:EntityType})
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000007.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000007.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000007.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,2 @@
+The name of the state variable is optional, but if defined cannot be an empty string or just white space characters. It should also start with an alpha-numeric character and end with a non-space character. It should not contain a ‘@’ character.
+(Reference \ref{defn:StateVariableDefinition})
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000008.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000008.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000008.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,2 @@
+Cardinality must be a positive non-zero integer.
+(Reference \ref{defn:EntityPoolNode})
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000009.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000009.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000009.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,3 @@
+If \attrib{cardinality} $>1$ then the descendant glyph must be displayed
+ as a multimer.
+(Reference \ref{defn:EntityPoolNode})
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000010.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000010.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000010.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,4 @@
+If the EPN is drawn directly on a \glyph{Map} then
+ \attrib{owning\_compartment} is not set. Interpretation is that EPN
+ belongs to an invisible default compartment.
+ (Reference \ref{defn:EntityPoolNode})
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000011.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000011.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000011.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,2 @@
+The appropriate subclass of \sbgnclass{CloneMarker} must be used
+ to distinguish logically identical instances of this class. (Reference \ref{defn:EntityPoolNode})
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000012.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000012.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000012.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,3 @@
+ \sbgnclass{EntityPoolNode} must be associated with at least
+ one \classref{SBGNArc} (degree $> 0$).
+ (Reference \ref{defn:EntityPoolNode})
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000013.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000013.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000013.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,3 @@
+the \sbgnclass{EmptySet} must be associated with at least
+ one \classref{SBGNArc} (degree $> 0$).
+ (Reference \ref{sec:sourceSink})
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000014.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000014.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000014.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,2 @@
+if a clone marker is used with the \sbgnclass{StatelessEPN} node it must be of type \sbgnclass{SimpleCloneMarker}.
+ (Reference \ref{defn:StatelessEPN})
\ No newline at end of file
Added: ProcessDiagram/trunk/validation-rules/000015.tex
===================================================================
--- ProcessDiagram/trunk/validation-rules/000015.tex (rev 0)
+++ ProcessDiagram/trunk/validation-rules/000015.tex 2012-05-24 15:43:40 UTC (rev 826)
@@ -0,0 +1,3 @@
+The \sbgnclass{UnspecifiedEntity} cannot have cardinality $>
+ 1$. This means there is no multimer glyph.
+ (Reference: \ref{sec:unspecifiedEntity})
\ 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...> - 2012-05-23 13:37:29
|
Revision: 825
http://sbgn.svn.sourceforge.net/sbgn/?rev=825&view=rev
Author: lenov
Date: 2012-05-23 13:37:17 +0000 (Wed, 23 May 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex
ProcessDiagram/trunk/UserManual/sources/refcard.aux
ProcessDiagram/trunk/UserManual/sources/refcard.tex
ProcessDiagram/trunk/UserManual/sources/symbols.aux
ProcessDiagram/trunk/UserManual/sources/symbols.tex
ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup
ProcessDiagram/trunk/UserManual/sources/symbols.tex~
Added Paths:
-----------
ProcessDiagram/trunk/UserManual/images/compartment.eps
ProcessDiagram/trunk/UserManual/images/compartment.pdf
ProcessDiagram/trunk/UserManual/images/compartment.png
ProcessDiagram/trunk/UserManual/images/compartment.svg
ProcessDiagram/trunk/UserManual/sources/compartment.tex
ProcessDiagram/trunk/UserManual/sources/submap.tex
Added: ProcessDiagram/trunk/UserManual/images/compartment.eps
===================================================================
--- ProcessDiagram/trunk/UserManual/images/compartment.eps (rev 0)
+++ ProcessDiagram/trunk/UserManual/images/compartment.eps 2012-05-23 13:37:17 UTC (rev 825)
@@ -0,0 +1,347 @@
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- 4844 strings out of 493848
- 65832 string characters out of 1152824
- 143136 words of memory out of 3000000
- 7842 multiletter control sequences out of 15000+50000
+ 4853 strings out of 493848
+ 66036 string characters out of 1152824
+ 143162 words of memory out of 3000000
+ 7848 multiletter control sequences out of 15000+50000
108192 words of font info for 85 fonts, out of 3000000 for 9000
714 hyphenation exceptions out of 8191
32i,8n,32p,1530b,290s stack positions out of 5000i,500n,10000p,200000b,50000s
@@ -1307,9 +1309,9 @@
ive/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texmf-texlive/fonts/type1/
public/txfonts/t1xtt.pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhv
b8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvbo8a.pfb>
-Output written on sbgn_PD-level1-user.pdf (21 pages, 1009025 bytes).
+Output written on sbgn_PD-level1-user.pdf (20 pages, 1016944 bytes).
PDF statistics:
- 347 PDF objects out of 1000 (max. 8388607)
+ 355 PDF objects out of 1000 (max. 8388607)
0 named destinations out of 1000 (max. 500000)
- 166 words of extra memory for PDF output out of 10000 (max. 10000000)
+ 171 words of extra memory for PDF output out of 10000 (max. 10000000)
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex 2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex 2012-05-23 13:37:17 UTC (rev 825)
@@ -24,8 +24,6 @@
%\include{sources/build}
%\include{sources/interpret}
-\appendix
-
\include{sources/refcard}
\backmatter
Added: ProcessDiagram/trunk/UserManual/sources/compartment.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/compartment.tex (rev 0)
+++ ProcessDiagram/trunk/UserManual/sources/compartment.tex 2012-05-23 13:37:17 UTC (rev 825)
@@ -0,0 +1,16 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Compartment
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\subsection{Glyph: \glyph{Compartment}}\label{sec:compartment}
+
+A compartment is a logical or physical structure that contains entity pool nodes. An \glyph{EPN} can only belong to one compartment. Therefore, the ``same'' biochemical species located in two different compartments are in fact two different ``pools'' and should be represented by two \glyph{EPNs}. 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 \glyph{EPNs}. A compartment can take \textbf{any} geometry. A compartment must always be entirely enclosed.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.3]{images/compartment}
+ \caption{The \PD glyph for \glyph{compartment}.}
+ \label{fig:compartment}
+\end{figure}
+
+To allow more aesthetically pleasing and understandable maps, 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.
\ No newline at end of file
Modified: ProcessDiagram/trunk/UserManual/sources/refcard.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/refcard.aux 2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/refcard.aux 2012-05-23 13:37:17 UTC (rev 825)
@@ -1,9 +1,6 @@
\relax
-\@writefile{toc}{\contentsline {chapter}{\numberline {A}Reference card}{18}}
-\@writefile{lof}{\addvspace {10\p@ }}
-\@writefile{lot}{\addvspace {10\p@ }}
\@setckpt{sources/refcard}{
-\setcounter{page}{20}
+\setcounter{page}{19}
\setcounter{equation}{0}
\setcounter{enumi}{0}
\setcounter{enumii}{0}
@@ -12,14 +9,14 @@
\setcounter{footnote}{0}
\setcounter{mpfootnote}{0}
\setcounter{part}{0}
-\setcounter{chapter}{1}
-\setcounter{section}{0}
-\setcounter{subsection}{3}
+\setcounter{chapter}{2}
+\setcounter{section}{6}
+\setcounter{subsection}{1}
\setcounter{subsubsection}{0}
\setcounter{paragraph}{0}
\setcounter{subparagraph}{0}
-\setcounter{figure}{0}
-\setcounter{table}{0}
+\setcounter{figure}{31}
+\setcounter{table}{5}
\setcounter{float@type}{4}
\setcounter{r@tfl@t}{0}
}
Modified: ProcessDiagram/trunk/UserManual/sources/refcard.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/refcard.tex 2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/refcard.tex 2012-05-23 13:37:17 UTC (rev 825)
@@ -1,4 +1 @@
-\chapter{Reference card}
-Print the summary of SBGN symbols on the next page for a quick reference.
-
\noindent\rotatebox{-90}{\scalebox{0.8}{\includegraphics{images/refcard}}}
Added: ProcessDiagram/trunk/UserManual/sources/submap.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/submap.tex (rev 0)
+++ ProcessDiagram/trunk/UserManual/sources/submap.tex 2012-05-23 13:37:17 UTC (rev 825)
@@ -0,0 +1,55 @@
+% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/ProcessDiagram/tags/L1V1.3Full/sources/submap.tex $
+
+\subsection{Glyph: \glyph{Submap}}
+\label{sec:submap}
+
+A \glyph{submap} is used to encapsulate processes (including all types of nodes and edges) within one glyph. The \glyph{submap} hides its content to the users, and display only input terminals (or ports), linked to \glyph{EPNs} (\sect{EPNs}). A \glyph{submap} is not equivalent to an \glyph{omitted process} (see \sect{omitted}). In the case of an SBGN description that is made available through a software tool, the content of a \glyph{submap} may be available to the tool. A user could then ask the tool to expand the \glyph{submap}, for instance by clicking on the icon representing the \glyph{submap}. The tool might then expand and show the \glyph{submap} within the same map (on the same canvas), or it might open it in a different canvas. In the case of an SBGN description made available in a book or a website, the content of the \glyph{submap} may be available on another page, possibly accessible via an hyperlink on the \glyph{submap}.
+
+\begin{glyphDescription}
+
+\glyphSboTerm SBO:0000395 ! encapsulating process
+
+\glyphContainer The \glyph{submap} is represented as a square box to remind the viewer that it is fundamentally a process.
+
+\glyphLabel The identification of the \glyph{submap} 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 center of the container box.
+
+\glyphAux A \glyph{submap} carries labeled terminals. When the \glyph{submap} is represented folded, those terminals are linked to external \glyph{EPNs} (\sect{EPNs}). In the unfolded view, exposing the internal structure of the \glyph{submap}, a set of \glyph{tags} point to the corresponding internal \glyph{EPNs} \sect{EPNs}.
+
+\end{glyphDescription}
+
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.22]{images/submap}
+ \caption{The \PD glyph for \glyph{submap}. (Upper part) folded submap. (Lower part) content of the submap.}
+ \label{fig:submap}
+\end{figure}
+
+\fig{submap-folded} represents a \glyph{submap} that transforms glucose into fructose-6-phosphate. The \glyph{submap} carries five terminals, four linked to EPNs and one linked to a \glyph{compartment}. The latter is particularly important in the case of EPNs present only in a \glyph{compartment} enclosed in a \glyph{submap}, and that are not linked to terminals themselves. Note that the terminals do not define a ``direction'', such as input or output. The flux of the reactions is determined by the context.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.4]{examples/submap-folded}
+ \caption{Example of a submap with contents elided.}
+ \label{fig:submap-folded}
+\end{figure}
+
+The map in \fig{submap-unfolded} represents an unfolded version of a \glyph{submap}. Here, anything outside the \glyph{submap} has disappeared, and the internal \glyph{tags} are not linked to the corresponding external \glyph{terminals}. Note the tag 5, linking the compartment ``mito'' of the \glyph{submap} to the compartment ``mito'' outside the \glyph{submap}. The compartment containing Glu6P is implicitly defined as the same as the compartment containing Glu and Fru6P. There is no ambiguity because if Glu and Fru6P were in different compartments, one of them should have been defined within the \glyph{submap}.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.35]{examples/submap-dissociated}
+ \caption{Example of an unfolded submap. The unfolded submap corresponds to the folded submap of \fig{submap-folded}.}
+ \label{fig:submap-unfolded}
+\end{figure}
+
+
+
+
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_PD-level1"
+% End:
+
Modified: ProcessDiagram/trunk/UserManual/sources/symbols.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.aux 2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.aux 2012-05-23 13:37:17 UTC (rev 825)
@@ -153,6 +153,11 @@
\newlabel{sec:not}{{2.5.3}{17}}
\@writefile{lof}{\contentsline {figure}{\numberline {2.30}{\ignorespaces The Process Description\xspace glyph for \emph {not}.}}{17}}
\newlabel{fig:not}{{2.30}{17}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.6}Representing compartments}{17}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.6.1}Glyph: \emph {Compartment}}{17}}
+\newlabel{sec:compartment}{{2.6.1}{17}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.31}{\ignorespaces The Process Description\xspace glyph for \emph {compartment}.}}{17}}
+\newlabel{fig:compartment}{{2.31}{17}}
\@setckpt{sources/symbols}{
\setcounter{page}{18}
\setcounter{equation}{0}
@@ -164,12 +169,12 @@
\setcounter{mpfootnote}{0}
\setcounter{part}{0}
\setcounter{chapter}{2}
-\setcounter{section}{5}
-\setcounter{subsection}{3}
+\setcounter{section}{6}
+\setcounter{subsection}{1}
\setcounter{subsubsection}{0}
\setcounter{paragraph}{0}
\setcounter{subparagraph}{0}
-\setcounter{figure}{30}
+\setcounter{figure}{31}
\setcounter{table}{5}
\setcounter{float@type}{4}
\setcounter{r@tfl@t}{0}
Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex 2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex 2012-05-23 13:37:17 UTC (rev 825)
@@ -82,20 +82,19 @@
\input{sources/or.tex}
\input{sources/not.tex}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Compartments
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% %\section{Container nodes}\label{sec:CNs}
+\section{Representing compartments}
+\input{sources/compartment.tex}
+
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%% Containers
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% %\section{Container nodes}\label{sec:CNs}
-%\section{Representing compartments}
-%
-%\input{sources/compartment.tex}
-%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%% Submap
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup 2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup 2012-05-23 13:37:17 UTC (rev 825)
@@ -58,33 +58,31 @@
\section{Arcs}\label{sec:arcs}
-Arcs are lines that link nodes of SBGN together. The symbols attached to their extremities indicate their meaning. \SBGNPDLone defines nine arcs. \glyph{consumption} (\sect{consumption}), \glyph{production} (\sect{production}), \glyph{modulation} (\sect{modulation}), \glyph{stimulation} (\sect{stimulation}), \glyph{catalysis} (\sect{catalysis}), \glyph{inhibition} (\sect{inhibition}), and \glyph{necessary stimulation} (\sect{necessary_stim}) connect \glyph{EPNs} to \glyph{PDs}.
+Arcs are lines that link nodes of SBGN together. The symbols attached to their extremities indicate their meaning. \SBGNPDLone defines nine arcs. \glyph{consumption} (\sect{consumption}), \glyph{production} (\sect{production}), \glyph{modulation} (\sect{modulation}), \glyph{stimulation} (\sect{stimulation}), \glyph{catalysis} (\sect{catalysis}), \glyph{inhibition} (\sect{inhibition}), and \glyph{necessary stimulation} (\sect{necessary_stim}) connect \glyph{EPNs} to \glyph{PDs}. \glyph{LogicArc} (\sect{logicArc}) link \glyph{EPNs} and \glyph{logic arcs}. \glyph{equivalenceArc} (\sect{equivalenceArc}) link nodes to \glyph{tag}. Arcs can take any shape, and are not restricted to segments of straight lines.
+
+\input{sources/consumption.tex}
+\input{sources/production.tex}
+\input{sources/modulation.tex}
+\input{sources/stimulation.tex}
+\input{sources/catalysis.tex}
+\input{sources/inhibition.tex}
+\input{sources/necessary_stim.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}
-% \input{sources/consumption.tex}
-% \input{sources/production.tex}
-% \input{sources/modulation.tex}
-% \input{sources/stimulation.tex}
-% \input{sources/catalysis.tex}
-% \input{sources/inhibition.tex}
-% \input{sources/necessary_stim.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}
-
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%% Containers
Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex~
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex~ 2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex~ 2012-05-23 13:37:17 UTC (rev 825)
@@ -69,34 +69,32 @@
\input{sources/necessary_stim.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}
-%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%% Logical operators
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% \section{Logical operators}\label{sec:logic}
-%
-% \input{sources/and.tex}
-% \input{sources/or.tex}
-% \input{sources/not.tex}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Compartments
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% %\section{Container nodes}\label{sec:CNs}
+\section{Representing compartments}
-
+\input{sources/compartment.tex}
+
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%% Containers
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% %\section{Container nodes}\label{sec:CNs}
-%\section{Representing compartments}
-%
-%\input{sources/compartment.tex}
-%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%% Submap
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2012-05-21 10:39:27
|
Revision: 824
http://sbgn.svn.sourceforge.net/sbgn/?rev=824&view=rev
Author: lenov
Date: 2012-05-21 10:39:18 +0000 (Mon, 21 May 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/images/dissociation.eps
ProcessDiagram/trunk/UserManual/images/dissociation.pdf
ProcessDiagram/trunk/UserManual/images/dissociation.png
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
ProcessDiagram/trunk/UserManual/sources/association.tex
ProcessDiagram/trunk/UserManual/sources/dissociation.tex
ProcessDiagram/trunk/UserManual/sources/symbols.aux
ProcessDiagram/trunk/UserManual/sources/symbols.tex
ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup
Added Paths:
-----------
ProcessDiagram/trunk/UserManual/images/and.eps
ProcessDiagram/trunk/UserManual/images/and.pdf
ProcessDiagram/trunk/UserManual/images/and.png
ProcessDiagram/trunk/UserManual/images/and.svg
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ProcessDiagram/trunk/UserManual/images/equivalence.pdf
ProcessDiagram/trunk/UserManual/images/equivalence.png
ProcessDiagram/trunk/UserManual/images/equivalence.svg
ProcessDiagram/trunk/UserManual/images/inhibition.eps
ProcessDiagram/trunk/UserManual/images/inhibition.pdf
ProcessDiagram/trunk/UserManual/images/inhibition.png
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ProcessDiagram/trunk/UserManual/images/modulation.pdf
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ProcessDiagram/trunk/UserManual/images/necessary_stim.pdf
ProcessDiagram/trunk/UserManual/images/necessary_stim.png
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ProcessDiagram/trunk/UserManual/images/phenotype.pdf
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ProcessDiagram/trunk/UserManual/images/production.pdf
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ProcessDiagram/trunk/UserManual/images/stimulation.png
ProcessDiagram/trunk/UserManual/images/stimulation.svg
ProcessDiagram/trunk/UserManual/sources/CVs.tex~
ProcessDiagram/trunk/UserManual/sources/and.tex
ProcessDiagram/trunk/UserManual/sources/and.tex~
ProcessDiagram/trunk/UserManual/sources/association.tex~
ProcessDiagram/trunk/UserManual/sources/catalysis.tex
ProcessDiagram/trunk/UserManual/sources/catalysis.tex~
ProcessDiagram/trunk/UserManual/sources/cloneMarker.tex.backup
ProcessDiagram/trunk/UserManual/sources/cloneMarker.tex~
ProcessDiagram/trunk/UserManual/sources/complex.tex~
ProcessDiagram/trunk/UserManual/sources/consumption.tex
ProcessDiagram/trunk/UserManual/sources/consumption.tex.backup
ProcessDiagram/trunk/UserManual/sources/consumption.tex~
ProcessDiagram/trunk/UserManual/sources/dissociation.tex~
ProcessDiagram/trunk/UserManual/sources/equivalenceArc.tex
ProcessDiagram/trunk/UserManual/sources/equivalenceArc.tex~
ProcessDiagram/trunk/UserManual/sources/front-page.tex~
ProcessDiagram/trunk/UserManual/sources/genetic.tex~
ProcessDiagram/trunk/UserManual/sources/inhibition.tex
ProcessDiagram/trunk/UserManual/sources/inhibition.tex~
ProcessDiagram/trunk/UserManual/sources/introduction.tex~
ProcessDiagram/trunk/UserManual/sources/latex-style.tex~
ProcessDiagram/trunk/UserManual/sources/logicArc.tex
ProcessDiagram/trunk/UserManual/sources/logicArc.tex~
ProcessDiagram/trunk/UserManual/sources/macromolecule.tex~
ProcessDiagram/trunk/UserManual/sources/modulation.tex
ProcessDiagram/trunk/UserManual/sources/modulation.tex~
ProcessDiagram/trunk/UserManual/sources/multimer.tex~
ProcessDiagram/trunk/UserManual/sources/necessary_stim.tex
ProcessDiagram/trunk/UserManual/sources/necessary_stim.tex~
ProcessDiagram/trunk/UserManual/sources/not.tex
ProcessDiagram/trunk/UserManual/sources/not.tex~
ProcessDiagram/trunk/UserManual/sources/omitted.tex.backup
ProcessDiagram/trunk/UserManual/sources/omitted.tex~
ProcessDiagram/trunk/UserManual/sources/or.tex
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ProcessDiagram/trunk/UserManual/sources/or.tex~
ProcessDiagram/trunk/UserManual/sources/pd-overview.tex~
ProcessDiagram/trunk/UserManual/sources/perturbing_agent.tex~
ProcessDiagram/trunk/UserManual/sources/phenotype.tex
ProcessDiagram/trunk/UserManual/sources/phenotype.tex~
ProcessDiagram/trunk/UserManual/sources/process.tex.backup
ProcessDiagram/trunk/UserManual/sources/process.tex~
ProcessDiagram/trunk/UserManual/sources/production.tex
ProcessDiagram/trunk/UserManual/sources/production.tex~
ProcessDiagram/trunk/UserManual/sources/refcard.aux
ProcessDiagram/trunk/UserManual/sources/simpleChemical.tex~
ProcessDiagram/trunk/UserManual/sources/sourceSink.tex.backup
ProcessDiagram/trunk/UserManual/sources/sourceSink.tex~
ProcessDiagram/trunk/UserManual/sources/stateVariable.tex~
ProcessDiagram/trunk/UserManual/sources/stimulation.tex
ProcessDiagram/trunk/UserManual/sources/stimulation.tex~
ProcessDiagram/trunk/UserManual/sources/symbols.tex~
ProcessDiagram/trunk/UserManual/sources/uncertain.tex~
ProcessDiagram/trunk/UserManual/sources/unitInformation.tex~
ProcessDiagram/trunk/UserManual/sources/unspecified.tex~
Added: ProcessDiagram/trunk/UserManual/images/and.eps
===================================================================
--- ProcessDiagram/trunk/UserManual/images/and.eps (rev 0)
+++ ProcessDiagram/trunk/UserManual/images/and.eps 2012-05-21 10:39:18 UTC (rev 824)
@@ -0,0 +1,230 @@
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Revision: 823
http://sbgn.svn.sourceforge.net/sbgn/?rev=823&view=rev
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From: <le...@us...> - 2012-05-20 11:59:46
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Revision: 822
http://sbgn.svn.sourceforge.net/sbgn/?rev=822&view=rev
Author: lenov
Date: 2012-05-20 11:59:35 +0000 (Sun, 20 May 2012)
Log Message:
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Modified Paths:
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Modified: ProcessDiagram/trunk/UserManual/images/uncertain.pdf
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Modified: ProcessDiagram/trunk/UserManual/images/uncertain.png
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Modified: ProcessDiagram/trunk/UserManual/images/uncertain.svg
===================================================================
--- ProcessDiagram/trunk/UserManual/images/uncertain.svg 2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/images/uncertain.svg 2012-05-20 11:59:35 UTC (rev 822)
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Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-05-20 11:59:35 UTC (rev 822)
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\openout2 = `sources/refcard.aux'.
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Appendix A.
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File: images/refcard.pdf Graphic file (type pdf)
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PDF statistics:
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Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/UserManual/sources/CVs.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/CVs.tex 2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/CVs.tex 2012-05-20 11:59:35 UTC (rev 822)
@@ -118,7 +118,7 @@
\subsubsection{Cardinality}
\label{sec:cardinality-cv}
-\SBGNPDLone defines a special unit of information usable on multimers for describing the number of monomers composing the multimer. \tab{cardinality-cv} shows the way in which the values must be written. Note that the value is an positive non-zero integer, and not (for example) a range. There is no provision in \SBGNPDLone for specifying a range in this context because it leads to problems of entity identifiability.
+\SBGNPDLone defines a special unit of information usable on multimers for describing the number of monomers composing the multimer. \tab{cardinality-cv} shows the way in which the values must be written. Note that the value is an positive non-zero integer, and not (for example) a range. There is at present no provision in \SBGNPDLone for specifying a range in this context because it leads to problems of entity identifiability.
\begin{table}[h]
\centering
Modified: ProcessDiagram/trunk/UserManual/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/front-page.tex 2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/front-page.tex 2012-05-20 11:59:35 UTC (rev 822)
@@ -11,7 +11,7 @@
\vspace*{0.5in}
\Large
-\textbf{Version 2.0}\\[0.1in]
+\textbf{Version 1.3}\\[0.1in]
\large
% Date: \sbgndate\\[0.25in]
Date: \today\\[0.25in]
Modified: ProcessDiagram/trunk/UserManual/sources/multimer.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/multimer.tex 2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/multimer.tex 2012-05-20 11:59:35 UTC (rev 822)
@@ -1,7 +1,7 @@
\subsection{Glyph: \glyph{Multimer}}
\label{sec:multimer}
-As its name implies, a multimer is an aggregation of multiple identical or pseudo-identical entities held together by non-covalent bonds. Thus, they are distinguished from polymers by the fact that the latter involve covalent bonds, and should be represented by \glyphs{macromolecules}. Here \emph{pseudo-identical} refers to the possibility that the entities differ chemically but retain some common global characteristic, such as a structure or function, and so can be considered identical within the context of the SBGN \PD. An example of this are the homologous subunits in a hetero-oligomeric receptor. SBGN \PD accepts multimers of \glyph{simple chemical} (\sect{simpleChemical}), \glyph{macromolecule} (\sect{macromolecule}), \glyph{nucleic acid feature} (\sect{genetic}) or \glyph{complex} (\sect{complex}). A \glyph{multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other as illustrated in \fig{multimer}.
+As its name implies, a multimer is an aggregation of multiple identical or pseudo-identical entities held together by non-covalent bonds. Thus, they are distinguished from polymers by the fact that the latter involve covalent bonds, and should be represented by \glyph{macromolecules}. Here \emph{pseudo-identical} refers to the possibility that the entities differ chemically but retain some common global characteristic, such as a structure or function, and so can be considered identical within the context of the SBGN \PD. An example of this are the homologous subunits in a hetero-oligomeric receptor. SBGN \PD accepts multimers of \glyph{simple chemical} (\sect{simpleChemical}), \glyph{macromolecule} (\sect{macromolecule}), \glyph{nucleic acid feature} (\sect{genetic}) or \glyph{complex} (\sect{complex}). A \glyph{multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other as illustrated in \fig{multimer}.
\begin{figure}[H]
\centering
Modified: ProcessDiagram/trunk/UserManual/sources/symbols.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.aux 2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.aux 2012-05-20 11:59:35 UTC (rev 822)
@@ -33,24 +33,64 @@
\newlabel{sec:perturbing agent}{{2.1.7}{7}}
\@writefile{lof}{\contentsline {figure}{\numberline {2.7}{\ignorespaces The Process Description\xspace glyph for \emph {perturbing agent}.}}{7}}
\newlabel{fig:perturbing agent}{{2.7}{7}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.1.8}Glyph: \emph {Multimer}}{7}}
+\newlabel{sec:multimer}{{2.1.8}{7}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.8}{\ignorespaces The Process Description\xspace glyph for \emph {multimer}. }}{7}}
+\newlabel{fig:multimer}{{2.8}{7}}
\@writefile{toc}{\contentsline {section}{\numberline {2.2}Decorations of the entity pool nodes}{7}}
\newlabel{sec:decorations}{{2.2}{7}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.1}Glyph: \emph {Unit of information}}{7}}
-\newlabel{sec:unitInfo}{{2.2.1}{7}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.8}{\ignorespaces The Process Description\xspace glyph for \emph {unit of information}.}}{7}}
-\newlabel{fig:unitInfo}{{2.8}{7}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.1}Glyph: \emph {Unit of information}}{8}}
+\newlabel{sec:unitInfo}{{2.2.1}{8}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.9}{\ignorespaces The Process Description\xspace glyph for \emph {unit of information}.}}{8}}
+\newlabel{fig:unitInfo}{{2.9}{8}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.2}Glyph: \emph {State variable}}{8}}
\newlabel{sec:stateVariable}{{2.2.2}{8}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.9}{\ignorespaces The Process Description\xspace glyph for \emph {state variable}.}}{8}}
-\newlabel{fig:state-var}{{2.9}{8}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.3}Glyph: \emph {Clone marker}}{8}}
-\newlabel{sec:cloneMarker}{{2.2.3}{8}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.10}{\ignorespaces The Process Description\xspace glyph for \emph {simple clone marker} applied to a \emph {simple chemical}}}{9}}
-\newlabel{fig:simpleCloneMarker}{{2.10}{9}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.11}{\ignorespaces The Process Description\xspace glyph for \emph {labeled clone marker} applied to a \emph {multimer} of \emph {macromolecules}.}}{9}}
-\newlabel{fig:labeledCloneMarker}{{2.11}{9}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.10}{\ignorespaces The Process Description\xspace glyph for \emph {state variable}.}}{8}}
+\newlabel{fig:state-var}{{2.10}{8}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.3}Glyph: \emph {Clone marker}}{9}}
+\newlabel{sec:cloneMarker}{{2.2.3}{9}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.11}{\ignorespaces The Process Description\xspace glyph for \emph {simple clone marker} applied to a \emph {simple chemical}}}{9}}
+\newlabel{fig:simpleCloneMarker}{{2.11}{9}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.12}{\ignorespaces The Process Description\xspace glyph for \emph {labeled clone marker} applied to a \emph {multimer} of \emph {macromolecules}.}}{9}}
+\newlabel{fig:labeledCloneMarker}{{2.12}{9}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.4}Controlled vocabularies used in SBGN Process Description\xspace Level\nobreakspace {}1\xspace }{9}}
+\newlabel{sec:CVs}{{2.2.4}{9}}
+\@writefile{toc}{\contentsline {subsubsection}{Entity pool node material types}{10}}
+\newlabel{sec:material-types-cv}{{2.2.4}{10}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.1}{\ignorespaces A sample of values from the \emph {material types} controlled vocabulary (Section\nobreakspace {}\ref {sec:material-types-cv}\xspace ).}}{10}}
+\newlabel{tab:material-types-cv}{{2.1}{10}}
+\@writefile{toc}{\contentsline {subsubsection}{Entity pool node conceptual types}{10}}
+\newlabel{sec:conceptual-types-cv}{{2.2.4}{10}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.2}{\ignorespaces A sample of values from the \emph {conceptual types} vocabulary (Section\nobreakspace {}\ref {sec:conceptual-types-cv}\xspace ).}}{10}}
+\newlabel{tab:conceptual-types-cv}{{2.2}{10}}
+\@writefile{toc}{\contentsline {subsubsection}{Macromolecule covalent modifications}{10}}
+\newlabel{sec:covalent-mod-cv}{{2.2.4}{10}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.3}{\ignorespaces A sample of values from the \emph {covalent modifications} vocabulary (Section\nobreakspace {}\ref {sec:covalent-mod-cv}\xspace ).}}{11}}
+\newlabel{tab:covalent-mod-cv}{{2.3}{11}}
+\@writefile{toc}{\contentsline {subsubsection}{Physical characteristics}{11}}
+\newlabel{sec:physical-characteristics-cv}{{2.2.4}{11}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.4}{\ignorespaces A sample of values from the \emph {physical characteristics} vocabulary (Section\nobreakspace {}\ref {sec:physical-characteristics-cv}\xspace ).}}{11}}
+\newlabel{tab:physical-characteristics-cv}{{2.4}{11}}
+\@writefile{toc}{\contentsline {subsubsection}{Cardinality}{11}}
+\newlabel{sec:cardinality-cv}{{2.2.4}{11}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.5}{\ignorespaces The format of the possible values for the \emph {cardinality} unit of information (Section\nobreakspace {}\ref {sec:cardinality-cv}\xspace ). Here, \texttt {\#} stands for the number; for example, ``\texttt {N:5}''.}}{12}}
+\newlabel{tab:cardinality-cv}{{2.5}{12}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.3}Process nodes}{12}}
+\newlabel{sec:PNs}{{2.3}{12}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.1}Glyph: \emph {Process}}{12}}
+\newlabel{sec:process}{{2.3.1}{12}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.13}{\ignorespaces The Process Description\xspace glyph for \emph {process}.}}{12}}
+\newlabel{fig:process}{{2.13}{12}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.2}Glyph: \emph {Omitted process}}{12}}
+\newlabel{sec:omitted}{{2.3.2}{12}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces The Process Description\xspace glyph for \emph {omitted process}.}}{12}}
+\newlabel{fig:omitted}{{2.14}{12}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.3}Glyph: \emph {Uncertain process}}{13}}
+\newlabel{sec:uncertain}{{2.3.3}{13}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces The Process Description\xspace glyph for an \emph {uncertain process}.}}{13}}
+\newlabel{fig:uncertain}{{2.15}{13}}
\@setckpt{sources/symbols}{
-\setcounter{page}{10}
+\setcounter{page}{14}
\setcounter{equation}{0}
\setcounter{enumi}{0}
\setcounter{enumii}{0}
@@ -60,13 +100,13 @@
\setcounter{mpfootnote}{0}
\setcounter{part}{0}
\setcounter{chapter}{2}
-\setcounter{section}{2}
+\setcounter{section}{3}
\setcounter{subsection}{3}
\setcounter{subsubsection}{0}
\setcounter{paragraph}{0}
\setcounter{subparagraph}{0}
-\setcounter{figure}{11}
-\setcounter{table}{0}
+\setcounter{figure}{15}
+\setcounter{table}{5}
\setcounter{float@type}{4}
\setcounter{r@tfl@t}{0}
}
Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex 2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex 2012-05-20 11:59:35 UTC (rev 822)
@@ -1,10 +1,14 @@
\chapter{Symbols used in SBGN Process Descriptions}
\label{chp:symbols}
-% Refactor the structure of this chapter. We need less sections and a simpler structure. For instance, auxiliary units must be defined in the EPN section.
-
An SBGN \PDm is mainly is bipartite graph, i.e. it is made up of two types of nodes that connect in an alternate way (some exceptions are described below, e.g. when \glyph{logical operators} or \glyph{tag} are used). The two types of nodes are the \glyph{process nodes} and the \glyph{entity pools nodes}, representing the things that are modified by processes. These nodes are connected by arcs. In addition, the \glyph{entity pools nodes} can be contained in \glyph{compartments}.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Entity pool nodes
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
\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, an 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. It really depends on what we want to represent. To belong to different compartments 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 when it comes to representing calcium release from the endoplasmic reticulum.
@@ -27,52 +31,21 @@
\input{sources/unitInformation.tex}
\input{sources/stateVariable.tex}
\input{sources/cloneMarker.tex}
+\input{sources/CVs.tex}
-% \input{sources/CVs.tex}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Process nodes
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%% Containers
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% %\section{Container nodes}\label{sec:CNs}
-% \section{Representing compartments}
-%
-% \input{sources/compartment.tex}
-%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%% Submap
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% \section{Submaps}
-% \input{sources/submap.tex}
-
-% \section{Referring to other Nodes}
-%
-% Reference nodes handle links or relationships between elements of a map and sub-map. At present there is only one reference glyph, \glyph{tag}, which can be used in a map refered to by a \glyph{submap} (\sect{submap}) or as an auxilary unit on the \glyph{submap}. The \glyph{clone marker} can also provide additional reference mechanisms and is discussed below (\sect{cloneMarker}).
-%
-% \input{sources/tag.tex}
-%
-%
-%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%% Process nodes
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% \section{Process nodes}\label{sec:PNs}
-%
-% Process nodes represent processes that transform one or several entity pools into one or several entity pools, identical or different. \SBGNPDLone defines a generic \glyph{process} (\sect{process}), as well as five more specific ones: the \glyph{omitted process} (\sect{omitted}), the \glyph{uncertain process} (\sect{uncertain}), the \glyph{association} (\sect{association}), the \glyph{dissociation} (\sect{dissociation}), and the \glyph{phenotype} (\sect{phenotype}). In future levels of the SBGN \PDl, more processes may be defined. (One can even envision the development of a controlled vocabulary of processes, as is done now for \glyph{EPNs}; see \sect{CVs}.)
-%
-% \input{sources/process.tex}
-% \input{sources/omitted.tex}
-% \input{sources/uncertain.tex}
+\section{Process nodes}\label{sec:PNs}
+
+Process nodes represent processes that transform one or several entity pools into one or several entity pools, identical or different. \SBGNPDLone defines a generic \glyph{process} (\sect{process}), as well as five more specific ones: the \glyph{omitted process} (\sect{omitted}), the \glyph{uncertain process} (\sect{uncertain}), the \glyph{association} (\sect{association}), the \glyph{dissociation} (\sect{dissociation}), and the \glyph{phenotype} (\sect{phenotype}).
+
+\input{sources/process.tex}
+\input{sources/omitted.tex}
+\input{sources/uncertain.tex}
% \input{sources/association.tex}
% \input{sources/dissociation.tex}
% \input{sources/phenotype.tex}
@@ -109,3 +82,33 @@
% \input{sources/and.tex}
% \input{sources/or.tex}
% \input{sources/not.tex}
+
+
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%% Containers
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% %\section{Container nodes}\label{sec:CNs}
+%\section{Representing compartments}
+%
+%\input{sources/compartment.tex}
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%% Submap
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% \section{Submaps}
+% \input{sources/submap.tex}
+
+% \section{Referring to other Nodes}
+%
+% Reference nodes handle links or relationships between elements of a map and sub-map. At present there is only one reference glyph, \glyph{tag}, which can be used in a map refered to by a \glyph{submap} (\sect{submap}) or as an auxilary unit on the \glyph{submap}. The \glyph{clone marker} can also provide additional reference mechanisms and is discussed below (\sect{cloneMarker}).
+%
+% \input{sources/tag.tex}
+%
+%
+%
Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup 2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup 2012-05-20 11:59:35 UTC (rev 822)
@@ -1,10 +1,14 @@
\chapter{Symbols used in SBGN Process Descriptions}
\label{chp:symbols}
-% Refactor the structure of this chapter. We need less sections and a simpler structure. For instance, auxiliary units must be defined in the EPN section.
-
An SBGN \PDm is mainly is bipartite graph, i.e. it is made up of two types of nodes that connect in an alternate way (some exceptions are described below, e.g. when \glyph{logical operators} or \glyph{tag} are used). The two types of nodes are the \glyph{process nodes} and the \glyph{entity pools nodes}, representing the things that are modified by processes. These nodes are connected by arcs. In addition, the \glyph{entity pools nodes} can be contained in \glyph{compartments}.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Entity pool nodes
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
\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, an 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. It really depends on what we want to represent. To belong to different compartments 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 when it comes to representing calcium release from the endoplasmic reticulum.
@@ -12,67 +16,34 @@
The \PDl contains six glyphs representing classes of material entities: \glyph{unspecified entity} (\sect{unspecifiedEntity}), \glyph{simple chemical} (\sect{simpleChemical}), \glyph{macromolecule} (\sect{macromolecule}), \glyph{nucleic acid feature} (\sect{genetic}), and \glyph{complex} (\sect{complex}). (Specific types of macromolecules, such as protein, RNA, DNA, polysaccharide, and specific simple chemicals are not defined by \PD but may be part of future levels of SBGN). In addition to the material entities, the \PDl represents two conceptual entities: An absorbing pool, called \glyph{source and sink} (\sect{sourceSink}), and a \glyph{perturbing agent} (\sect{perturbing agent}). Material and conceptual entities can optionally carry auxiliary units such as \glyph{units of information} (\sect{unitInfo}), \glyph{state variables} (\sect{stateVariable}) and \glyph{clone markers} (\sect{cloneMarker}).
\input{sources/unspecified.tex}
- \input{sources/macromolecule.tex}
+\input{sources/macromolecule.tex}
\input{sources/simpleChemical.tex}
-% \input{sources/genetic.tex}
-% \input{sources/complex.tex}
-% \input{sources/sourceSink.tex}
-% \input{sources/perturbing_agent.tex}
-%
-% \section{Modification of the entity pool nodes}
+\input{sources/genetic.tex}
+\input{sources/complex.tex}
+\input{sources/sourceSink.tex}
+\input{sources/perturbing_agent.tex}
+\input{sources/multimer.tex}
-% \subsection{Auxiliary Units}
-%
-% Auxiliary units are glyphs that decorate other glyphs, providing additional information that may be useful to the reader. These can provide annotation (\glyph{unit of information}), state information (\glyph{state variable}) or indicate duplication of entity pool nodes (\glyph{clone marker}).
-%
-% \input{sources/unitInformation.tex}
-% \input{sources/stateVariable.tex}
-% \input{sources/cloneMarker.tex}
+\section{Decorations of the entity pool nodes}\label{sec:decorations}
-% \input{sources/CVs.tex}
+SBGN \PD provides glyphs that decorate other glyphs, providing additional information that may be useful to the reader. These can provide annotation (\glyph{unit of information}), state information (\glyph{state variable}) or indicate duplication of entity pool nodes (\glyph{clone marker}).
-% \input{sources/multimer.tex}
+\input{sources/unitInformation.tex}
+\input{sources/stateVariable.tex}
+\input{sources/cloneMarker.tex}
+\input{sources/CVs.tex}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Process nodes
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%% Containers
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% %\section{Container nodes}\label{sec:CNs}
-% \section{Representing compartments}
-%
-% \input{sources/compartment.tex}
-%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%% Submap
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% \section{Submaps}
-% \input{sources/submap.tex}
-
-% \section{Referring to other Nodes}
-%
-% Reference nodes handle links or relationships between elements of a map and sub-map. At present there is only one reference glyph, \glyph{tag}, which can be used in a map refered to by a \glyph{submap} (\sect{submap}) or as an auxilary unit on the \glyph{submap}. The \glyph{clone marker} can also provide additional reference mechanisms and is discussed below (\sect{cloneMarker}).
-%
-% \input{sources/tag.tex}
-%
-%
-%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%% Process nodes
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% \section{Process nodes}\label{sec:PNs}
-%
-% Process nodes represent processes that transform one or several entity pools into one or several entity pools, identical or different. \SBGNPDLone defines a generic \glyph{process} (\sect{process}), as well as five more specific ones: the \glyph{omitted process} (\sect{omitted}), the \glyph{uncertain process} (\sect{uncertain}), the \glyph{association} (\sect{association}), the \glyph{dissociation} (\sect{dissociation}), and the \glyph{phenotype} (\sect{phenotype}). In future levels of the SBGN \PDl, more processes may be defined. (One can even envision the development of a controlled vocabulary of processes, as is done now for \glyph{EPNs}; see \sect{CVs}.)
-%
-% \input{sources/process.tex}
+\section{Process nodes}\label{sec:PNs}
+
+Process nodes represent processes that transform one or several entity pools into one or several entity pools, identical or different. \SBGNPDLone defines a generic \glyph{process} (\sect{process}), as well as five more specific ones: the \glyph{omitted process} (\sect{omitted}), the \glyph{uncertain process} (\sect{uncertain}), the \glyph{association} (\sect{association}), the \glyph{dissociation} (\sect{dissociation}), and the \glyph{phenotype} (\sect{phenotype}).
+
+\input{sources/process.tex}
% \input{sources/omitted.tex}
% \input{sources/uncertain.tex}
% \input{sources/association.tex}
@@ -111,3 +82,33 @@
% \input{sources/and.tex}
% \input{sources/or.tex}
% \input{sources/not.tex}
+
+
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%% Containers
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% %\section{Container nodes}\label{sec:CNs}
+%\section{Representing compartments}
+%
+%\input{sources/compartment.tex}
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%% Submap
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% \section{Submaps}
+% \input{sources/submap.tex}
+
+% \section{Referring to other Nodes}
+%
+% Reference nodes handle links or relationships between elements of a map and sub-map. At present there is only one reference glyph, \glyph{tag}, which can be used in a map refered to by a \glyph{submap} (\sect{submap}) or as an auxilary unit on the \glyph{submap}. The \glyph{clone marker} can also provide additional reference mechanisms and is discussed below (\sect{cloneMarker}).
+%
+% \input{sources/tag.tex}
+%
+%
+%
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2012-05-20 05:28:27
|
Revision: 821
http://sbgn.svn.sourceforge.net/sbgn/?rev=821&view=rev
Author: lenov
Date: 2012-05-20 05:28:21 +0000 (Sun, 20 May 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/sources/multimer.tex
ProcessDiagram/trunk/UserManual/sources/symbols.tex
Modified: ProcessDiagram/trunk/UserManual/sources/multimer.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/multimer.tex 2012-05-04 17:24:18 UTC (rev 820)
+++ ProcessDiagram/trunk/UserManual/sources/multimer.tex 2012-05-20 05:28:21 UTC (rev 821)
@@ -1,46 +1,11 @@
-% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/ProcessDiagram/tags/L1V1.3Full/sources/multimer.tex $
-
\subsection{Glyph: \glyph{Multimer}}
\label{sec:multimer}
-As its name implies, a multimer is an aggregation of multiple identical or pseudo-identical entities held together by non-covalent bonds (Thus, they are distinguished from polymers by the fact that the later involve covalent bonds). Here, \emph{pseudo-identical} refers to the possibility that the entities differ chemically but retain some common global characteristic, such as a structure or function, and so can be considered identical within the context of the SBGN \PD. An example of this are the homologous subunits in a hetero-oligomeric receptor. SBGN \PD accepts multimers of \glyph{simple chemical} (\sect{simpleChemical}), \glyph{macromolecule} (\sect{macromolecule}), \glyph{nucleic acid feature} (\sect{genetic}) or \glyph{complex} (\sect{complex}).
+As its name implies, a multimer is an aggregation of multiple identical or pseudo-identical entities held together by non-covalent bonds. Thus, they are distinguished from polymers by the fact that the latter involve covalent bonds, and should be represented by \glyphs{macromolecules}. Here \emph{pseudo-identical} refers to the possibility that the entities differ chemically but retain some common global characteristic, such as a structure or function, and so can be considered identical within the context of the SBGN \PD. An example of this are the homologous subunits in a hetero-oligomeric receptor. SBGN \PD accepts multimers of \glyph{simple chemical} (\sect{simpleChemical}), \glyph{macromolecule} (\sect{macromolecule}), \glyph{nucleic acid feature} (\sect{genetic}) or \glyph{complex} (\sect{complex}). A \glyph{multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other as illustrated in \fig{multimer}.
-\begin{glyphDescription}
-
-\glyphSboTerm %SBO:0000286 ! multimer
-\begin{tabular}{l l}
-Macromolecule & SBO:0000420 ! multimer of macromolecules \\
-Complex & SBO:0000418 ! multimer of complexes \\
-Nucleic Acid Feature & SBO:0000419 ! multimer of informational molecule segments \\
-Simple Chemical & SBO:0000421 ! multimer of simple chemicals
-\end{tabular}
-
-\glyphContainer A \glyph{multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other. \fig{multimer} illustrates the glyph.
-
-\glyphLabel A \glyph{multimer} has no identity on its own. However, the first of the monomers carries an identifying label. The label is 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 top monomer's container. The label may spill outside of the container.
-
-\glyphAux A \glyph{multimer} can carry state variables that can add information about its state (\sect{stateVariable}). The state of a multimer is therefore defined as the vector of all its state variables. Note that a \glyph{state variable} carried by a multimer actually applies to each of the constituent monomers individually. If instead the state variables are meant to apply to the whole multimeric assembly, a \glyph{macromolecule} (\sect{macromolecule}) should be used instead of \glyph{multimer}. An assembly containing some state variables applicable to the components, and others state variable applicable to the assembly (for instance opening of a channel and phosphorylation of each of its subunits) should be represented by a \glyph{complex} (\sect{complex}).
-
-A \glyph{multimer} can also carry one or several \glyph{units of information} (\sect{unitInfo}). The information can characterize a domain, such as a binding site. Particular \glyph{units of information} exist for describing the material type (\sect{material-types-cv}), the conceptual type (\sect{conceptual-types-cv}), and the cardinality (\sect{cardinality-cv}) of the multimer. Note that a \glyph{unit of information} carried by a multimer actually applies to each of the constituent monomers individually. If instead a \glyph{unit of information} should be applicable to the whole multimeric assembly, a \glyph{macromolecule} should be used (\sect{macromolecule}). An assembly containing units of information applying to the components, and others to the assembly should be represented by a \glyph{complex} (\sect{complex}).
-
-A \glyph{multimer} may also carry a \glyph{clone marker} (\sect{cloneMarker}).
-
-\end{glyphDescription}
-
-
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/multimer}
- \caption{The \PD glyph for \glyph{multimer} with an additional unit of information containing the cardinality.}
+ \caption{The \PD glyph for \glyph{multimer}. }
\label{fig:multimer}
\end{figure}
-
-
-
-
-
-
-% The following is for [X]Emacs users. Please leave in place.
-% Local Variables:
-% TeX-master: "../sbgn_PD-level1"
-% End:
Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex 2012-05-04 17:24:18 UTC (rev 820)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex 2012-05-20 05:28:21 UTC (rev 821)
@@ -18,6 +18,7 @@
\input{sources/complex.tex}
\input{sources/sourceSink.tex}
\input{sources/perturbing_agent.tex}
+\input{sources/multimer.tex}
\section{Decorations of the entity pool nodes}\label{sec:decorations}
@@ -29,7 +30,6 @@
% \input{sources/CVs.tex}
-% \input{sources/multimer.tex}
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2012-05-04 17:24:27
|
Revision: 820
http://sbgn.svn.sourceforge.net/sbgn/?rev=820&view=rev
Author: lenov
Date: 2012-05-04 17:24:18 +0000 (Fri, 04 May 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
ProcessDiagram/trunk/UserManual/sources/cloneMarker.tex
ProcessDiagram/trunk/UserManual/sources/stateVariable.tex
ProcessDiagram/trunk/UserManual/sources/symbols.aux
ProcessDiagram/trunk/UserManual/sources/symbols.tex
Added Paths:
-----------
ProcessDiagram/trunk/UserManual/images/complex.eps
ProcessDiagram/trunk/UserManual/images/complex.pdf
ProcessDiagram/trunk/UserManual/images/complex.png
ProcessDiagram/trunk/UserManual/images/complex.svg
ProcessDiagram/trunk/UserManual/images/genetic-plain.eps
ProcessDiagram/trunk/UserManual/images/genetic-plain.graffle
ProcessDiagram/trunk/UserManual/images/genetic-plain.pdf
ProcessDiagram/trunk/UserManual/images/genetic-plain.svg
ProcessDiagram/trunk/UserManual/images/genetic.eps
ProcessDiagram/trunk/UserManual/images/genetic.pdf
ProcessDiagram/trunk/UserManual/images/genetic.png
ProcessDiagram/trunk/UserManual/images/genetic.svg
ProcessDiagram/trunk/UserManual/images/labeledCloneMarker.eps
ProcessDiagram/trunk/UserManual/images/labeledCloneMarker.pdf
ProcessDiagram/trunk/UserManual/images/labeledCloneMarker.png
ProcessDiagram/trunk/UserManual/images/labeledCloneMarker.svg
ProcessDiagram/trunk/UserManual/images/macromolecule-plain.eps
ProcessDiagram/trunk/UserManual/images/macromolecule-plain.graffle
ProcessDiagram/trunk/UserManual/images/macromolecule-plain.pdf
ProcessDiagram/trunk/UserManual/images/macromolecule-plain.png
ProcessDiagram/trunk/UserManual/images/macromolecule-plain.svg
ProcessDiagram/trunk/UserManual/images/macromolecule.eps
ProcessDiagram/trunk/UserManual/images/macromolecule.pdf
ProcessDiagram/trunk/UserManual/images/macromolecule.png
ProcessDiagram/trunk/UserManual/images/macromolecule.svg
ProcessDiagram/trunk/UserManual/images/perturbing_agent.eps
ProcessDiagram/trunk/UserManual/images/perturbing_agent.pdf
ProcessDiagram/trunk/UserManual/images/perturbing_agent.png
ProcessDiagram/trunk/UserManual/images/perturbing_agent.svg
ProcessDiagram/trunk/UserManual/images/refcard.eps
ProcessDiagram/trunk/UserManual/images/refcard.pdf
ProcessDiagram/trunk/UserManual/images/refcard.png
ProcessDiagram/trunk/UserManual/images/refcard.svg
ProcessDiagram/trunk/UserManual/images/simpleChemical.ai
ProcessDiagram/trunk/UserManual/images/simpleChemical.eps
ProcessDiagram/trunk/UserManual/images/simpleChemical.pdf
ProcessDiagram/trunk/UserManual/images/simpleChemical.png
ProcessDiagram/trunk/UserManual/images/simpleChemical.svg
ProcessDiagram/trunk/UserManual/images/simpleCloneMarker.eps
ProcessDiagram/trunk/UserManual/images/simpleCloneMarker.pdf
ProcessDiagram/trunk/UserManual/images/simpleCloneMarker.png
ProcessDiagram/trunk/UserManual/images/simpleCloneMarker.svg
ProcessDiagram/trunk/UserManual/images/sourceSink.eps
ProcessDiagram/trunk/UserManual/images/sourceSink.pdf
ProcessDiagram/trunk/UserManual/images/sourceSink.png
ProcessDiagram/trunk/UserManual/images/sourceSink.svg
ProcessDiagram/trunk/UserManual/images/stateVariable.eps
ProcessDiagram/trunk/UserManual/images/stateVariable.pdf
ProcessDiagram/trunk/UserManual/images/stateVariable.png
ProcessDiagram/trunk/UserManual/images/stateVariable.svg
ProcessDiagram/trunk/UserManual/images/uncertain.eps
ProcessDiagram/trunk/UserManual/images/uncertain.pdf
ProcessDiagram/trunk/UserManual/images/uncertain.png
ProcessDiagram/trunk/UserManual/images/uncertain.svg
ProcessDiagram/trunk/UserManual/images/unitInformation.eps
ProcessDiagram/trunk/UserManual/images/unitInformation.pdf
ProcessDiagram/trunk/UserManual/images/unitInformation.png
ProcessDiagram/trunk/UserManual/images/unitInformation.svg
ProcessDiagram/trunk/UserManual/images/unspecified.eps
ProcessDiagram/trunk/UserManual/images/unspecified.pdf
ProcessDiagram/trunk/UserManual/images/unspecified.png
ProcessDiagram/trunk/UserManual/images/unspecified.svg
Added: ProcessDiagram/trunk/UserManual/images/complex.eps
===================================================================
--- ProcessDiagram/trunk/UserManual/images/complex.eps (rev 0)
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From: <hua...@us...> - 2012-03-08 21:50:26
|
Revision: 819
http://sbgn.svn.sourceforge.net/sbgn/?rev=819&view=rev
Author: huaiyumi
Date: 2012-03-08 21:50:16 +0000 (Thu, 08 Mar 2012)
Log Message:
-----------
1. Add glyph process. 2. Modify descriptions for biological activity and phenotype glyph. 3. Modify related sections See revision history (Appendix C) for more details.
Modified Paths:
--------------
ActivityFlow/trunk/examples/Action_potential.eps
ActivityFlow/trunk/examples/Action_potential.pdf
ActivityFlow/trunk/examples/Action_potential.png
ActivityFlow/trunk/examples/Action_potential.svg
ActivityFlow/trunk/images/refcard.eps
ActivityFlow/trunk/images/refcard.pdf
ActivityFlow/trunk/images/refcard.png
ActivityFlow/trunk/images/refcard.svg
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/acknowledgments.tex
ActivityFlow/trunk/sources/biologicalActivity.tex
ActivityFlow/trunk/sources/examples.tex
ActivityFlow/trunk/sources/front-page.tex
ActivityFlow/trunk/sources/glyphs.tex
ActivityFlow/trunk/sources/phenotype.tex
ActivityFlow/trunk/sources/refcard.tex
ActivityFlow/trunk/sources/syntax.tex
Added Paths:
-----------
ActivityFlow/trunk/images/process.eps
ActivityFlow/trunk/images/process.pdf
ActivityFlow/trunk/images/process.png
ActivityFlow/trunk/images/process.svg
ActivityFlow/trunk/sources/process.tex
ActivityFlow/trunk/sources/revision_history.tex
Modified: ActivityFlow/trunk/examples/Action_potential.eps
===================================================================
--- ActivityFlow/trunk/examples/Action_potential.eps 2012-03-07 22:00:46 UTC (rev 818)
+++ ActivityFlow/trunk/examples/Action_potential.eps 2012-03-08 21:50:16 UTC (rev 819)
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[truncated message content] |
|
From: <hua...@us...> - 2012-03-07 22:00:56
|
Revision: 818
http://sbgn.svn.sourceforge.net/sbgn/?rev=818&view=rev
Author: huaiyumi
Date: 2012-03-07 22:00:46 +0000 (Wed, 07 Mar 2012)
Log Message:
-----------
1. Remove perturbation as an activity node.
2. Add perturbation as unit of information.
3. Modify perturbation glyphs in affected figures.
4. Remove perturbation from tables in the syntax section.
Modified Paths:
--------------
ActivityFlow/trunk/examples/Action_potential.eps
ActivityFlow/trunk/examples/Action_potential.pdf
ActivityFlow/trunk/examples/Action_potential.png
ActivityFlow/trunk/examples/Action_potential.svg
ActivityFlow/trunk/examples/PPAR.eps
ActivityFlow/trunk/examples/PPAR.pdf
ActivityFlow/trunk/examples/PPAR.png
ActivityFlow/trunk/examples/PPAR.svg
ActivityFlow/trunk/examples/ex-positiveInfluence.eps
ActivityFlow/trunk/examples/ex-positiveInfluence.pdf
ActivityFlow/trunk/examples/ex-positiveInfluence.png
ActivityFlow/trunk/examples/ex-positiveInfluence.svg
ActivityFlow/trunk/images/refcard.eps
ActivityFlow/trunk/images/refcard.pdf
ActivityFlow/trunk/images/refcard.png
ActivityFlow/trunk/images/refcard.svg
ActivityFlow/trunk/images/unitInformation.png
ActivityFlow/trunk/images/unitInformation_ba.eps
ActivityFlow/trunk/images/unitInformation_ba.pdf
ActivityFlow/trunk/images/unitInformation_ba.png
ActivityFlow/trunk/images/unitInformation_ba.svg
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/acknowledgments.tex
ActivityFlow/trunk/sources/glyphs.tex
ActivityFlow/trunk/sources/syntax.tex
ActivityFlow/trunk/sources/unitInformation.tex
Modified: ActivityFlow/trunk/examples/Action_potential.eps
===================================================================
--- ActivityFlow/trunk/examples/Action_potential.eps 2012-03-05 22:44:30 UTC (rev 817)
+++ ActivityFlow/trunk/examples/Action_potential.eps 2012-03-07 22:00:46 UTC (rev 818)
@@ -1,4727 +1,2222 @@
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[truncated message content] |
|
From: <le...@us...> - 2012-03-05 22:44:38
|
Revision: 817
http://sbgn.svn.sourceforge.net/sbgn/?rev=817&view=rev
Author: lenov
Date: 2012-03-05 22:44:30 +0000 (Mon, 05 Mar 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bib
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex
ProcessDiagram/trunk/UserManual/sources/complex.tex
ProcessDiagram/trunk/UserManual/sources/genetic.tex
ProcessDiagram/trunk/UserManual/sources/introduction.aux
ProcessDiagram/trunk/UserManual/sources/introduction.tex
ProcessDiagram/trunk/UserManual/sources/introduction.tex.backup
ProcessDiagram/trunk/UserManual/sources/macromolecule.tex
ProcessDiagram/trunk/UserManual/sources/perturbing_agent.tex
ProcessDiagram/trunk/UserManual/sources/simpleChemical.tex
ProcessDiagram/trunk/UserManual/sources/sourceSink.tex
ProcessDiagram/trunk/UserManual/sources/stateVariable.tex
ProcessDiagram/trunk/UserManual/sources/symbols.aux
ProcessDiagram/trunk/UserManual/sources/symbols.tex
ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup
ProcessDiagram/trunk/UserManual/sources/unitInformation.tex
ProcessDiagram/trunk/UserManual/sources/unspecified.tex
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux 2012-03-05 22:44:30 UTC (rev 817)
@@ -1,6 +1,7 @@
\relax
\@input{sources/introduction.aux}
\@input{sources/symbols.aux}
+\@input{sources/refcard.aux}
\bibstyle{unsrt}
\bibdata{sbgn_PD-level1-user}
\bibcite{LeNovere:2009p1}{1}
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bib
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bib 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bib 2012-03-05 22:44:30 UTC (rev 817)
@@ -138,6 +138,14 @@
pages = {36}
}
+@Article{Moodie:2011,
+ author = {Moodie, Stuart and Le Nov\`{e}re, Nicolas and Demir, Emek and Mi, Huaiyu and Vill\'{e}ger, Alice},
+ title = {Systems Biology Graphical Notation: Process Description language Level 1},
+ journal = {Nature Precedings},
+ year = {2011},
+ url = {http://dx.doi.org/10.1038/npre.2011.3721.4}
+}
+
@Article{Pirson:2000,
author = {I. Pirson and N. Fortemaison and C. Jacobs and S. Dremier and J. E. Dumont and C. Maenhaut},
title = {The visual display of regulatory information and networks},
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg 2012-03-05 22:44:30 UTC (rev 817)
@@ -2,11 +2,13 @@
The top-level auxiliary file: sbgn_PD-level1-user.aux
A level-1 auxiliary file: sources/introduction.aux
A level-1 auxiliary file: sources/symbols.aux
+A level-1 auxiliary file: sources/refcard.aux
The style file: unsrt.bst
Database file #1: sbgn_PD-level1-user.bib
+Warning--I didn't find a database entry for "Moodie2011"
You've used 1 entry,
1791 wiz_defined-function locations,
- 456 strings with 4402 characters,
+ 459 strings with 4441 characters,
and the built_in function-call counts, 750 in all, are:
= -- 26
> -- 119
@@ -45,3 +47,4 @@
while$ -- 3
width$ -- 2
write$ -- 15
+(There was 1 warning)
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-03-05 22:44:30 UTC (rev 817)
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2011.11.28) 31 JAN 2012 09:36
+This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2011.11.28) 5 MAR 2012 19:46
entering extended mode
%&-line parsing enabled.
**sbgn_PD-level1-user.tex
@@ -866,7 +866,7 @@
`rotating' package detected
`float' package detected
) (./sources/latex-macros.tex) (./sbgn_PD-level1-user.aux
-(./sources/introduction.aux) (./sources/symbols.aux))
+(./sources/introduction.aux) (./sources/symbols.aux) (./sources/refcard.aux))
\openout1 = `sbgn_PD-level1-user.aux'.
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 11.
@@ -1027,209 +1027,243 @@
(Font) Font shape `T1/phv/b/n' tried instead on input line 6.
LaTeX Font Info: Font shape `T1/phv/b/n' will be
(Font) scaled to size 21.64548pt on input line 6.
+
+LaTeX Warning: Citation `Moodie2011' on page 1 undefined on input line 12.
+
LaTeX Font Info: Font shape `T1/phv/bx/n' in size <14.4> not available
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LaTeX Font Info: Font shape `T1/phv/b/n' will be
-(Font) scaled to size 12.52792pt on input line 17.
+(Font) scaled to size 12.52792pt on input line 14.
<images/MAPK-only.pdf, id=9, 345.29pt x 337.26pt>
File: images/MAPK-only.pdf Graphic file (type pdf)
<use images/MAPK-only.pdf>
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- 30.
-
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LaTeX Warning: Reference `sec:stateVariable' on page 1 undefined on input line
-30.
+24.
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+Overfull \hbox (13.03523pt too wide) in paragraph at lines 44--22
+[]\T1/futs/m/n/10.95 The eas-i-est and best way to get in-volved in SBGN dis-cu
+s-sions is to join the sbg...@ca...
+ []
+
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Chapter 2.
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+<use images/unspecified.pdf> [4
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+<use images/unitInformation.pdf>)) [7 <./images/sourceSink.pdf> <./images/pertu
+rbing_agent.pdf> <./images/unitInformation.pdf>]
+\openout2 = `sources/refcard.aux'.
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+ (./sources/refcard.tex
+Appendix A.
+<images/refcard.pdf, id=112, 798.985pt x 575.14874pt>
+File: images/refcard.pdf Graphic file (type pdf)
+ <use images/refcard.pdf>)
+Overfull \hbox (7.15172pt too wide) in paragraph at lines 4--29
+[]
+ []
-) [4
+[8
-] (./sbgn_PD-level1-user.bbl) [5
+] [9 <./images/refcard.pdf>] (./sbgn_PD-level1-user.bbl) [10
-] (./sbgn_PD-level1-user.aux
-(./sources/introduction.aux) (./sources/symbols.aux))
+]
+(./sbgn_PD-level1-user.aux (./sources/introduction.aux) (./sources/symbols.aux)
+(./sources/refcard.aux))
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PDF statistics:
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+ 56 words of extra memory for PDF output out of 10000 (max. 10000000)
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex 2012-03-05 22:44:30 UTC (rev 817)
@@ -26,7 +26,7 @@
\appendix
-%\include{sources/refcard}
+\include{sources/refcard}
\backmatter
Modified: ProcessDiagram/trunk/UserManual/sources/complex.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/complex.tex 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sources/complex.tex 2012-03-05 22:44:30 UTC (rev 817)
@@ -6,25 +6,12 @@
\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 other complexes. The resulting entity may have its own identity, properties and function in an SBGN map.
+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 map. 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.
-\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 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{An example \PD glyph for \glyph{complex}.}
+ \caption{The \PD glyph for \glyph{complex}.}
\label{fig:complex}
\end{figure}
Modified: ProcessDiagram/trunk/UserManual/sources/genetic.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/genetic.tex 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sources/genetic.tex 2012-03-05 22:44:30 UTC (rev 817)
@@ -3,37 +3,11 @@
\subsection{Glyph: \glyph{Nucleic acid feature}}
\label{sec:genetic}
-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 map.
+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 a transcript. The label of this EPN and its \emph{units of information} (see section \ref{unitInformation}) are often important for making the purpose clear to the reader of a map. 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.
-\begin{glyphDescription}
-
-\glyphSboTerm SBO:0000354 ! informational molecule segment
-
-\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{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{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 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 \glyph{nucleic acid feature}.
-
-A \glyph{nucleic acid feature} may also carry a \glyph{clone marker}
-(\sect{cloneMarker}).
-
-\end{glyphDescription}
-
-
\begin{figure}[H]
\centering
- \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 an additional state variable and a
- unit of information on the right.}
+ \includegraphics[width = 1.25in]{images/genetic}
+ \caption{The \PD glyph for \glyph{nucleic acid feature}.}
\label{fig:genetic}
\end{figure}
-
-% The following is for [X]Emacs users. Please leave in place.
-% Local Variables:
-% TeX-master: "../sbgn_PD-level1"
-% End:
Modified: ProcessDiagram/trunk/UserManual/sources/introduction.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/introduction.aux 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sources/introduction.aux 2012-03-05 22:44:30 UTC (rev 817)
@@ -1,5 +1,6 @@
\relax
\citation{LeNovere:2009p1}
+\citation{Moodie2011}
\@writefile{toc}{\contentsline {chapter}{\numberline {1}Introduction}{1}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
@@ -9,6 +10,7 @@
\newlabel{fig:eg1}{{1.1}{2}}
\@writefile{toc}{\contentsline {section}{\numberline {1.2}SBGN levels and versions}{2}}
\newlabel{sec:sbgn-levels}{{1.2}{2}}
+\citation{Moodie2011}
\@writefile{toc}{\contentsline {section}{\numberline {1.3}How to get more information}{3}}
\newlabel{sec:info}{{1.3}{3}}
\@setckpt{sources/introduction}{
Modified: ProcessDiagram/trunk/UserManual/sources/introduction.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/introduction.tex 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sources/introduction.tex 2012-03-05 22:44:30 UTC (rev 817)
@@ -6,29 +6,22 @@
\chapter{Introduction}
%Here put a general but short introduction to the needs of standardizing the representation of pathways.
-With the rise of systems and synthetic biology, the use of graphical representations of pathways and networks to describe biological systems has become pervasive. It was therefore important to use a consistent notation that would allow people to interpret those maps easily without the need of extensive legends. Furthermore, activities like synthetic biology, that reconstruct biological systems, needs to exchange their description unambiguously, as engineers exchange circuit diagrams.
+With the rise of systems and synthetic biology, the use of graphical representations of pathways and networks to describe biological systems has become pervasive. It was therefore important to use a consistent notation that would allow people to interpret those maps easily and quickly, without the need of extensive legends. Furthermore, activities like synthetic biology, that reconstruct biological systems, need to exchange their descriptions unambiguously, as engineers exchange circuit diagrams.
-The goal of the Systems Biology Graphical Notation (SBGN) is to standardize the graphical/visual
-representation of biochemical and cellular processes. SBGN
-defines comprehensive sets of symbols with precise semantics, together with
-detailed syntactic rules defining their use. It also describes the manner
-in which such graphical information should be interpreted. SBGN is made up of three different and complementary languages \cite{LeNovere:2009p1}. This document describes the graphical elements composing the \emph{\PDl{}} of SBGN.
+The goal of the Systems Biology Graphical Notation (SBGN) is to standardize the graphical/visual representation of biochemical and cellular processes. SBGN defines comprehensive sets of symbols with precise semantics, together with
+detailed syntactic rules defining their use. It also describes the manner in which such graphical information should be interpreted. SBGN is made up of three different and complementary languages \cite{LeNovere:2009p1}. This document presents the graphical elements composing the \emph{\PDl{}} of SBGN. It is not a normative description, but rather a document aimed at end-users. People, such as software developers, looking for a normative description of SBGN \PDs should rather read the technical specification of the language \cite{Moodie2011}.
\section{Overview of SBGN \PDs}
\label{sec:PD-overview}
-To quickly describe what SBGN \PDl is about, we let's give a brief overview of some of the relevant concepts with the help of an example shown in \fig{eg1}. It is a simple map 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 \PDl by lines with arrows and other decorations. In this particular map, all of the processes happen to be the same: processes catalyzed by biochemical entities. The directions of the arrows indicate the direction of the processes; for example, unphosphorylated RAF kinase processes to phosphorylated RAF kinase via a process catalyzed by RAS. Although ATP and ADP are shown as incidental to the phosphorylations on this particular graph, they are involved in the same process as the proteins getting phosphorylated. The small circles on the nodes for RAF and other entity pools represent state variables (in this case, phosphorylation sites).
+To quickly describe what SBGN \PDl is about, let's give a brief overview of some of the relevant concepts with the help of an example shown in \fig{eg1}. It is a simple map 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 \PDl by lines with arrows and other decorations. In this particular map, all of the processes happen to be the same: processes catalyzed by biochemical entities. The directions of the arrows indicate the direction of the processes; for example, unphosphorylated RAF kinase proceeds to phosphorylated RAF kinase via a process catalyzed by RAS. Although ATP and ADP are shown as incidental to the phosphorylations on this particular graph, they are involved in the same process as the proteins getting phosphorylated. The small circles on the nodes for RAF and other entity pools represent state variables (in this case, phosphorylation sites).
% Redo the figure with colors
\begin{figure}[h]
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.8]{images/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 macromolecule nodes in this map are adorned with state
- variables (\sect{stateVariable}) representing phosphorylation states. This map uses one type of process node, the process node
- (\sect{process}), and three kind of connecting arc, consumption (\sect{consumption}), production (\sect{production}) and catalysis
- (\sect{catalysis}). Finally, some entity pool nodes have dark bands along their bottoms; these are clone markers (\sect{cloneMarker}) indicating that the same pool nodes appear multiple times in the map.}
+ \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 macromolecule nodes in this map are adorned with state variables (\sect{stateVariable}) representing phosphorylation states. This map uses one type of process node, the process node (\sect{process}), and three kind of connecting arc, consumption (\sect{consumption}), production (\sect{production}) and catalysis (\sect{catalysis}). Finally, some entity pool nodes have dark bands along their bottoms; these are clone markers (\sect{cloneMarker}) indicating that the same pool nodes appear multiple times in the map.}
\label{fig:eg1}
\end{figure}
@@ -37,44 +30,15 @@
\section{SBGN levels and versions}
\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 need a vast language that most newcomers
-would shun as being too complex. Thus, the SBGN community followed an idea
-used in the development of other standards, i.e. 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 need a vast language that most newcomers would shun as being too complex. Thus, the SBGN community followed an idea used in the development of other standards, i.e. stratify language development into levels.
-A \emph{level} of one of the SBGN languages 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. Within \emph{levels},
-\emph{versions} represent small evolution of a language, that may
-involve new glyphs, refined semantics, but no fundamental change of
-the way maps are to be generated and interpreted. In addition new
-versions should be backwards compatible, \ie \PD maps that conform to
-an earlier version of the \PDl within the same level should still be
-valid. This does not apply to a new levels.
+A \emph{level} of one of the SBGN languages 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. Within \emph{levels}, \emph{versions} represent small evolution of a language, that may involve new glyphs, refined semantics, but no fundamental change of the way maps are to be generated and interpreted. In addition new versions should be backwards compatible, \ie \PD maps that conform to an earlier version of the \PDl within the same level should still be valid. This does not apply to a new levels.
-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 or version. In this way, the development
-of SBGN languages is envisioned to proceed in stages, with each higher
-levels adding richness compared to the levels below it.
+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 or version. In this way, the development of SBGN languages is envisioned to proceed in stages, with each higher levels adding richness compared to the levels below it.
\section{How to get more information}
\label{sec:info}
-Normative specification
+The normative description of the language is the technical specification \cite{Moodie2011}. It is available from the SBGN website (\url{http://sbgn.org/}). This website is a portal for all things to the notation. In addition to the specifications, there are examples of maps, FAQs, and informations on part and forthcoming meetings.
-The SBGN website (\url{http://sbgn.org/}) is a portal for all things
-related to SBGN.
-% Description of the website content
-
-SBGN discussion list (sbgn-discuss\@caltech.edu). The easiest and best way to get involved in SBGN
-discussions is to join the mailing list and participate.
-
-SBGN announce list
-
-Face-to-face meetings of the SBGN community are announced on the website as
-well as the mailing list.
+The easiest and best way to get involved in SBGN discussions is to join the sbg...@ca... mailing list. If you only want the announcements of meetings and new specifications, you can join the very low flux mailing list sbg...@li... instead.
Modified: ProcessDiagram/trunk/UserManual/sources/introduction.tex.backup
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/introduction.tex.backup 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sources/introduction.tex.backup 2012-03-05 22:44:30 UTC (rev 817)
@@ -1,4 +1,3 @@
-% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/ProcessDiagram/trunk/sources/introduction.tex $
% =============================================================================
% introduction
@@ -7,62 +6,46 @@
\chapter{Introduction}
%Here put a general but short introduction to the needs of standardizing the representation of pathways.
+With the rise of systems and synthetic biology, the use of graphical representations of pathways and networks to describe biological systems has become pervasive. It was therefore important to use a consistent notation that would allow people to interpret those maps easily and quickly, without the need of extensive legends. Furthermore, activities like synthetic biology, that reconstruct biological systems, need to exchange their descriptions unambiguously, as engineers exchange circuit diagrams.
-The goal of the \textbf{S}ystems \textbf{B}iology \textbf{G}raphical
-\textbf{N}otation (SBGN) is to standardize the graphical/visual
-representation of biochemical and cellular processes. SBGN
-defines comprehensive sets of symbols with precise semantics, together with
-detailed syntactic rules defining their use. It also describes the manner
-in which such graphical information should be interpreted \cite{LeNovere:2009p1}.
+The goal of the Systems Biology Graphical Notation (SBGN) is to standardize the graphical/visual representation of biochemical and cellular processes. SBGN defines comprehensive sets of symbols with precise semantics, together with
+detailed syntactic rules defining their use. It also describes the manner in which such graphical information should be interpreted. SBGN is made up of three different and complementary languages \cite{LeNovere:2009p1}. This document describes the graphical elements composing the \emph{\PDl{}} of SBGN.
-% Brief introduction to the three languages.
+\section{Overview of SBGN \PDs}
+\label{sec:PD-overview}
-This document describes the graphical elements composing the \emph{\PDl{}} of SBGN.
+To quickly describe what SBGN \PDl is about, let's give a brief overview of some of the relevant concepts with the help of an example shown in \fig{eg1}. It is a simple map 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 \PDl by lines with arrows and other decorations. In this particular map, all of the processes happen to be the same: processes catalyzed by biochemical entities. The directions of the arrows indicate the direction of the processes; for example, unphosphorylated RAF kinase proceeds to phosphorylated RAF kinase via a process catalyzed by RAS. Although ATP and ADP are shown as incidental to the phosphorylations on this particular graph, they are involved in the same process as the proteins getting phosphorylated. The small circles on the nodes for RAF and other entity pools represent state variables (in this case, phosphorylation sites).
-% Here put a brief version of the introduction present in the glyph section of the PD specification.
-%
-%\section{Overview}
-%
-%\input{sources/pd-overview.tex}
+% Redo the figure with colors
+\begin{figure}[h]
+ \centering
+ \vspace*{-0.75em}
+ \includegraphics[scale=0.8]{images/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 macromolecule nodes in this map are adorned with state variables (\sect{stateVariable}) representing phosphorylation states. This map uses one type of process node, the process node (\sect{process}), and three kind of connecting arc, consumption (\sect{consumption}), production (\sect{production}) and catalysis (\sect{catalysis}). Finally, some entity pool nodes have dark bands along their bottoms; these are clone markers (\sect{cloneMarker}) indicating that the same pool nodes appear multiple times in the map.}
+ \label{fig:eg1}
+\end{figure}
+The essence of the \PDs is \emph{change}: it shows how different entities in the system process 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 one type of entity is transformed into another is conveyed by a \emph{process node} and arcs between entity pool nodes and process nodes indicate an influence by the entities on the processes. In the case of \fig{eg1}, those arcs describe consumption \sect{consumption}, production \sect{production} and 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 details of this and other aspects of \PD notation are explained in the rest of this chapter.
+
\section{SBGN levels and versions}
\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 need a vast language that most newcomers
-would shun as being too complex. Thus, the SBGN community followed an idea
-used in the development of other standards, i.e. 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 need a vast language that most newcomers would shun as being too complex. Thus, the SBGN community followed an idea used in the development of other standards, i.e. stratify language development into levels.
-A \emph{level} of one of the SBGN languages 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. Within \emph{levels},
-\emph{versions} represent small evolution of a language, that may
-involve new glyphs, refined semantics, but no fundamental change of
-the way maps are to be generated and interpreted. In addition new
-versions should be backwards compatible, \ie \PD maps that conform to
-an earlier version of the \PDl within the same level should still be
-valid. This does not apply to a new levels.
+A \emph{level} of one of the SBGN languages 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. Within \emph{levels}, \emph{versions} represent small evolution of a language, that may involve new glyphs, refined semantics, but no fundamental change of the way maps are to be generated and interpreted. In addition new versions should be backwards compatible, \ie \PD maps that conform to an earlier version of the \PDl within the same level should still be valid. This does not apply to a new levels.
-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 or version. In this way, the development
-of SBGN languages is envisioned to proceed in stages, with each higher
-levels adding richness compared to the levels below it.
+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 or version. In this way, the development of SBGN languages is envisioned to proceed in stages, with each higher levels adding richness compared to the levels below it.
\section{How to get more information}
\label{sec:info}
-% Normative specification
+Normative specification
The SBGN website (\url{http://sbgn.org/}) is a portal for all things
related to SBGN.
% Description of the website content
-SBGN discussion list (\mailto{sbg...@ca...}). The easiest and best way to get involved in SBGN
+SBGN discussion list (sbgn-discuss\@caltech.edu). The easiest and best way to get involved in SBGN
discussions is to join the mailing list and participate.
SBGN announce list
Modified: ProcessDiagram/trunk/UserManual/sources/macromolecule.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/macromolecule.tex 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sources/macromolecule.tex 2012-03-05 22:44:30 UTC (rev 817)
@@ -3,31 +3,12 @@
\subsection{Glyph: \glyph{Macromolecule}}
\label{sec:macromolecule}
-Many biological processes involve \emph{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, \SBGNPDLone 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 map is then clarified using its label and decorations, as will become clear below. (Future levels of SBGN may subclass the \glyph{macromolecule} and introduce different glyphs to differentiate between types of macromolecules.)
+Many biological processes involve \emph{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, \SBGNPDLone 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 map is then clarified using its label and decorations, as will become clear below. A \glyph{macromolecule} is represented by a rectangular container with rounded corners, as illustrated in \fig{macromolecule}.
-\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 variables.
-
-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})
-
-\end{glyphDescription}
-
\begin{figure}[H]
\centering
- \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.}
+ \includegraphics[width = 1.25in]{images/macromolecule-plain}
+ \caption{The \PD glyph for \glyph{macromolecule}.}
\label{fig:macromolecule}
\end{figure}
Modified: ProcessDiagram/trunk/UserManual/sources/perturbing_agent.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/perturbing_agent.tex 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sources/perturbing_agent.tex 2012-03-05 22:44:30 UTC (rev 817)
@@ -8,28 +8,9 @@
pulse or a change in temperature; they can also be more complex and not
well-defined phenomena, for instance the outcome of a biological process, an experimental
setup, or a mutation. For these situations, SBGN provides the
-\glyph{perturbing agent} glyph. It is an EPN, and represents the amount to perturbing agent applied to a process.
-
-\begin{glyphDescription}
-
-\glyphSboTerm SBO:0000405 ! perturbing agent
-
-\glyphContainer A \glyph{perturbing agent} is represented by a modified hexagon
+\glyph{perturbing agent} glyph. It is an EPN, and represents the amount to perturbing agent applied to a process. A \glyph{perturbing agent} is represented by a modified hexagon
having two opposite concave faces, as illustrated in \fig{perturbing agent}.
-\glyphLabel A \glyph{perturbing agent} 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
-\glyph{perturbing agent} container. The label may spill outside of the container.
-
-\glyphAux A \glyph{perturbing agent} may carry a \glyph{clone marker}
-(\sect{cloneMarker}).
-
-A \glyph{perturbing agent} can optionally carry one or more \glyph{units of information} (\sect{unitInfo}). A controlled vocaulary is available to describing the physical characteristic of the perturbing agent (see \sect{physical-characteristics-cv}).
-
-\end{glyphDescription}
-
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/perturbing_agent}
Modified: ProcessDiagram/trunk/UserManual/sources/simpleChemical.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/simpleChemical.tex 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sources/simpleChemical.tex 2012-03-05 22:44:30 UTC (rev 817)
@@ -1,33 +1,13 @@
-% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/ProcessDiagram/tags/L1V1.3Full/sources/simpleChemical.tex $
\subsection{Glyph: \glyph{Simple chemical}}
\label{sec:simpleChemical}
-A simple chemical in SBGN is defined as the opposite of a macromolecule (\sect{macromolecule}): it is a chemical compound that is \emph{not} formed by the covalent linking of pseudo-identical residues. Examples of simple chemicals are an atom, a monoatomic ion, a salt, a radical, a solid metal, a crystal, etc.
+In SBGN \PDs, a simple chemical is defined as the opposite of a macromolecule (\sect{macromolecule}): it is a chemical compound that is \emph{not} formed by the covalent linking of pseudo-identical residues. Examples of simple chemicals are an atom, a monoatomic ion, a salt, a radical, a solid metal, a crystal, etc. A \glyph{simple chemical} is represented by a circular
+container, as depicted in \fig{simpleChemical}. To avoid confusion with the Unspecified Entity (\ref{sec:unspecifiedEntity}), this glyph must remain a circle and cannot be deformed into an eclipse.
-\begin{glyphDescription}
-
-\glyphSboTerm SBO:0000247 ! simple chemical
-
-\glyphContainer A \glyph{simple chemical} is represented by a circular
-container, as depicted in \fig{simpleChemical}. To avoid confusion
-with the Unspecified Entity (\ref{sec:unspecifiedEntity}), this glyph
-must remain a circle and cannot be deformed into an eclipse.
-
-\glyphLabel The identification of the \glyph{simple chemical} 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 center of the circular container. The label is permitted to spill outside the container.
-
-\glyphAux A \glyph{simple chemical} may be decorated with one or more \glyph{units of information} (\sect{unitInfo}). A particular \glyph{unit of information} describes the material type. A \glyph{simple chemical} may also carry a \glyph{clone marker} (\sect{cloneMarker}).
-
-\end{glyphDescription}
-
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/simpleChemical}
\caption{The \PD glyph for \glyph{simple chemical}.}
\label{fig:simpleChemical}
\end{figure}
-
-% The following is for [X]Emacs users. Please leave in place.
-% Local Variables:
-% TeX-master: "../sbgn_PD-level1"
-% End:
Modified: ProcessDiagram/trunk/UserManual/sources/sourceSink.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/sourceSink.tex 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sources/sourceSink.tex 2012-03-05 22:44:30 UTC (rev 817)
@@ -16,42 +16,18 @@
(respectively, output) into (resp. from) a compartment without explicitly
representing a transport process from a source (resp. to a target).
-For these and other situations, SBGN defines two glyphs that use the same symbol for explicitly
-representing the involvement of an unspecified source or sink. The symbol
+For these and other situations, SBGN defines a glyph for explicitly
+representing the involvement of an unspecified source or sink. A \glyph{source} or \glyph{sink} is represented by the mathematical symbol for ``empty
+set'', that is, a circle crossed by a bar linking the upper-right and
+lower-left corners of an invisible square drawn around the circle ($\emptyset$).
+\fig{sourceSink} illustrates this. The symbol should be linked to one
+and only one edge in a map. The symbol
used in SBGN is borrowed from the mathematical symbol for ``empty set'',
but it is important to note that it does not actually represent a true
absence of everything or a physical void---it represents the absence of the
corresponding structures in the model, that is, the fact that these sources
-or sinks are conceptually outside the scope of the map. The reason that we
-regard the \glyph{Source} and \glyph{Sink} as different glyphs is that they have different
-syntax and semantics (the former only connects to a \glyph{Consumption} arc and the latter
-a \glyph{Production} arc). This is mainly an issue for software tools and those mapping to
-and from SBGN from other notations of exchange formats.
+or sinks are conceptually outside the scope of the map.
-A frequently asked question is, why bother having an explicit symbol at
-all? The reason is that one cannot simply use an arc that does not
-terminate on a node, because the dangling end could be mistaken to be
-pointing to another node in the map. This is specially true if the
-map is rescaled, causing the spacing of elements in the map to
-change. The availability and use of an explicit symbol for sources and
-sinks is critical.
-
-\begin{glyphDescription}
-
-\glyphSboTerm SBO:0000291 ! empty set
-
-\glyphContainer A \glyph{source} or \glyph{sink} is represented by the mathematical symbol for ``empty
-set'', that is, a circle crossed by a bar linking the upper-right and
-lower-left corners of an invisible square drawn around the circle ($\emptyset$).
-\fig{sourceSink} illustrates this. The symbol should be linked to one
-and only one edge in a map.
-
-\glyphLabel A \glyph{source} or \glyph{sink} does not carry any labels.
-
-\glyphAux A \glyph{source} or \glyph{sink} does not carry any auxiliary items.
-
-\end{glyphDescription}
-
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/sourceSink}
@@ -60,11 +36,3 @@
\end{figure}
-
-
-
-
-% The following is for [X]Emacs users. Please leave in place.
-% Local Variables:
-% TeX-master: "../sbgn_PD-level1"
-% End:
Modified: ProcessDiagram/trunk/UserManual/sources/stateVariable.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/stateVariable.tex 2012-01-31 15:35:18 UTC (rev 816)
+++ ProcessDiagram/trunk/UserManual/sources/stateVariable.tex 2012-03-05 22:44:30 UTC (rev 817)
@@ -3,22 +3,10 @@
\subsection{Glyph: \glyph{State variable}}
\label{sec:stateVariable}
-Many biological entities such as molecules can exist in different \emph{states}, meaning different physical or informational configurations. These states can arise for a variety of reasons. For example, macromolecules can be subject to post-synthesis modifications, wherein residues of the macromolecules (amino acids, nucleosides, or glucid residues) are modified through covalent linkage to other chemicals. Other examples of states are alternative conformations as in the closed/open/desensitized conformations of a transmembrane channel, and the active/inactive forms of an enzyme.
+Many biological entities, such as molecules, can exist in different \emph{states}, meaning different physical or informational configurations. These states can arise for a variety of reasons. For example, macromolecules can be subject to post-synthesis modifications, wherein residues of the macromolecules (amino acids, nucleosides, or glucid residues) are modified through covalent linkage to other chemicals. Other examples of states are alternative conformations as in the closed/open/desensitized conformations of a transmembrane channel, and the active/inactive forms of an enzyme.
-SBGN provides a means of associating one or more \glyph{state variables} with an entity; each such variable can be used to represent a dimension along which the state of the overall entity can vary. When an entity can ex...
[truncated message content] |
|
From: <le...@us...> - 2012-01-31 15:35:32
|
Revision: 816
http://sbgn.svn.sourceforge.net/sbgn/?rev=816&view=rev
Author: lenov
Date: 2012-01-31 15:35:18 +0000 (Tue, 31 Jan 2012)
Log Message:
-----------
Added Paths:
-----------
ProcessDiagram/trunk/UserManual/
ProcessDiagram/trunk/UserManual/Makefile
ProcessDiagram/trunk/UserManual/README.txt
ProcessDiagram/trunk/UserManual/images/
ProcessDiagram/trunk/UserManual/images/MAPK-only.ai
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ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex
ProcessDiagram/trunk/UserManual/sources/
ProcessDiagram/trunk/UserManual/sources/CVs.tex
ProcessDiagram/trunk/UserManual/sources/cloneMarker.tex
ProcessDiagram/trunk/UserManual/sources/complex-epn-eg.tex
ProcessDiagram/trunk/UserManual/sources/complex.tex
ProcessDiagram/trunk/UserManual/sources/front-page.tex
ProcessDiagram/trunk/UserManual/sources/genetic.tex
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ProcessDiagram/trunk/UserManual/sources/introduction.tex
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ProcessDiagram/trunk/UserManual/sources/pd-overview.log
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ProcessDiagram/trunk/UserManual/sources/perturbing_agent.tex
ProcessDiagram/trunk/UserManual/sources/simpleChemical.tex
ProcessDiagram/trunk/UserManual/sources/sourceSink.tex
ProcessDiagram/trunk/UserManual/sources/stateVariable.tex
ProcessDiagram/trunk/UserManual/sources/symbols.aux
ProcessDiagram/trunk/UserManual/sources/symbols.tex
ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup
ProcessDiagram/trunk/UserManual/sources/tag.tex
ProcessDiagram/trunk/UserManual/sources/unitInformation.tex
ProcessDiagram/trunk/UserManual/sources/unspecified.tex
Added: ProcessDiagram/trunk/UserManual/Makefile
===================================================================
--- ProcessDiagram/trunk/UserManual/Makefile (rev 0)
+++ ProcessDiagram/trunk/UserManual/Makefile 2012-01-31 15:35:18 UTC (rev 816)
@@ -0,0 +1,31 @@
+.PHONY: clean, dist_clean
+
+MAIN = sbgn_PD-level1-user
+
+LATEX = pdflatex
+BIBTEX = bibtex
+
+all default: images examples
+ $(MAKE) -C examples
+ $(MAKE) -C images
+ $(LATEX) $(MAIN).tex
+ $(LATEX) $(MAIN).tex
+ $(BIBTEX) $(MAIN)
+ $(LATEX) $(MAIN).tex
+
+clean:
+ $(MAKE) -C images clean
+ $(MAKE) -C examples clean
+ -rm -f *.bbl
+ -rm -f *.blg
+ -rm -f *.out
+ -rm -f *.dvi
+ -rm -f *.toc
+ -rm -f *.aux
+ -rm -f *.log
+ -rm -f *.tmp
+ -rm -f *.prv
+ -rm -f sbgn_PD-level1-user.fdb_latexmk
+
+dist_clean: clean
+ -rm -f *.pdf
Added: ProcessDiagram/trunk/UserManual/README.txt
===================================================================
--- ProcessDiagram/trunk/UserManual/README.txt (rev 0)
+++ ProcessDiagram/trunk/UserManual/README.txt 2012-01-31 15:35:18 UTC (rev 816)
@@ -0,0 +1,13 @@
+
+ User manual for the
+
+ ----------------------------------------
+ Systems Biology Graphical Notation (SBGN)
+ Process Diagrams Level 1.3
+ ----------------------------------------
+
+ For more information about SBGN, visit:
+ http://sbgn.org
+
+ Please join the sbgn-discuss mailing list by visiting
+ http://sbgn.org/Forums
Added: ProcessDiagram/trunk/UserManual/images/MAPK-only.ai
===================================================================
--- ProcessDiagram/trunk/UserManual/images/MAPK-only.ai (rev 0)
+++ ProcessDiagram/trunk/UserManual/images/MAPK-only.ai 2012-01-31 15:35:18 UTC (rev 816)
@@ -0,0 +1,1616 @@
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|
From: <stu...@us...> - 2011-11-16 20:00:44
|
Revision: 815
http://sbgn.svn.sourceforge.net/sbgn/?rev=815&view=rev
Author: stumoodie
Date: 2011-11-16 20:00:35 +0000 (Wed, 16 Nov 2011)
Log Message:
-----------
More revisions. Still to alphabeticise, but otherwise ready for review.
Modified Paths:
--------------
ProcessDiagram/trunk/examples/submap-dissociated.svg
ProcessDiagram/trunk/examples/submap-folded.svg
ProcessDiagram/trunk/examples/submap-unfolded.svg
ProcessDiagram/trunk/images/cloningrules-eg.svg
ProcessDiagram/trunk/images/entitytypeuml.svg
ProcessDiagram/trunk/images/epnuml.svg
ProcessDiagram/trunk/images/exampleuml.svg
ProcessDiagram/trunk/images/sbgn_model_revised/128173
ProcessDiagram/trunk/images/sbgn_model_revised/134957.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/45.session
ProcessDiagram/trunk/images/uml_example/128173.diagram
ProcessDiagram/trunk/images/uml_example/45.session
ProcessDiagram/trunk/images/uml_example/uml_example.prj
ProcessDiagram/trunk/sbgn_PD-level1.pdf
ProcessDiagram/trunk/sbgn_PD-level1.tex
ProcessDiagram/trunk/sources/glyphs.tex
ProcessDiagram/trunk/sources/latex-macros.tex
ProcessDiagram/trunk/sources/latex-style.tex
Property Changed:
----------------
ProcessDiagram/trunk/examples/
Property changes on: ProcessDiagram/trunk/examples
___________________________________________________________________
Added: svn:ignore
+ *.pdf
Modified: ProcessDiagram/trunk/examples/submap-dissociated.svg
===================================================================
--- ProcessDiagram/trunk/examples/submap-dissociated.svg 2011-11-15 21:48:24 UTC (rev 814)
+++ ProcessDiagram/trunk/examples/submap-dissociated.svg 2011-11-16 20:00:35 UTC (rev 815)
@@ -58,15 +58,15 @@
objecttolerance="10"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
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inkscape:cy="196.93646"
inkscape:document-units="px"
inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
- inkscape:window-width="1341"
- inkscape:window-height="746"
+ inkscape:window-width="1827"
+ inkscape:window-height="1006"
inkscape:window-x="1598"
inkscape:window-y="106"
showguides="true"
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x="902.13672"
sodipodi:role="line">4</tspan></text>
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y="255.07971"
style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
id="tspan2813">GPI</tspan></text>
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Modified: ProcessDiagram/trunk/examples/submap-folded.svg
===================================================================
--- ProcessDiagram/trunk/examples/submap-folded.svg 2011-11-15 21:48:24 UTC (rev 814)
+++ ProcessDiagram/trunk/examples/submap-folded.svg 2011-11-16 20:00:35 UTC (rev 815)
@@ -58,17 +58,17 @@
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+ inkscape:cy="138.81931"
inkscape:document-units="px"
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width="1052.3622px"
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- inkscape:window-height="746"
- inkscape:window-x="1549"
- inkscape:window-y="214"
+ inkscape:window-width="1952"
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style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
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xml:space="preserve"
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Modified: ProcessDiagram/trunk/examples/submap-unfolded.svg
===================================================================
--- ProcessDiagram/trunk/examples/submap-unfolded.svg 2011-11-15 21:48:24 UTC (rev 814)
+++ ProcessDiagram/trunk/examples/submap-unfolded.svg 2011-11-16 20:00:35 UTC (rev 815)
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inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
- inkscape:zoom="0.59178761"
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+ inkscape:zoom="1.2529253"
+ inkscape:cx="-207.12962"
inkscape:cy="193.1699"
inkscape:document-units="px"
inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
- inkscape:window-width="1341"
- inkscape:window-height="1022"
+ inkscape:window-width="2169"
+ inkscape:window-height="1249"
inkscape:window-x="1544"
inkscape:window-y="58"
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@@ -105,15 +105,6 @@
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id="tspan3253">mitom</tspan></text>
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Modified: ProcessDiagram/trunk/images/cloningrules-eg.svg
===================================================================
--- ProcessDiagram/trunk/images/cloningrules-eg.svg 2011-11-15 21:48:24 UTC (rev 814)
+++ ProcessDiagram/trunk/images/cloningrules-eg.svg 2011-11-16 20:00:35 UTC (rev 815)
@@ -79,11 +79,11 @@
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inkscape:pageshadow="2"
- inkscape:zoom="0.77041077"
- inkscape:cx="311.20242"
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+ inkscape:zoom="0.91503662"
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inkscape:window-width="1744"
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inkscape:snap-intersection-paths="true"
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+ inkscape:object-nodes="true"
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+ inkscape:connector-curvature="0"
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+ d="m 138.93557,312.86638 107.7535,-58.9482"
style="fill:none;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
- d="m 243.80952,253.70672 87.84315,0"
+ sodipodi:nodetypes="cc" />
+ <path
+ style="fill:none;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ d="m 246.68907,253.91818 85,0"
id="path3894"
inkscape:connector-curvature="0"
sodipodi:nodetypes="cc" />
<path
style="fill:none;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
- d="m 135.35014,202.61428 110.2521,51.09244"
+ d="m 135.35014,202.61428 111.33893,51.3039"
id="path3898"
- inkscape:connector-curvature="0" />
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="cc" />
<path
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- <path
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@@ -479,7 +484,7 @@
x="476.86273"
y="288.6647"
style="font-size:20px" /></flowRegion><flowPara
- id="flowPara4447"></flowPara></flowRoot> <flowRoot
+ id="flowPara4447" /></flowRoot> <flowRoot
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@@ -570,7 +575,7 @@
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sodipodi:ry="20.5"
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sodipodi:ry="20.5"
sodipodi:rx="20.5"
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Modified: ProcessDiagram/trunk/images/entitytypeuml.svg
===================================================================
--- ProcessDiagram/trunk/images/entitytypeuml.svg 2011-11-15 21:48:24 UTC (rev 814)
+++ ProcessDiagram/trunk/images/entitytypeuml.svg 2011-11-16 20:00:35 UTC (rev 815)
@@ -3,13 +3,13 @@
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<svg width="968" height="427" version="1.1" xmlns="http://www.w3.org/2000/svg">
<g>
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="834" y="305" width="3" height="47" />
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- <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="660" y="301" width="174" height="48" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="747" y="318">StateVariableDefinition</text>
- <line stroke="black" stroke-opacity="1" x1="660" y1="321" x2="834" y2="321" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="664" y="338">name : string</text>
- <line stroke="black" stroke-opacity="1" x1="660" y1="341" x2="834" y2="341" />
+ <rect fill="#808080" stroke="none" stroke-opacity="1" x="534" y="119" width="3" height="47" />
+ <rect fill="#808080" stroke="none" stroke-opacity="1" x="420" y="163" width="117" height="3" />
+ <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="416" y="115" width="118" height="48" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" font-style="italic" text-anchor="middle" x="475" y="132">EntityPoolNode</text>
+ <line stroke="black" stroke-opacity="1" x1="416" y1="135" x2="534" y2="135" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="420" y="152">cardinality : int</text>
+ <line stroke="black" stroke-opacity="1" x1="416" y1="155" x2="534" y2="155" />
</g>
<g>
<rect fill="#808080" stroke="none" stroke-opacity="1" x="798" y="110" width="3" height="65" />
@@ -22,17 +22,22 @@
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</g>
<g>
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="534" y="119" width="3" height="47" />
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- <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="416" y="115" width="118" height="48" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" font-style="italic" text-anchor="middle" x="475" y="132">EntityPoolNode</text>
- <line stroke="black" stroke-opacity="1" x1="416" y1="135" x2="534" y2="135" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="420" y="152">cardinality : int</text>
- <line stroke="black" stroke-opacity="1" x1="416" y1="155" x2="534" y2="155" />
+ <rect fill="#808080" stroke="none" stroke-opacity="1" x="834" y="305" width="3" height="47" />
+ <rect fill="#808080" stroke="none" stroke-opacity="1" x="664" y="349" width="173" height="3" />
+ <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="660" y="301" width="174" height="48" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="747" y="318">StateVariableDefinition</text>
+ <line stroke="black" stroke-opacity="1" x1="660" y1="321" x2="834" y2="321" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="664" y="338">name : string</text>
+ <line stroke="black" stroke-opacity="1" x1="660" y1="341" x2="834" y2="341" />
</g>
<g>
- <line stroke="black" stroke-opacity="1" x1="701" y1="141" x2="695" y2="135" />
- <line stroke="black" stroke-opacity="1" x1="701" y1="141" x2="695" y2="147" />
+ <line stroke="black" stroke-opacity="1" x1="893" y1="140" x2="893" y2="324" />
+</g>
+<g>
+ <line stroke="black" stroke-opacity="1" x1="802" y1="140" x2="893" y2="140" />
+ <polygon fill="#000000" stroke="black" stroke-opacity="1" points="802,140 808,134 814,140 808,146" />
+</g>
+<g>
<line stroke="black" stroke-opacity="1" x1="538" y1="141" x2="701" y2="141" />
<polygon fill="#ffffff" stroke="black" stroke-opacity="1" points="538,141 544,135 550,141 544,147" />
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@@ -40,13 +45,14 @@
<line stroke="black" stroke-opacity="1" x1="893" y1="324" x2="838" y2="324" />
</g>
<g>
- <line stroke="black" stroke-opacity="1" x1="893" y1="140" x2="893" y2="324" />
+ <rect fill="#808080" stroke="none" stroke-opacity="1" x="157" y="273" width="3" height="35" />
+ <rect fill="#808080" stroke="none" stroke-opacity="1" x="59" y="305" width="101" height="3" />
+ <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="55" y="269" width="102" height="36" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" font-style="italic" text-anchor="middle" x="106" y="286">StatelessEPN</text>
+ <line stroke="black" stroke-opacity="1" x1="55" y1="289" x2="157" y2="289" />
+ <line stroke="black" stroke-opacity="1" x1="55" y1="297" x2="157" y2="297" />
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<g>
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<rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="316" y="270" width="92" height="36" />
@@ -55,36 +61,28 @@
<line stroke="black" stroke-opacity="1" x1="316" y1="298" x2="408" y2="298" />
</g>
<g>
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="157" y="273" width="3" height="35" />
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- <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="55" y="269" width="102" height="36" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" font-style="italic" text-anchor="middle" x="106" y="286">StatelessEPN</text>
- <line stroke="black" stroke-opacity="1" x1="55" y1="289" x2="157" y2="289" />
- <line stroke="black" stroke-opacity="1" x1="55" y1="297" x2="157" y2="297" />
+ <line stroke="black" stroke-opacity="1" x1="107" y1="218" x2="477" y2="218" />
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- <line stroke="black" stroke-opacity="1" x1="471" y1="173" x2="483" y2="173" />
+ <line stroke="black" stroke-opacity="1" x1="363" y1="269" x2="363" y2="218" />
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<g>
<line stroke="black" stroke-opacity="1" x1="363" y1="218" x2="477" y2="218" />
</g>
<g>
- <line stroke="black" stroke-opacity="1" x1="363" y1="269" x2="363" y2="218" />
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<line stroke="black" stroke-opacity="1" x1="477" y1="218" x2="477" y2="173" />
<line stroke="black" stroke-opacity="1" x1="477" y1="167" x2="471" y2="173" />
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<line stroke="black" stroke-opacity="1" x1="471" y1="173" x2="483" y2="173" />
</g>
<g>
- <line stroke="black" stroke-opacity="1" x1="107" y1="218" x2="477" y2="218" />
+ <line stroke="black" stroke-opacity="1" x1="107" y1="268" x2="107" y2="218" />
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<g>
- <line stroke="black" stroke-opacity="1" x1="107" y1="268" x2="107" y2="218" />
+ <line stroke="black" stroke-opacity="1" x1="477" y1="218" x2="477" y2="173" />
+ <line stroke="black" stroke-opacity="1" x1="477" y1="167" x2="471" y2="173" />
+ <line stroke="black" stroke-opacity="1" x1="477" y1="167" x2="483" y2="173" />
+ <line stroke="black" stroke-opacity="1" x1="471" y1="173" x2="483" y2="173" />
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<g>
<rect fill="#808080" stroke="none" stroke-opacity="1" x="413" y="367" width="3" height="47" />
@@ -96,82 +94,85 @@
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<g>
- <line stroke="black" stroke-opacity="1" x1="659" y1="326" x2="653" y2="320" />
- <line stroke="black" stroke-opacity="1" x1="659" y1="326" x2="653" y2="332" />
- <line stroke="black" stroke-opacity="1" x1="538" y1="326" x2="659" y2="326" />
+ <line stroke="black" stroke-opacity="1" x1="315" y1="290" x2="241" y2="290" />
+ <polygon fill="#000000" stroke="black" stroke-opacity="1" points="315,290 309,296 303,290 309,284" />
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<g>
- <line stroke="black" stroke-opacity="1" x1="538" y1="389" x2="538" y2="326" />
+ <line stroke="black" stroke-opacity="1" x1="241" y1="290" x2="241" y2="389" />
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<g>
+ <line stroke="black" stroke-opacity="1" x1="241" y1="389" x2="306" y2="389" />
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+<g>
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<polygon fill="#ffffff" stroke="black" stroke-opacity="1" points="417,389 423,383 429,389 423,395" />
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<g>
- <line stroke="black" stroke-opacity="1" x1="241" y1="389" x2="306" y2="389" />
+ <line stroke="black" stroke-opacity="1" x1="538" y1="389" x2="538" y2="326" />
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<g>
- <line stroke="black" stroke-opacity="1" x1="241" y1="290" x2="241" y2="389" />
+ <line stroke="black" stroke-opacity="1" x1="659" y1="326" x2="653" y2="320" />
+ <line stroke="black" stroke-opacity="1" x1="659" y1="326" x2="653" y2="332" />
+ <line stroke="black" stroke-opacity="1" x1="538" y1="326" x2="659" y2="326" />
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<g>
- <line stroke="black" stroke-opacity="1" x1="315" y1="290" x2="241" y2="290" />
- <polygon fill="#000000" stroke="black" stroke-opacity="1" points="315,290 309,296 303,290 309,284" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="848" y="347">*</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="427" y="412">1..*</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="812" y="134">owning_entity_type</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="641" y="349">1</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="371" y="135">epns</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="589" y="320">definition</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="182" y="135">owning_compartment</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="548" y="164">1..*</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="399" y="164">*</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="683" y="164">1</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="182" y="164">0..1</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="615" y="135">entity_type</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="254" y="383">states</text>
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<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="297" y="313">1</text>
-</g>
-<g>
<text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="223" y="284">owning_epn</text>
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<g>
<text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="290" y="412">*</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="254" y="383">states</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="297" y="313">1</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="182" y="164">0..1</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="615" y="135">entity_type</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="399" y="164">*</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="548" y="135">pools</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="182" y="135">owning_compartment</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="683" y="164">1</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="371" y="135">epns</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="548" y="164">1..*</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="812" y="163">1</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="589" y="320">definition</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="812" y="134">owning_entity_type</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="641" y="349">1</text>
</g>
<g>
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="848" y="347">*</text>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="427" y="412">1..*</text>
</g>
<g>
<text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="848" y="318">state_definitions</text>
</g>
<g>
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="812" y="163">1</text>
+</g>
+<g>
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<rect fill="#808080" stroke="none" stroke-opacity="1" x="62" y="172" width="109" height="3" />
<rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="58" y="106" width="110" height="66" />
Modified: ProcessDiagram/trunk/images/epnuml.svg
===================================================================
--- ProcessDiagram/trunk/images/epnuml.svg 2011-11-15 21:48:24 UTC (rev 814)
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[truncated message content] |
|
From: <stu...@us...> - 2011-11-15 21:48:36
|
Revision: 814
http://sbgn.svn.sourceforge.net/sbgn/?rev=814&view=rev
Author: stumoodie
Date: 2011-11-15 21:48:24 +0000 (Tue, 15 Nov 2011)
Log Message:
-----------
Pretty much complete first draft.
Modified Paths:
--------------
ProcessDiagram/trunk/examples/macromolecule-CaMKII.svg
ProcessDiagram/trunk/images/attributevalueuml.svg
ProcessDiagram/trunk/images/auxiliaryunituml.svg
ProcessDiagram/trunk/images/compartmentuml.svg
ProcessDiagram/trunk/images/complexsubunituml.svg
ProcessDiagram/trunk/images/crossreferenceuml.svg
ProcessDiagram/trunk/images/epnuml.svg
ProcessDiagram/trunk/images/equivalencearcuml.svg
ProcessDiagram/trunk/images/nonstoichprocessuml.svg
ProcessDiagram/trunk/images/process.svg
ProcessDiagram/trunk/images/processumlview.svg
ProcessDiagram/trunk/images/refcard.svg
ProcessDiagram/trunk/images/sbgn_model_revised/128173
ProcessDiagram/trunk/images/sbgn_model_revised/128173.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/134829.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/134957.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/135085.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/141613.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/141869.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/148397.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/154925.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/161453.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168109.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168237.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168365.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/175149.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/181677.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/188205.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/194861.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/201389.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/208301.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/208429.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/45.session
ProcessDiagram/trunk/images/sbgnumloverview.svg
ProcessDiagram/trunk/images/simpleChemical.svg
ProcessDiagram/trunk/images/simpleChemicalMultimer.svg
ProcessDiagram/trunk/images/stateVariable.svg
ProcessDiagram/trunk/images/statefulepnuml.svg
ProcessDiagram/trunk/images/statelessepnuml.svg
ProcessDiagram/trunk/images/statevariableviewuml.svg
ProcessDiagram/trunk/images/submapnodeuml.svg
ProcessDiagram/trunk/images/unitInformation.svg
ProcessDiagram/trunk/sbgn_PD-level1.bib
ProcessDiagram/trunk/sbgn_PD-level1.pdf
ProcessDiagram/trunk/sources/concepts.tex
ProcessDiagram/trunk/sources/glyphs.tex
ProcessDiagram/trunk/sources/introduction.tex
ProcessDiagram/trunk/sources/latex-macros.tex
ProcessDiagram/trunk/sources/latex-style.tex
ProcessDiagram/trunk/sources/revision_history.tex
Added Paths:
-----------
ProcessDiagram/trunk/images/cloningrules-eg.svg
ProcessDiagram/trunk/images/entitytypeuml.svg
ProcessDiagram/trunk/images/exampleuml.svg
ProcessDiagram/trunk/images/reversible.svg
ProcessDiagram/trunk/images/sbgn_model_revised/214957.diagram
ProcessDiagram/trunk/images/sbgnnodearcuml.svg
ProcessDiagram/trunk/images/submapglyph.svg
ProcessDiagram/trunk/images/uml_example/
ProcessDiagram/trunk/images/uml_example/128173.diagram
ProcessDiagram/trunk/images/uml_example/45.session
ProcessDiagram/trunk/images/uml_example/cpp_includes
ProcessDiagram/trunk/images/uml_example/generation_settings
ProcessDiagram/trunk/images/uml_example/idl_includes
ProcessDiagram/trunk/images/uml_example/java_imports
ProcessDiagram/trunk/images/uml_example/python_imports
ProcessDiagram/trunk/images/uml_example/stereotypes
ProcessDiagram/trunk/images/uml_example/tools
ProcessDiagram/trunk/images/uml_example/uml_example.prj
Removed Paths:
-------------
ProcessDiagram/trunk/images/simpleChemical.ai
Modified: ProcessDiagram/trunk/examples/macromolecule-CaMKII.svg
===================================================================
--- ProcessDiagram/trunk/examples/macromolecule-CaMKII.svg 2011-11-09 20:32:54 UTC (rev 813)
+++ ProcessDiagram/trunk/examples/macromolecule-CaMKII.svg 2011-11-15 21:48:24 UTC (rev 814)
@@ -108,9 +108,9 @@
objecttolerance="10"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
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@@ -189,66 +189,24 @@
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Modified: ProcessDiagram/trunk/images/attributevalueuml.svg
===================================================================
--- ProcessDiagram/trunk/images/attributevalueuml.svg 2011-11-09 20:32:54 UTC (rev 813)
+++ ProcessDiagram/trunk/images/attributevalueuml.svg 2011-11-15 21:48:24 UTC (rev 814)
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- <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="833" y="264">name : string</text>
- <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="833" y="280">cardinality : int</text>
- <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="833" y="296">natures : cv</text>
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+ <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" font-weight="bold" font-style="italic" text-anchor="middle" x="797" y="263">EntityPoolNode</text>
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- <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="437" y="113">natures : cv</text>
- <line stroke="black" stroke-opacity="1" x1="434" y1="115" x2="537" y2="115" />
+ <line stroke="black" stroke-opacity="1" x1="429" y1="270" x2="423" y2="264" />
+ <line stroke="black" stroke-opacity="1" x1="429" y1="270" x2="423" y2="276" />
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+ <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="433" y="114" width="103" height="57" />
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+ <line stroke="black" stroke-opacity="1" x1="433" y1="131" x2="536" y2="131" />
+ <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="436" y="146">name : string</text>
+ <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="436" y="162">natures : cv</text>
+ <line stroke="black" stroke-opacity="1" x1="433" y1="164" x2="536" y2="164" />
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<line stroke="black" stroke-opacity="1" x1="486" y1="239" x2="480" y2="233" />
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- <polygon fill="#000000" stroke="black" stroke-opacity="1" points="486,125 492,131 486,137 480,131" />
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<g>
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<text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="552" y="290">*</text>
</g>
<g>
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+ <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="721" y="290">1</text>
</g>
<g>
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+ <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="43" y="264">children</text>
</g>
<g>
- <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="810" y="290">1</text>
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</g>
<g>
- <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="43" y="264">children</text>
+ <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="99" y="224">1</text>
</g>
<g>
- <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="86" y="290">*</text>
+ <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="295" y="264">displayed_attributes</text>
</g>
<g>
- <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="95" y="225">1</text>
+ <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="413" y="291">*</text>
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<g>
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</g>
<g>
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+ <text font-family="Helvetica" font-size="14" fill="#000000" xml:space="preserve" x="470" y="233">*</text>
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Modified: ProcessDiagram/trunk/images/auxiliaryunituml.svg
===================================================================
--- ProcessDiagram/trunk/images/auxiliaryunituml.svg 2011-11-09 20:32:54 UTC (rev 813)
+++ ProcessDiagram/trunk/images/auxiliaryunituml.svg 2011-11-15 21:48:24 UTC (rev 814)
@@ -3,15 +3,6 @@
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<g>
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<line stroke="black" stroke-opacity="1" x1="994" y1="291" x2="1092" y2="291" />
</g>
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+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="535" y="423">annotation_text : string</text>
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+ <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="563" y="82" width="98" height="36" />
<text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" font-style="italic" text-anchor="middle" x="612" y="99">AuxiliaryUnit</text>
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<line stroke="black" stroke-opacity="1" x1="563" y1="110" x2="661" y2="110" />
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<g>
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<text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="892" y="280">StateVariable</text>
<line stroke="black" stroke-opacity="1" x1="839" y1="283" x2="945" y2="283" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="843" y="300">name : string</text>
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- <line stroke="black" stroke-opacity="1" x1="839" y1="321" x2="945" y2="321" />
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Added: ProcessDiagram/trunk/images/cloningrules-eg.svg
===================================================================
--- ProcessDiagram/trunk/images/cloningrules-eg.svg (rev 0)
+++ ProcessDiagram/trunk/images/cloningrules-eg.svg 2011-11-15 21:48:24 UTC (rev 814)
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|
From: <stu...@us...> - 2011-11-09 20:33:04
|
Revision: 813
http://sbgn.svn.sourceforge.net/sbgn/?rev=813&view=rev
Author: stumoodie
Date: 2011-11-09 20:32:54 +0000 (Wed, 09 Nov 2011)
Log Message:
-----------
Complete rough draft. Needs more refinement, but most of content there.
Modified Paths:
--------------
ProcessDiagram/trunk/examples/compartment_overlapping.svg
ProcessDiagram/trunk/examples/ex-annotation.svg
ProcessDiagram/trunk/examples/modulation-nAChR.svg
ProcessDiagram/trunk/examples/process-dimerisation.svg
ProcessDiagram/trunk/examples/stoichEx1.svg
ProcessDiagram/trunk/images/annotation.svg
ProcessDiagram/trunk/images/auxiliaryunituml.svg
ProcessDiagram/trunk/images/complexsubunituml.svg
ProcessDiagram/trunk/images/epnuml.svg
ProcessDiagram/trunk/images/glyphauxuml.svg
ProcessDiagram/trunk/images/labeledCloneMarker.svg
ProcessDiagram/trunk/images/logicaloperatoruml.svg
ProcessDiagram/trunk/images/nonstoichprocessuml.svg
ProcessDiagram/trunk/images/sbgn_model_revised/128173
ProcessDiagram/trunk/images/sbgn_model_revised/128173.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/134829.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/134957.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/141869.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/154925.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/161453.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168109.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168237.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168365.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/174893.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/175021.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/181677.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/188205.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/45.session
ProcessDiagram/trunk/images/sbgnumloverview.svg
ProcessDiagram/trunk/images/stoichprocessuml.svg
ProcessDiagram/trunk/images/submapnodeuml.svg
ProcessDiagram/trunk/sbgn_PD-level1.pdf
ProcessDiagram/trunk/sbgn_PD-level1.tex
ProcessDiagram/trunk/sources/front-page.tex
ProcessDiagram/trunk/sources/glyphs.tex
ProcessDiagram/trunk/sources/latex-style.tex
ProcessDiagram/trunk/sources/toc.tex
Added Paths:
-----------
ProcessDiagram/trunk/images/clonemarkeruml.svg
ProcessDiagram/trunk/images/crossreferenceuml.svg
ProcessDiagram/trunk/images/equivalencearcuml.svg
ProcessDiagram/trunk/images/fluxarcuml.svg
ProcessDiagram/trunk/images/logicarcuml.svg
ProcessDiagram/trunk/images/modulationarcuml.svg
ProcessDiagram/trunk/images/sbgn_model_revised/194733.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/194861.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/201389.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/201517.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/201645.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/201773.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/208301.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/208429.diagram
ProcessDiagram/trunk/images/statevariableviewuml.svg
ProcessDiagram/trunk/images/stoichlabellayout.svg
ProcessDiagram/trunk/images/submapterminal.svg
Modified: ProcessDiagram/trunk/examples/compartment_overlapping.svg
===================================================================
--- ProcessDiagram/trunk/examples/compartment_overlapping.svg 2011-11-07 17:37:36 UTC (rev 812)
+++ ProcessDiagram/trunk/examples/compartment_overlapping.svg 2011-11-09 20:32:54 UTC (rev 813)
@@ -32,7 +32,7 @@
objecttolerance="10"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
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inkscape:cy="148.71953"
inkscape:document-units="px"
@@ -169,7 +169,7 @@
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inkscape:connector-curvature="0" />
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+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
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width="82.832512"
height="24.243662"
Modified: ProcessDiagram/trunk/examples/ex-annotation.svg
===================================================================
--- ProcessDiagram/trunk/examples/ex-annotation.svg 2011-11-07 17:37:36 UTC (rev 812)
+++ ProcessDiagram/trunk/examples/ex-annotation.svg 2011-11-09 20:32:54 UTC (rev 813)
@@ -9,11 +9,11 @@
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xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
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sodipodi:version="0.32"
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+ inkscape:version="0.48.2 r9819"
version="1.0"
sodipodi:docname="ex-annotation.svg"
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inkscape:pageshadow="2"
- inkscape:zoom="2.0563262"
- inkscape:cx="777.5276"
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inkscape:document-units="px"
inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
- inkscape:window-width="1321"
- inkscape:window-height="777"
+ inkscape:window-width="2068"
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id="guide2990"
- position="1064"
+ position="483.21875,-534.70593"
orientation="vertical" />
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id="guide3940"
- position="850.64737,697.92153"
+ position="269.86612,163.2156"
orientation="horizontal" />
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id="guide3942"
- position="395.56201,140.05545"
+ position="-185.21924,-394.65048"
orientation="horizontal" />
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id="guide3249"
- position="192.68317,360.94796"
+ position="-388.09808,-173.75797"
orientation="1,0" />
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id="guide3251"
- position="339.19342,419.99604"
+ position="-241.58783,-114.70989"
orientation="1,0" />
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+ position="104.9972,-201.08398"
orientation="1,0" />
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id="guide4660"
- position="712.30988,611.60284"
+ position="131.52863,76.896907"
orientation="1,0" />
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id="guide4662"
- position="781.27984,724.37812"
+ position="200.49859,189.67219"
orientation="1,0" />
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id="guide4664"
- position="764.29819,467.01784"
+ position="183.51694,-67.68809"
orientation="1,0" />
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id="guide4666"
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+ position="-72.50181,190.95088"
orientation="0,1" />
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id="guide3349"
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+ position="-342.36913,-179.97355"
orientation="1,0" />
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id="guide3353"
- position="417.33222,573.60981"
+ position="-163.44903,38.903877"
orientation="-0.70710678,0.70710678" />
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id="guide3355"
- position="833.52534,593.29108"
+ position="252.74409,58.585147"
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- position="216.2136,367.16355"
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- d="M 0,0 L 5,-5 L -12.5,0 L 5,5 L 0,0 z"
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Modified: ProcessDiagram/trunk/examples/modulation-nAChR.svg
===================================================================
--- ProcessDiagram/trunk/examples/modulation-nAChR.svg 2011-11-07 17:37:36 UTC (rev 812)
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Modified: ProcessDiagram/trunk/examples/process-dimerisation.svg
===================================================================
--- ProcessDiagram/trunk/examples/process-dimerisation.svg 2011-11-07 17:37:36 UTC (rev 812)
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sodipodi:rx="58.336308"
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sodipodi:cx="776.55475"
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+ style="fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
sodipodi:type="arc" />
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id="text6200"
y="300.12769"
x="697.41541"
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+ style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;font-family:Bitstream Vera Sans"
xml:space="preserve"><tspan
id="tspan6202"
style="font-size:28px;font-weight:normal;text-align:center;text-anchor:middle"
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sodipodi:role="line">LAC</tspan></text>
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y="263.86426"
- x="568.55597"
+ x="553.90771"
height="26.555647"
width="29.21854"
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+ style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:3;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0" />
<text
sodipodi:linespacing="125%"
id="text3151"
y="285.60651"
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+ x="562.73962"
+ style="font-size:20px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:start;line-height:125%;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;font-family:Arial"
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y="285.60651"
- x="577.21533"
+ x="562.73962"
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sodipodi:role="line">1</tspan></text>
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Modified: ProcessDiagram/trunk/examples/stoichEx1.svg
===================================================================
--- ProcessDiagram/trunk/examples/stoichEx1.svg 2011-11-07 17:37:36 UTC (rev 812)
+++ ProcessDiagram/trunk/examples/stoichEx1.svg 2011-11-09 20:32:54 UTC (rev 813)
@@ -1,5 +1,6 @@
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+
<svg
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:cc="http://creativecommons.org/ns#"
@@ -12,10 +13,10 @@
height="1052.3622047"
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sodipodi:version="0.32"
- inkscape:version="0.46"
- sodipodi:docbase="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/examples"
+ inkscape:version="0.48.2 r9819"
sodipodi:docname="stoichEx1.svg"
- inkscape:output_extension="org.inkscape.output.svg.inkscape">
+ inkscape:output_extension="org.inkscape.output.svg.inkscape"
+ version="1.1">
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inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
- inkscape:zoom="3.7282914"
- inkscape:cx="238.34123"
+ inkscape:zoom="5.3812643"
+ inkscape:cx="277.28534"
inkscape:cy="706.84313"
inkscape:document-units="px"
inkscape:current-layer="layer1"
showguides="true"
inkscape:guide-bbox="true"
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+ inkscape:window-width="1334"
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+ inkscape:window-x="1898"
+ inkscape:window-y="98"
+ showgrid="false"
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width="9.4658356"
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height="9.4657154"
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y="-54.97028"
transform="matrix(-0.7952153,-0.6063272,-0.6063272,0.7952153,0,0)" />
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+ sodipodi:role="line"
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+ height="9.4663448"
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+ transform="matrix(5.2379496e-4,-0.99999986,0.99999986,5.2379496e-4,0,0)" />
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+ sodipodi:role="line"
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x="285.71597"
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Modified: ProcessDiagram/trunk/images/annotation.svg
===================================================================
--- ProcessDiagram/trunk/images/annotation.svg 2011-11-07 17:37:36 UTC (rev 812)
+++ ProcessDiagram/trunk/images/annotation.svg 2011-11-09 20:32:54 UTC (rev 813)
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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+
<svg
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:cc="http://creativecommons.org/ns#"
@@ -8,12 +9,11 @@
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xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- width="1052.3622"
- height="744.09448"
+ width="386.4375"
+ height="348.3125"
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sodipodi:version="0.32"
- inkscape:version="0.46"
- sodipodi:docbase="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/EntityRelationship/Level1/images"
+ inkscape:version="0.48.2 r9819"
sodipodi:docname="annotation.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape"
version="1.0"
@@ -40,23 +40,28 @@
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inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
- inkscape:zoom="1.1687991"
- inkscape:cx="526.18109"
- inkscape:cy="372.04724"
+ inkscape:zoom="0.94268752"
+ inkscape:cx="105.17092"
+ inkscape:cy="160.43079"
inkscape:document-units="px"
inkscape:current-layer="layer1"
showguides="true"
inkscape:guide-bbox="true"
inkscape:window-width="1024"
inkscape:window-height="749"
- inkscape:window-x="-5"
- inkscape:window-y="0"
+ inkscape:window-x="2375"
+ inkscape:window-y="113"
width="1052.3622px"
height="744.09448px"
- showgrid="false">
+ showgrid="false"
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+ fit-margin-left="0"
+ fit-margin-right="0"
+ fit-margin-bottom="0"
+ inkscape:window-maximized="0">
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- position="286.88332"
+ position="-296.46875,219.38259"
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</sodipodi:namedview>
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inkscape:label="Layer 1"
inkscape:groupmode="layer"
id="layer1"
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+ transform="translate(-650.36633,-537.87925)">
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- id="rect2872" />
+ style="fill:none;stroke:#000000;stroke-width:5;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ d="m 298.96875,330.78125 0,210 64.5625,0 -16.65625,133.3125 55.1875,-133.3125 278.34375,0 0,-156.65625 -62.375,-53.34375 -319.0625,0 z"
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xml:space="preserve"
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+ style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;font-family:Bitstream Vera Sans"
x="725.71777"
y="678.80914"
id="text2890"><tspan
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+ id="path2400"
+ inkscape:connector-curvature="0" />
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</svg>
Modified: ProcessDiagram/trunk/images/auxiliaryunituml.svg
===================================================================
--- ProcessDiagram/trunk/images/auxiliaryunituml.svg 2011-11-07 17:37:36 UTC (rev 812)
+++ ProcessDiagram/trunk/images/auxiliaryunituml.svg 2011-11-09 20:32:54 UTC (rev 813)
@@ -1,8 +1,17 @@
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+<svg width="1108" height="450" version="1.1" xmlns="http://www.w3.org/2000/svg">
<g>
+ <rect fill="#808080" stroke="none" stroke-opacity="1" x="691" y="390" width="3" height="47" />
+ <rect fill="#808080" stroke="none" stroke-opacity="1" x="535" y="434" width="159" height="3" />
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[truncated message content] |
|
From: <stu...@us...> - 2011-11-07 17:37:45
|
Revision: 812
http://sbgn.svn.sourceforge.net/sbgn/?rev=812&view=rev
Author: stumoodie
Date: 2011-11-07 17:37:36 +0000 (Mon, 07 Nov 2011)
Log Message:
-----------
Well on way to writing spec.
Modified Paths:
--------------
ProcessDiagram/trunk/Makefile
ProcessDiagram/trunk/examples/compartment_overlapping.svg
ProcessDiagram/trunk/examples/submap-dissociated.svg
ProcessDiagram/trunk/examples/submap-folded.svg
ProcessDiagram/trunk/examples/submap-unfolded.svg
ProcessDiagram/trunk/images/complexsubunituml.svg
ProcessDiagram/trunk/images/emptysetuml.svg
ProcessDiagram/trunk/images/epnuml.svg
ProcessDiagram/trunk/images/genetic.svg
ProcessDiagram/trunk/images/geneticMultimer.svg
ProcessDiagram/trunk/images/glyphauxuml.svg
ProcessDiagram/trunk/images/sbgn_model_revised/128173
ProcessDiagram/trunk/images/sbgn_model_revised/128173.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/134829.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/134957.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/135085.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/141613.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/141741.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/141869.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/45.session
ProcessDiagram/trunk/images/sbgnumloverview.svg
ProcessDiagram/trunk/images/statefulepnuml.svg
ProcessDiagram/trunk/images/statelessepnuml.svg
ProcessDiagram/trunk/images/submap.svg
ProcessDiagram/trunk/sbgn_PD-level1.pdf
ProcessDiagram/trunk/sources/glyphs.tex
ProcessDiagram/trunk/sources/latex-macros.tex
ProcessDiagram/trunk/sources/latex-style.tex
Added Paths:
-----------
ProcessDiagram/trunk/images/attributevalueuml.svg
ProcessDiagram/trunk/images/auxiliaryunituml.svg
ProcessDiagram/trunk/images/compartmentuml.svg
ProcessDiagram/trunk/images/logicaloperatoruml.svg
ProcessDiagram/trunk/images/nonstoichprocessuml.svg
ProcessDiagram/trunk/images/processumlview.svg
ProcessDiagram/trunk/images/sbgn_model_revised/148397.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/154925.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/161453.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/161581.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168109.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168237.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168365.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168493.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/168877.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/174893.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/175021.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/175149.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/181677.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/188205.diagram
ProcessDiagram/trunk/images/stoichprocessuml.svg
ProcessDiagram/trunk/images/submapnodeuml.svg
Modified: ProcessDiagram/trunk/Makefile
===================================================================
--- ProcessDiagram/trunk/Makefile 2011-11-01 16:33:16 UTC (rev 811)
+++ ProcessDiagram/trunk/Makefile 2011-11-07 17:37:36 UTC (rev 812)
@@ -5,7 +5,7 @@
# $HeadURL$
# =============================================================================
-.PHONY: clean, dist_clean, images, examples
+.PHONY: clean, dist_clean
MAIN = sbgn_PD-level1
@@ -13,20 +13,16 @@
BIBTEX = bibtex
all default: images examples
+ $(MAKE) -C examples
+ $(MAKE) -C images
$(LATEX) $(MAIN).tex
$(LATEX) $(MAIN).tex
$(BIBTEX) $(MAIN)
$(LATEX) $(MAIN).tex
-images:
- $(MAKE) -C images
-
-examples:
- $(MAKE) -C images
-
-
clean:
$(MAKE) -C images clean
+ $(MAKE) -C examples clean
-rm -f *.bbl
-rm -f *.blg
-rm -f *.out
Modified: ProcessDiagram/trunk/examples/compartment_overlapping.svg
===================================================================
--- ProcessDiagram/trunk/examples/compartment_overlapping.svg 2011-11-01 16:33:16 UTC (rev 811)
+++ ProcessDiagram/trunk/examples/compartment_overlapping.svg 2011-11-07 17:37:36 UTC (rev 812)
@@ -1,24 +1,25 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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+
<svg
xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:cc="http://web.resource.org/cc/"
+ xmlns:cc="http://creativecommons.org/ns#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:svg="http://www.w3.org/2000/svg"
xmlns="http://www.w3.org/2000/svg"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- width="744.09448819"
- height="1052.3622047"
+ width="895.75616"
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id="svg18713"
sodipodi:version="0.32"
- inkscape:version="0.45.1"
- sodipodi:docbase="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/examples"
+ inkscape:version="0.48.2 r9819"
sodipodi:docname="compartment_overlapping.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape"
inkscape:export-filename="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/examples/compartment_overlapping.png"
inkscape:export-xdpi="150"
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+ inkscape:export-ydpi="150"
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inkscape:document-units="px"
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inkscape:window-width="1360"
inkscape:window-height="1020"
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+ inkscape:window-x="1812"
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transform="scale(1.0237215,0.9768282)"><tspan
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xml:space="preserve"><tspan
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+ style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
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width="82.832512"
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@@ -143,7 +152,7 @@
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xml:space="preserve"
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+ style="fill:none;stroke:#7d7d7d;stroke-width:9;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
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@@ -168,7 +178,7 @@
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Modified: ProcessDiagram/trunk/examples/submap-dissociated.svg
===================================================================
--- ProcessDiagram/trunk/examples/submap-dissociated.svg 2011-11-01 16:33:16 UTC (rev 811)
+++ ProcessDiagram/trunk/examples/submap-dissociated.svg 2011-11-07 17:37:36 UTC (rev 812)
@@ -1,20 +1,20 @@
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+
<svg
xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:cc="http://web.resource.org/cc/"
+ xmlns:cc="http://creativecommons.org/ns#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:svg="http://www.w3.org/2000/svg"
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xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- width="1052.3622"
- height="744.09448"
+ width="681.77167"
+ height="532.71014"
id="svg2"
sodipodi:version="0.32"
- inkscape:version="0.45.1"
+ inkscape:version="0.48.2 r9819"
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sodipodi:docname="submap-dissociated.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape">
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inkscape:stockid="Arrow1Mend"
orient="auto"
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- transform="scale(0.4) rotate(180) translate(10,0)" />
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
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+ transform="matrix(-0.4,0,0,-0.4,-4,0)"
+ inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow1Lend"
orient="auto"
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+ refX="0"
id="Arrow1Lend"
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+ style="overflow:visible">
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id="path2978"
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- style="fill-rule:evenodd;stroke:#000000;stroke-width:1.0pt;marker-start:none;"
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+ inkscape:connector-curvature="0" />
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xml:space="preserve"
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+ style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;font-family:Bitstream Vera Sans"
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y="363.16055"
id="text3354"><tspan
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+ style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;font-family:Bitstream Vera Sans"
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id="text3362"><tspan
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+ style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;font-family:Bitstream Vera Sans"
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xml:space="preserve"><tspan
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id="text3183"
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xml:space="preserve"><tspan
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style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
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<rect
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+ style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:3;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
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style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
id="tspan2813">GPI</tspan></text>
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Modified: ProcessDiagram/trunk/examples/submap-folded.svg
===================================================================
--- ProcessDiagram/trunk/examples/submap-folded.svg 2011-11-01 16:33:16 UTC (rev 811)
+++ ProcessDiagram/trunk/examples/submap-folded.svg 2011-11-07 17:37:36 UTC (rev 812)
@@ -1,20 +1,20 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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+
<svg
xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:cc="http://web.resource.org/cc/"
+ xmlns:cc="http://creativecommons.org/ns#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:svg="http://www.w3.org/2000/svg"
xmlns="http://www.w3.org/2000/svg"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- width="1052.3622"
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+ height="458.37775"
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sodipodi:version="0.32"
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sodipodi:docname="submap-folded.svg"
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<marker
inkscape:stockid="Arrow1Mend"
orient="auto"
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- refX="0.0"
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+ refX="0"
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+ style="overflow:visible">
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<marker
inkscape:stockid="Arrow1Lend"
orient="auto"
- refY="0.0"
- refX="0.0"
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+ refX="0"
id="Arrow1Lend"
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+ style="overflow:visible">
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id="path2978"
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- style="fill-rule:evenodd;stroke:#000000;stroke-width:1.0pt;marker-start:none;"
- transform="scale(0.8) rotate(180) translate(12.5,0)" />
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
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inkscape:pageshadow="2"
- inkscape:zoom="2"
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+ inkscape:cx="283.40859"
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inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
inkscape:window-width="1345"
inkscape:window-height="746"
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showguides="true"
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+ fit-margin-bottom="0">
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orientation="vertical"
- position="721.24884"
+ position="580.98975,-238.89088"
id="guide2990" />
<sodipodi:guide
orientation="vertical"
- position="347.54298"
+ position="207.28389,-238.89088"
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orientation="horizontal"
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[truncated message content] |
|
From: <stu...@us...> - 2011-11-01 16:33:26
|
Revision: 811
http://sbgn.svn.sourceforge.net/sbgn/?rev=811&view=rev
Author: stumoodie
Date: 2011-11-01 16:33:16 +0000 (Tue, 01 Nov 2011)
Log Message:
-----------
Added makefile to generate examples and removed derived image files. Also added more text - work in progress
Modified Paths:
--------------
ProcessDiagram/trunk/Makefile
ProcessDiagram/trunk/examples/insulin.svg
ProcessDiagram/trunk/examples/macromolecule-CaMKII.svg
ProcessDiagram/trunk/images/glyphauxuml.svg
ProcessDiagram/trunk/images/mapuml.svg
ProcessDiagram/trunk/images/sbgn_model_revised/128173
ProcessDiagram/trunk/images/sbgn_model_revised/128173.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/134701.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/134829.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/141741.diagram
ProcessDiagram/trunk/images/sbgn_model_revised/45.session
ProcessDiagram/trunk/images/sbgn_model_revised/sbgn_model_revised.prj
ProcessDiagram/trunk/images/sbgnumloverview.svg
ProcessDiagram/trunk/sbgn_PD-level1.pdf
ProcessDiagram/trunk/sources/concepts.tex
ProcessDiagram/trunk/sources/glyphs.tex
ProcessDiagram/trunk/sources/latex-style.tex
Added Paths:
-----------
ProcessDiagram/trunk/examples/Makefile
Removed Paths:
-------------
ProcessDiagram/trunk/examples/IFNGeneRef.eps
ProcessDiagram/trunk/examples/IFNGeneRef.pdf
ProcessDiagram/trunk/examples/IFNGeneRef.png
ProcessDiagram/trunk/examples/MAPK-only.ai
ProcessDiagram/trunk/examples/MAPK-only.eps
ProcessDiagram/trunk/examples/MAPK-only.pdf
ProcessDiagram/trunk/examples/MAPK-only.png
ProcessDiagram/trunk/examples/MAPK.eps
ProcessDiagram/trunk/examples/MAPK.pdf
ProcessDiagram/trunk/examples/MAPK.png
ProcessDiagram/trunk/examples/association-MPF.eps
ProcessDiagram/trunk/examples/association-MPF.pdf
ProcessDiagram/trunk/examples/association-MPF.png
ProcessDiagram/trunk/examples/association-multimerisation.eps
ProcessDiagram/trunk/examples/association-multimerisation.pdf
ProcessDiagram/trunk/examples/association-multimerisation.png
ProcessDiagram/trunk/examples/association-unamed.eps
ProcessDiagram/trunk/examples/association-unamed.pdf
ProcessDiagram/trunk/examples/association-unamed.png
ProcessDiagram/trunk/examples/cloning.eps
ProcessDiagram/trunk/examples/cloning.pdf
ProcessDiagram/trunk/examples/cloning.png
ProcessDiagram/trunk/examples/compartment-3comp.eps
ProcessDiagram/trunk/examples/compartment-3comp.pdf
ProcessDiagram/trunk/examples/compartment-3comp.png
ProcessDiagram/trunk/examples/compartment-cell-wrong.eps
ProcessDiagram/trunk/examples/compartment-cell-wrong.pdf
ProcessDiagram/trunk/examples/compartment-cell-wrong.png
ProcessDiagram/trunk/examples/compartment-cell.eps
ProcessDiagram/trunk/examples/compartment-cell.pdf
ProcessDiagram/trunk/examples/compartment-cell.png
ProcessDiagram/trunk/examples/compartment_overlapping.eps
ProcessDiagram/trunk/examples/compartment_overlapping.pdf
ProcessDiagram/trunk/examples/compartment_overlapping.png
ProcessDiagram/trunk/examples/compartment_overlapping_wrong.eps
ProcessDiagram/trunk/examples/compartment_overlapping_wrong.pdf
ProcessDiagram/trunk/examples/compartment_overlapping_wrong.png
ProcessDiagram/trunk/examples/dissociation-ribosome.eps
ProcessDiagram/trunk/examples/dissociation-ribosome.pdf
ProcessDiagram/trunk/examples/dissociation-ribosome.png
ProcessDiagram/trunk/examples/dissociation-ribosome_small.png
ProcessDiagram/trunk/examples/ex-annotation.eps
ProcessDiagram/trunk/examples/ex-annotation.pdf
ProcessDiagram/trunk/examples/ex-annotation.png
ProcessDiagram/trunk/examples/glycolysis.eps
ProcessDiagram/trunk/examples/glycolysis.pdf
ProcessDiagram/trunk/examples/glycolysis.png
ProcessDiagram/trunk/examples/insulin.eps
ProcessDiagram/trunk/examples/insulin.pdf
ProcessDiagram/trunk/examples/insulin.png
ProcessDiagram/trunk/examples/macromolecule-CaMKII.eps
ProcessDiagram/trunk/examples/macromolecule-CaMKII.pdf
ProcessDiagram/trunk/examples/macromolecule-CaMKII.png
ProcessDiagram/trunk/examples/macromolecule-GluR.eps
ProcessDiagram/trunk/examples/macromolecule-GluR.pdf
ProcessDiagram/trunk/examples/macromolecule-GluR.png
ProcessDiagram/trunk/examples/modulation-VOC.eps
ProcessDiagram/trunk/examples/modulation-VOC.pdf
ProcessDiagram/trunk/examples/modulation-VOC.png
ProcessDiagram/trunk/examples/modulation-nAChR.eps
ProcessDiagram/trunk/examples/modulation-nAChR.pdf
ProcessDiagram/trunk/examples/modulation-nAChR.png
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ProcessDiagram/trunk/examples/muscle.pdf
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ProcessDiagram/trunk/examples/necessary_stim-genetic.pdf
ProcessDiagram/trunk/examples/necessary_stim-genetic.png
ProcessDiagram/trunk/examples/necessary_stim-transport.eps
ProcessDiagram/trunk/examples/necessary_stim-transport.pdf
ProcessDiagram/trunk/examples/necessary_stim-transport.png
ProcessDiagram/trunk/examples/process-dimerisation.eps
ProcessDiagram/trunk/examples/process-dimerisation.pdf
ProcessDiagram/trunk/examples/process-dimerisation.png
ProcessDiagram/trunk/examples/process-modulated.eps
ProcessDiagram/trunk/examples/process-modulated.pdf
ProcessDiagram/trunk/examples/process-modulated.png
ProcessDiagram/trunk/examples/process-phosphorylation.eps
ProcessDiagram/trunk/examples/process-phosphorylation.pdf
ProcessDiagram/trunk/examples/process-phosphorylation.png
ProcessDiagram/trunk/examples/process-reaction.eps
ProcessDiagram/trunk/examples/process-reaction.pdf
ProcessDiagram/trunk/examples/process-reaction.png
ProcessDiagram/trunk/examples/process-reversible.eps
ProcessDiagram/trunk/examples/process-reversible.pdf
ProcessDiagram/trunk/examples/process-reversible.png
ProcessDiagram/trunk/examples/process-translocation.eps
ProcessDiagram/trunk/examples/process-translocation.pdf
ProcessDiagram/trunk/examples/process-translocation.png
ProcessDiagram/trunk/examples/sbgn_edge_taxonomy.pdf
ProcessDiagram/trunk/examples/sbgn_node_taxonomy.pdf
ProcessDiagram/trunk/examples/stimulation-example1.eps
ProcessDiagram/trunk/examples/stimulation-example1.pdf
ProcessDiagram/trunk/examples/stimulation-example1.png
ProcessDiagram/trunk/examples/stoichEx1.eps
ProcessDiagram/trunk/examples/stoichEx1.pdf
ProcessDiagram/trunk/examples/stoichEx1.png
ProcessDiagram/trunk/examples/submap-dissociated.eps
ProcessDiagram/trunk/examples/submap-dissociated.pdf
ProcessDiagram/trunk/examples/submap-dissociated.png
ProcessDiagram/trunk/examples/submap-folded.eps
ProcessDiagram/trunk/examples/submap-folded.pdf
ProcessDiagram/trunk/examples/submap-folded.png
ProcessDiagram/trunk/examples/submap-unfolded.eps
ProcessDiagram/trunk/examples/submap-unfolded.pdf
ProcessDiagram/trunk/examples/submap-unfolded.png
ProcessDiagram/trunk/examples/wrongStateVariables.eps
ProcessDiagram/trunk/examples/wrongStateVariables.pdf
ProcessDiagram/trunk/examples/wrongStateVariables.png
Modified: ProcessDiagram/trunk/Makefile
===================================================================
--- ProcessDiagram/trunk/Makefile 2011-10-31 14:55:16 UTC (rev 810)
+++ ProcessDiagram/trunk/Makefile 2011-11-01 16:33:16 UTC (rev 811)
@@ -5,14 +5,14 @@
# $HeadURL$
# =============================================================================
-.PHONY: clean, dist_clean, images
+.PHONY: clean, dist_clean, images, examples
MAIN = sbgn_PD-level1
LATEX = pdflatex
BIBTEX = bibtex
-all default: images
+all default: images examples
$(LATEX) $(MAIN).tex
$(LATEX) $(MAIN).tex
$(BIBTEX) $(MAIN)
@@ -21,11 +21,22 @@
images:
$(MAKE) -C images
+examples:
+ $(MAKE) -C images
+
clean:
- -rm *.aux
$(MAKE) -C images clean
+ -rm -f *.bbl
+ -rm -f *.blg
+ -rm -f *.out
+ -rm -f *.dvi
+ -rm -f *.toc
+ -rm -f *.aux
+ -rm -f *.log
+ -rm -f *.tmp
+ -rm -f *.prv
+ -rm -f sbgn_PD-level1.fdb_latexmk
-
dist_clean: clean
- -rm *.pdf
\ No newline at end of file
+ -rm -f *.pdf
Deleted: ProcessDiagram/trunk/examples/IFNGeneRef.eps
===================================================================
--- ProcessDiagram/trunk/examples/IFNGeneRef.eps 2011-10-31 14:55:16 UTC (rev 810)
+++ ProcessDiagram/trunk/examples/IFNGeneRef.eps 2011-11-01 16:33:16 UTC (rev 811)
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|
From: <stu...@us...> - 2011-10-31 14:55:25
|
Revision: 810
http://sbgn.svn.sourceforge.net/sbgn/?rev=810&view=rev
Author: stumoodie
Date: 2011-10-31 14:55:16 +0000 (Mon, 31 Oct 2011)
Log Message:
-----------
Updated to ignore *.pdf and modifed clean taregt
Modified Paths:
--------------
ProcessDiagram/trunk/images/Makefile
Property Changed:
----------------
ProcessDiagram/trunk/images/
Property changes on: ProcessDiagram/trunk/images
___________________________________________________________________
Added: svn:ignore
+ *.pdf
Modified: ProcessDiagram/trunk/images/Makefile
===================================================================
--- ProcessDiagram/trunk/images/Makefile 2011-10-31 14:49:08 UTC (rev 809)
+++ ProcessDiagram/trunk/images/Makefile 2011-10-31 14:55:16 UTC (rev 810)
@@ -15,8 +15,6 @@
clean:
- -rm *.pdf
- -rm *.eps
- -rm *.png
+ -rm -f *.pdf
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <stu...@us...> - 2011-10-31 14:49:18
|
Revision: 809
http://sbgn.svn.sourceforge.net/sbgn/?rev=809&view=rev
Author: stumoodie
Date: 2011-10-31 14:49:08 +0000 (Mon, 31 Oct 2011)
Log Message:
-----------
Deleted derived image files so that they are now generated by the makefile.
Modified Paths:
--------------
ProcessDiagram/trunk/sbgn_PD-level1.pdf
Removed Paths:
-------------
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Deleted: ProcessDiagram/trunk/images/and.eps
===================================================================
--- ProcessDiagram/trunk/images/and.eps 2011-10-31 14:37:56 UTC (rev 808)
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