sbgn-svn-commit Mailing List for Systems Biology Graphical Notation (Page 26)

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Revision: 330
          http://sbgn.svn.sourceforge.net/sbgn/?rev=330&view=rev
Author:   mhucka
Date:     2008-06-11 18:51:25 -0700 (Wed, 11 Jun 2008)

Log Message:
-----------
Changed uses of description environment to glyphDescription.

Modified Paths:
--------------
    trunk/documents/specifications/ProcessDiagram/Level1/sources/association.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/catalysis.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/compartment.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/complex.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/consumption.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/dissociation.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/inhibition.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/logicArc.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/modulation.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/omitted.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/production.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/stimulation.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/submap.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/transition.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/trigger.tex
    trunk/documents/specifications/ProcessDiagram/Level1/sources/uncertain.tex

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/association.tex
===================================================================

--- trunk/documents/specifications/ProcessDiagram/Level1/sources/association.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/association.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -6,33 +6,33 @@
 
 The association between two EPNs represents the non-covalent binding of the biological objects represented by those EPNs into a larger complex.
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ SBO:0000177 ! binding.
  \item[origin]\mbox{}\\ More than one \glyph{consumption} arcss (section \ref{sec:consumption}).
  \item[target]\mbox{}\\  One \glyph{production} arc (section \ref{sec:production}).
  \item[node]\mbox{}\\ An \glyph{association} between several entities is represented by a filled disc.
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{images/association}}
+\scalebox{0.3}{\includegraphics{images/association}}
 \end{center}
 
 The following example illustrates the association of two cyclin and CDC2 kinase into the Maturation Promoting Factor in ST.
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/association-MPF}}
+\scalebox{0.3}{\includegraphics{examples/association-MPF}}
 \end{center}
 
 The following example illustrates the association of a pentameric macromolecule (a nicotinic acetylcholine receptor) with a simple chemical (the local anesthetic chlorpromazin) in an unamed complex, in an ST diagram. 
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/association-unamed}}
+\scalebox{0.3}{\includegraphics{examples/association-unamed}}
 \end{center}
 
 An association does not obligatory results in the formation of a \glyph{complex}, but can also produce a \glyph{multimer}. See the formation of the hemoglobin below.
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/association-multimerisation}}
+\scalebox{0.3}{\includegraphics{examples/association-multimerisation}}
 \end{center}
 \normalcolor
 

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/catalysis.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/catalysis.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/catalysis.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -7,12 +7,12 @@
 A catalysis is a particular case of stimulation, where the effector affects
 positively the flux of a process represented by the target transition. The positive effect on the transition is due to the lowering of the activation energy of a reaction.
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ SBO:0000172 ! catalysis
  \item[origin]\mbox{}\\ Any EPN (section~\ref{sec:EPNs}) or any logical operator (section~\ref{sec:logic}).
  \item[target]\mbox{}\\ Any transition node (section~\ref{sec:PNs}).
  \item[node]\mbox{}\\ The target extremity of a \glyph{catalysis} carries an empty circle.
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
 \scalebox{0.5}{\includegraphics{images/catalysis}}

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/compartment.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/compartment.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/compartment.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -4,17 +4,13 @@
 %\color{blue}
 \subsection{Glyph: \glyph{Compartment}}\label{sec:compartment}
 
-\subsubsection{Introduction}
-
 In order to describe biochemical and cellular events, it is useful to
 define the notion of pools. A pool is an ensemble of participants that
 can be considered identical relatively to the events they are involved
 into. A compartment is a logical or physical subset of the event space
 that contains pools.
 
-\subsubsection{Specification}
-
-\begin{description}
+\begin{glyphDescription}
 \glyphSboTerm  SBO:0000289 ! functional compartment 
 \glyphContainer A compartment is represented by a surface
   enclosed in a continuous border or located between continuous borders. These borders should be noticeably thicker than the borders of the EPNs. A compartment can take \textbf{any} geometry. A compartment must always be entirely enclosed.
@@ -30,23 +26,23 @@
   temperature or voltage, see \ref{sec:unitInfo}.
   The center of the bounding box of a \glyph{unit of information} is
   located on the midline of the border of the compartment. 
-\end{description}
+\end{glyphDescription}
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{images/compartment}}
+\scalebox{0.3}{\includegraphics{images/compartment}}
 \end{center}
 
 
 It is important to note that a compartment never contains another compartment, but may surround it. Two ``adjacents'' compartments are not separated by one line, but by \textbf{two} lines. The following example represents a cell made up of a nucleus surrounded by the cytoplasm.
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/compartment-cell}}
+\scalebox{0.3}{\includegraphics{examples/compartment-cell}}
 \end{center}
 
 The following example represents three adjacent compartments. Two of the compartments carry units of information. Notice the fact that those units of information do not overlap several membrane boundaries.
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/compartment-3comp}}
+\scalebox{0.3}{\includegraphics{examples/compartment-3comp}}
 \end{center}
 
 To make drawing aestetically more pleasing and understandable, comparments are
@@ -56,7 +52,7 @@
 placement of compartments:
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{images/compartment_overlapping}}
+\scalebox{0.3}{\includegraphics{images/compartment_overlapping}}
 \end{center}
 
 Overlapped (hidden) part of the compartment should not contain any object,
@@ -64,9 +60,6 @@
 correct:
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/compartment_overlapping_wrong}}
+\scalebox{0.3}{\includegraphics{examples/compartment_overlapping_wrong}}
 \end{center}
 
-
-\normalcolor
-\newpage

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/complex.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/complex.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/complex.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -4,13 +4,9 @@
 %\color{blue}
 \subsection{Glyph: \glyph{Complex}}\label{sec:complex}
 
-\subsubsection{Introduction}
-
 A \glyph{complex} node represents a biochemical entity composed of other biochemical entities, whether macromolecules, simple chemicals, multimers, or themselves complexes. 
 
-\subsubsection{Specification}
-
-\begin{description}
+\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 octogonal 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.
@@ -26,10 +22,8 @@
   The center of the bounding box of a \glyph{unit of information} is
   located on the midline of the border of the complex. A \glyph{complex} may
   carry a \glyph{clone marker} (see section~\ref{sec:cloneMarker}).
-\end{description}
+\end{glyphDescription}
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{images/complex}}
+\scalebox{0.3}{\includegraphics{images/complex}}
 \end{center}
-\normalcolor
-\newpage

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/consumption.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/consumption.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/consumption.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -7,12 +7,12 @@
 \glyph{Consumption} is the arc used to represent the fact that an entity only affects a process,
 but is not affected by it. 
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ To be determined.
  \item[origin]\mbox{}\\ Any EPN (section \ref{sec:EPNs}).
  \item[target]\mbox{}\\ Any process node (section~\ref{sec:PNs}).
  \item[end-points]\mbox{}\\ No particular symbol is used to represent a source.
- \end{description}
+ \end{glyphDescription}
 
 
 A cardinality label may be associated with \glyph{consumption} (section \ref{sec:consumption}) or 

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/dissociation.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/dissociation.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/dissociation.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -6,17 +6,13 @@
 
 The dissociation of a EPN into two EPNs represents the rupture of a non-covalent binding between the biological entities represented by those EPNs.
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ SBO:0000180 ! dissociation
  \item[origin]\mbox{}\\ One \glyph{consumption} arc (section \ref{sec:consumption}).
  \item[target]\mbox{}\\  More than one \glyph{production} arc (section \ref{sec:production}).
  \item[node]\mbox{}\\ A \glyph{dissociation} between several entities is represented by two concentric empty discs. A simple empty disc could be, in some cases, confused with the \glyph{modulation} (section \ref{sec:modulation}).
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{images/dissociation}}
+\scalebox{0.3}{\includegraphics{images/dissociation}}
 \end{center}
-\normalcolor
-\newpage
-
-\newpage

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/inhibition.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/inhibition.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/inhibition.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -7,12 +7,12 @@
 
 An inhibition affects \textbf{negatively } the flux of a process represented by the target transition. This inhibition can be for instance a competitive inhibition or an allosteric inhibition. 
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ SBO:0000169 ! inhibition
  \item[origin]\mbox{}\\ Any EPN (section~\ref{sec:EPNs}) or any logical operator (section~\ref{sec:logic}).
  \item[target]\mbox{}\\ Any transition node (section~\ref{sec:PNs}).
  \item[node]\mbox{}\\ The target extremity of an \glyph{inhibition} carries a bar perpendicular to the arc.
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
 \scalebox{0.5}{\includegraphics{images/inhibition}}

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/logicArc.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/logicArc.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/logicArc.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -7,12 +7,12 @@
 \glyph{Logic arc} is the arc used to represent the fact that an entity influences
 outcome of logic operator. 
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ To be determined.
  \item[origin]\mbox{}\\ Any EPN (section \ref{sec:EPNs}) or logical operator (section~\ref{sec:logic}).
  \item[target]\mbox{}\\ Any logical operator (section~\ref{sec:logic}).
  \item[end-points]\mbox{}\\ No particular symbol is used to represent a source.
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
 \scalebox{0.5}{\includegraphics{images/logicArc}}

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/modulation.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/modulation.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/modulation.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -10,12 +10,12 @@
 conditions, for instance the concentration of the intervening
 participants. A \glyph{modulation} can also be used when one does not know the precise direction of the effect.
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ SBO:0000168 ! control
  \item[origin]\mbox{}\\ Any EPN (section~\ref{sec:EPNs}) or any logical operator (section~\ref{sec:logic}).
  \item[target]\mbox{}\\ Any transition node (section~\ref{sec:PNs}).
  \item[end-points]\mbox{}\\ The target extremity of a \glyph{modulation} carries an empty diamond.
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
 \scalebox{0.5}{\includegraphics{images/modulation}}

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/omitted.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/omitted.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/omitted.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -6,15 +6,15 @@
 
 Omitted processes are processes that are known to exist, but are omitted from the diagram for the sake of clarity or parsimony. A single \glyph{omitted process} can represent any number of actual processes. The omitted process is different from a module.
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ To be determined
  \item[origin]\mbox{}\\ One or several \glyph{consumption} arcs (section \ref{sec:consumption}) or one or several \glyph{production} arcs (section~\ref{sec:production}).
  \item[target]\mbox{}\\ One or several \glyph{production} arcs(section \ref{sec:production}).
  \item[node]\mbox{}\\ Omitted processes are represented as a transition containing a double slanted NW-SE line separated by an empty space.
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{images/omitted}}
+\scalebox{0.3}{\includegraphics{images/omitted}}
 \end{center}
 \normalcolor
 

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/production.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/production.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/production.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -8,12 +8,12 @@
 produced by a process. In the case of a reversible transition, the 
 \glyph{production} arc also acts as a \glyph{consumption} arc.
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ To be determined.
  \item[origin]\mbox{}\\ Any process node (section~\ref{sec:PNs}), or module (section~\ref{sec:submap}).
  \item[target]\mbox{}\\ Any EPN (section \ref{sec:EPNs}).
  \item[end-points]\mbox{}\\ The target extremity of a \glyph{production} carries a filled arrowhead.
- \end{description}
+ \end{glyphDescription}
 
 A cardinality label can be associated with \glyph{production} arc indicating the stoichiometry of a process.
 

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/stimulation.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/stimulation.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/stimulation.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -7,12 +7,12 @@
 
 A stimulation affects \textbf{positively} the flux of a process represented by the target transition. This stimulation can be for instance a catalysis or a positive allosteric regulation. Note that \glyph{catalysis} exists independently in SBGN, see section \ref{sec:catalysis}.
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ SBO:0000170 ! stimulation
  \item[origin]\mbox{}\\ Any EPN (section~\ref{sec:EPNs}) or any logical operator (section~\ref{sec:logic}).
  \item[target]\mbox{}\\ Any transition node (section~\ref{sec:PNs}).
  \item[end point]\mbox{}\\ The target extremity of a \glyph{stimulation} carries an empty arrowhead.
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
 \scalebox{0.5}{\includegraphics{images/stimulation}}

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/submap.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/submap.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/submap.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -6,29 +6,29 @@
 
 A \glyph{submap} is used to encapsulate a certain number of processes (including all types of nodes and edges) within one glyph. The module hides its content to the users, and display only input terminals (or ports). A module is not equivalent to an omitted process (see section~\ref{sec:omitted}). In the case of an SBGN diagram available through a software tool, the content of a module may be available to the tool. A user could then ask the tool to expand the module, for instance by clicking on the module icon, that would expand the module within the same diagram (on the same canvas) or open it in a different canvas.
 
-\begin{description}
+\begin{glyphDescription}
 \glyphSboTerm to be determined
 \glyphContainer The \glyph{submap} is represented as a square box, to remind that it is fundamentaly 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 submap is represented folded, those terminals are linked to external EPNs (section~\ref{sec:EPNs}) or containers (section~\ref{sec:CNs}). In the unfolded view, exposing the internal structure of the submap, a set of \glyph{tags} point to the corresponding internal EPNs (section~\ref{sec:EPNs}) or containers (section~\ref{sec:CNs}).
-\end{description}
+\end{glyphDescription}
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{images/submap}}
+\scalebox{0.3}{\includegraphics{images/submap}}
 \end{center}
 
 The following diagram represents a \glyph{submap} that transforms glucose into fructose-6-phosphate. The \glyph{submap} carry 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{center}
-\scalebox{0.5}{\includegraphics{examples/submap-folded}}
+\scalebox{0.3}{\includegraphics{examples/submap-folded}}
 \end{center}
 
 The following diagram represents an unfolded version of the submap. Here, anything outside the 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 submap to the to the compartment ``mito'' outside the submap. The compartment containing Glu6P is implicitely defined as the same than the compartment containing Glu and Fru6p. There is no ambiguity because if Glu and Fru6 were in different compartments, one of them should have been defined within the submap.
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/submap-dissociated}}
+\scalebox{0.3}{\includegraphics{examples/submap-dissociated}}
 \end{center}
-\normalcolor
 
 
+

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/transition.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/transition.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/transition.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -6,15 +6,15 @@
 
 A transition is a process transforming a set of states or entities in another set of states or entities.
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ SBO:0000167 ! reaction
  \item[origin]\mbox{}\\ One or several \glyph{consumption} arcs (section \ref{sec:consumption}) or one or several \glyph{production} arcs (section~\ref{sec:production}).
  \item[target]\mbox{}\\ One or several \glyph{production} arcs (section \ref{sec:production}).
  \item[node]\mbox{}\\ A transition is represented by a square box. The arcs linking it to the state/entity nodes are attached to the center of opposite sides. The modulatory arcs point to the other two sides. A \glyph{transition} connected to \glyph{production} arcs on opposite sides is a reversible transition.
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{images/transition}}
+\scalebox{0.3}{\includegraphics{images/transition}}
 \end{center}
 
 A transition is the basic process node in SBGN. It describes a process that transforms a given set of biochemical entities --- macromolecules, simple 
@@ -28,37 +28,37 @@
 represent the phosphorylation of a protein in a state transition diagram.
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/transition-phosphorylation}}
+\scalebox{0.3}{\includegraphics{examples/transition-phosphorylation}}
 \end{center}
 
 The following example illustrates the use of a \glyph{transition} node to represent an reaction between two reactants that generates three products. 
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/transition-reaction}}
+\scalebox{0.3}{\includegraphics{examples/transition-reaction}}
 \end{center}
 
 The following example illustrates the use of a \glyph{transition} node to represent a translocation. The large round-cornered rectangle represents a compartment border (see section \ref{sec:compartment}).
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/transition-translocation}}
+\scalebox{0.3}{\includegraphics{examples/transition-translocation}}
 \end{center}
 
 The following example illustrates the use of a \glyph{transition} node to represent the reversible opening and closing of an ionic channel in a state transition diagram.
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{examples/transition-reversible}}
+\scalebox{0.3}{\includegraphics{examples/transition-reversible}}
 \end{center}
 
 When such a reversible process is assymetrically modulated, it should be represented by two different processes in State Transition. The following example illustrates the use of two \glyph{transition} 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{center}
-\scalebox{0.5}{\includegraphics{examples/transition-modulated}}
+\scalebox{0.3}{\includegraphics{examples/transition-modulated}}
 \end{center}
 
 The following example 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{center}
-\scalebox{0.5}{\includegraphics{examples/transition-dimerisation}}
+\scalebox{0.3}{\includegraphics{examples/transition-dimerisation}}
 \end{center}
 
 \normalcolor

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/trigger.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/trigger.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/trigger.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -7,12 +7,12 @@
 
 A trigger effect, or absolute stimulation, is a stimulation that is necessary for a process to take place. A process modulated by a trigger can only occur when this trigger is active.
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ SBO:0000171 ! necessary stimulation
  \item[origin]\mbox{}\\ Any EPN (section~\ref{sec:EPNs}) or any logical operator (section~\ref{sec:logic}).
  \item[target]\mbox{}\\ Any transition node (section~\ref{sec:PNs}).
  \item[node]\mbox{}\\ The target extremity of a \glyph{trigger} carries an open arrow (to remind that it is a \glyph{stimulation}) coming after a larger vertical bar.
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
 \scalebox{0.5}{\includegraphics{images/trigger}}

Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/uncertain.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/uncertain.tex	2008-06-12 01:43:09 UTC (rev 329)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/uncertain.tex	2008-06-12 01:51:25 UTC (rev 330)
@@ -6,14 +6,14 @@
 
 Uncertain processes are processes that may not exist. A single \glyph{uncertain process} can represent any number of actual processes.
 
-\begin{description}
+\begin{glyphDescription}
  \item[SBO]\mbox{}\\ To be determined
  \item[origin]\mbox{}\\ One or several \glyph{consumption} arcs (section \ref{sec:consumption}) or one or several \glyph{production} arcs (section \ref{sec:production}).
  \item[target]\mbox{}\\ One or several \glyph{production} arcs (section \ref{sec:production}).
  \item[node]\mbox{}\\ Uncertain processes are represented as a transition containing a questionmark.
- \end{description}
+ \end{glyphDescription}
 
 \begin{center}
-\scalebox{0.5}{\includegraphics{images/uncertain}}
+\scalebox{0.3}{\includegraphics{images/uncertain}}
 \end{center}
 \normalcolor


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sbgn-svn-commit Mailing List for Systems Biology Graphical Notation (Page 26)

sbgn-svn-commit — Notification of commits to the SVN repository