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:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/images/uncertain.eps
ProcessDiagram/trunk/UserManual/images/uncertain.pdf
ProcessDiagram/trunk/UserManual/images/uncertain.png
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ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
ProcessDiagram/trunk/UserManual/sources/CVs.tex
ProcessDiagram/trunk/UserManual/sources/front-page.tex
ProcessDiagram/trunk/UserManual/sources/multimer.tex
ProcessDiagram/trunk/UserManual/sources/symbols.aux
ProcessDiagram/trunk/UserManual/sources/symbols.tex
ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup
Modified: ProcessDiagram/trunk/UserManual/images/uncertain.eps
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+ inkscape:window-maximized="0">
<sodipodi:guide
orientation="vertical"
position="301.42857"
@@ -82,6 +87,7 @@
<dc:format>image/svg+xml</dc:format>
<dc:type
rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title></dc:title>
</cc:Work>
</rdf:RDF>
</metadata>
@@ -125,7 +131,7 @@
height="41.42857"
width="44.285713"
id="rect2829"
- style="opacity:1;fill:white;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:5;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
+ style="opacity:1;fill:#ffffc8;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:5;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
<text
xml:space="preserve"
style="font-size:12px;font-style:normal;font-weight:normal;fill:black;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans"
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)
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2012.5.4) 4 MAY 2012 18:21
+This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2012.5.4) 20 MAY 2012 08:09
entering extended mode
%&-line parsing enabled.
**sbgn_PD-level1-user.tex
@@ -1062,9 +1062,6 @@
(Font) Font shape `T1/futs/b/n' tried instead on input line 24.
-LaTeX Warning: Reference `sec:process' on page 1 undefined on input line 24.
-
-
LaTeX Warning: Reference `sec:consumption' on page 1 undefined on input line 24
.
@@ -1076,9 +1073,6 @@
LaTeX Warning: Reference `sec:catalysis' on page 1 undefined on input line 24.
-LaTeX Warning: Reference `sec:process' on page 1 undefined on input line 24.
-
-
LaTeX Warning: Reference `sec:consumption' on page 1 undefined on input line 24
.
@@ -1188,53 +1182,104 @@
<images/perturbing_agent.pdf, id=83, 265.99374pt x 110.4125pt>
File: images/perturbing_agent.pdf Graphic file (type pdf)
-<use images/perturbing_agent.pdf>) (./sources/unitInformation.tex
-
-LaTeX Warning: Reference `sec:CVs' on page 7 undefined on input line 8.
-
-<images/unitInformation.pdf, id=84, 263.98625pt x 109.40875pt>
+<use images/perturbing_agent.pdf>) (./sources/multimer.tex
+<images/multimer.pdf, id=84, 329.23pt x 217.81375pt>
+File: images/multimer.pdf Graphic file (type pdf)
+ <use images/multimer.pdf>) (./sources/unitInformation.tex [7 <./images/sourceS
+ink.pdf> <./images/perturbing_agent.pdf> <./images/multimer.pdf>]
+<images/unitInformation.pdf, id=113, 263.98625pt x 109.40875pt>
File: images/unitInformation.pdf Graphic file (type pdf)
-<use images/unitInformation.pdf>) (./sources/stateVariable.tex [7 <./images/sou
-rceSink.pdf> <./images/perturbing_agent.pdf> <./images/unitInformation.pdf>]
-<images/stateVariable.pdf, id=109, 263.98625pt x 111.41624pt>
+<use images/unitInformation.pdf>) (./sources/stateVariable.tex
+<images/stateVariable.pdf, id=114, 263.98625pt x 111.41624pt>
File: images/stateVariable.pdf Graphic file (type pdf)
<use images/stateVariable.pdf>) (./sources/cloneMarker.tex
LaTeX Warning: Reference `sec:submap' on page 8 undefined on input line 5.
-<images/simpleCloneMarker.pdf, id=110, 170.6375pt x 171.64125pt>
+[8 <./images/unitInformation.pdf> <./images/stateVariable.pdf>]
+<images/simpleCloneMarker.pdf, id=130, 170.6375pt x 171.64125pt>
File: images/simpleCloneMarker.pdf Graphic file (type pdf)
-<use images/simpleCloneMarker.pdf> [8 <./images/stateVariable.pdf>]
+<use images/simpleCloneMarker.pdf>
Overfull \hbox (0.13669pt too wide) in paragraph at lines 16--17
[]\T1/futs/m/n/10.95 Unlike the \T1/futs/m/it/10.95 sim-ple clone marker\T1/fut
s/m/n/10.95 , the \T1/futs/m/it/10.95 la-beled clone marker \T1/futs/m/n/10.95
in-cludes (un-sur-pris-ingly, given its name)
[]
-<images/labeledCloneMarker.pdf, id=120, 323.2075pt x 215.80624pt>
+<images/labeledCloneMarker.pdf, id=131, 323.2075pt x 215.80624pt>
File: images/labeledCloneMarker.pdf Graphic file (type pdf)
-<use images/labeledCloneMarker.pdf>)) [9 <./images/simpleCloneMarker.pdf> <./im
-ages/labeledCloneMarker.pdf>]
+<use images/labeledCloneMarker.pdf>) (./sources/CVs.tex [9 <./images/simpleClon
+eMarker.pdf> <./images/labeledCloneMarker.pdf>] [10]
+
+LaTeX Warning: Reference `sec:phenotype' on page 11 undefined on input line 99.
+
+
+LaTeX Font Info: Font shape `T1/txtt/m/it' in size <10> not available
+(Font) Font shape `T1/txtt/m/sl' tried instead on input line 135.
+
+LaTeX Warning: `h' float specifier changed to `ht'.
+
+)
+
+LaTeX Warning: Reference `sec:association' on page 11 undefined on input line 4
+4.
+
+
+LaTeX Warning: Reference `sec:dissociation' on page 11 undefined on input line
+44.
+
+
+LaTeX Warning: Reference `sec:phenotype' on page 11 undefined on input line 44.
+
+
+[11] (./sources/process.tex
+
+LaTeX Warning: Reference `sec:consumption' on page 12 undefined on input line 8
+.
+
+
+LaTeX Warning: Reference `sec:production' on page 12 undefined on input line 8.
+
+
+
+LaTeX Warning: Reference `sec:arcs' on page 12 undefined on input line 8.
+
+<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
+
+LaTeX Warning: Reference `sec:submap' on page 12 undefined on input line 7.
+
+<images/omitted.pdf, id=158, 244.915pt x 84.315pt>
+File: images/omitted.pdf Graphic file (type pdf)
+ <use images/omitted.pdf>)
+(./sources/uncertain.tex [12 <./images/process.pdf> <./images/omitted.pdf>]
+<images/uncertain.pdf, id=168, 244.915pt x 84.315pt>
+File: images/uncertain.pdf Graphic file (type pdf)
+
+<use images/uncertain.pdf>)) [13 <./images/uncertain.pdf>]
\openout2 = `sources/refcard.aux'.
- (./sources/refcard.tex
+
+(./sources/refcard.tex
Appendix A.
-<images/refcard.pdf, id=140, 798.985pt x 575.14874pt>
+<images/refcard.pdf, id=178, 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
[]
[]
-[10
+[14
-] [11 <./images/refcard.pdf>] (./sbgn_PD-level1-user.bbl) [12
+] [15 <./images/refcard.pdf>] (./sbgn_PD-level1-user.bbl) [16
@@ -1247,24 +1292,24 @@
)
Here is how much of TeX's memory you used:
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- 62052 string characters out of 1152824
- 140498 words of memory out of 3000000
- 7717 multiletter control sequences out of 15000+50000
- 110908 words of font info for 85 fonts, out of 3000000 for 9000
+ 4720 strings out of 493848
+ 63167 string characters out of 1152824
+ 142739 words of memory out of 3000000
+ 7759 multiletter control sequences out of 15000+50000
+ 112722 words of font info for 88 fonts, out of 3000000 for 9000
714 hyphenation exceptions out of 8191
- 32i,7n,32p,1530b,290s stack positions out of 5000i,500n,10000p,200000b,50000s
+ 32i,8n,32p,1530b,290s stack positions out of 5000i,500n,10000p,200000b,50000s
{/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}</usr/share/texmf-texli
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-urw/helvetic/uhvb8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvb
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-Output written on sbgn_PD-level1-user.pdf (13 pages, 888985 bytes).
+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 (17 pages, 926607 bytes).
PDF statistics:
- 189 PDF objects out of 1000 (max. 8388607)
+ 229 PDF objects out of 1000 (max. 8388607)
0 named destinations out of 1000 (max. 500000)
- 71 words of extra memory for PDF output out of 10000 (max. 10000000)
+ 91 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/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@...}
\setcounter{r@...}
}
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}
+%
+%
+%
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