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From: <tcz...@us...> - 2016-06-09 05:46:31
|
Revision: 950
http://sourceforge.net/p/sbgn/code/950
Author: tczauderna
Date: 2016-06-09 05:46:28 +0000 (Thu, 09 Jun 2016)
Log Message:
-----------
fixed type in latex source for front page
compiled latest version of the draft
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/front-page.tex
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/front-page.tex 2016-06-09 04:54:03 UTC (rev 949)
+++ ProcessDiagram/trunk/Specification/sources/front-page.tex 2016-06-09 05:46:28 UTC (rev 950)
@@ -38,7 +38,7 @@
Emek Demir & \emph{OHSU, USA}\\
Robin Haw & \emph{Ontario Institute for Cancer Research, Canada}\\
Augustin Luna & \emph{Dana-Farber Cancer Institute, USA}\\
-Alexander Mazein & \emph(EISBM, Lyon, France)\\
+Alexander Mazein & \emph{EISBM, Lyon, France}\\
Huaiyu Mi & \emph{University of Southern California, USA}\\
Nicolas \lenov & \emph{Babraham Institute, UK}\\
Falk Schreiber & \emph{University of Konstanz, Germany}\\
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hua...@us...> - 2016-06-09 04:54:06
|
Revision: 949
http://sourceforge.net/p/sbgn/code/949
Author: huaiyumi
Date: 2016-06-09 04:54:03 +0000 (Thu, 09 Jun 2016)
Log Message:
-----------
Update PD author affiliations
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sources/front-page.tex
Modified: ProcessDiagram/trunk/Specification/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/front-page.tex 2016-06-09 04:23:56 UTC (rev 948)
+++ ProcessDiagram/trunk/Specification/sources/front-page.tex 2016-06-09 04:54:03 UTC (rev 949)
@@ -35,13 +35,13 @@
\begin{tabular}{l>{\hspace*{15pt}}r}
Stuart Moodie & \emph{Eight Pillars Ltd, UK}\\
Tobias Czauderna & \emph{Monash University, Australia}\\
-Emek Demir & \emph{Memorial Sloan-Kettering Institute, USA}\\
+Emek Demir & \emph{OHSU, USA}\\
Robin Haw & \emph{Ontario Institute for Cancer Research, Canada}\\
-Augustin Luna & \emph{Memorial Sloan-Kettering Institute, USA}\\
-Alexander Mazein & \emph(European Institute for Systems Biology and Medicine, Lyon, France)\\
+Augustin Luna & \emph{Dana-Farber Cancer Institute, USA}\\
+Alexander Mazein & \emph(EISBM, Lyon, France)\\
Huaiyu Mi & \emph{University of Southern California, USA}\\
Nicolas \lenov & \emph{Babraham Institute, UK}\\
-Falk Schreiber & \emph{Monash University, Australia \& MLU Halle, Germany}\\
+Falk Schreiber & \emph{University of Konstanz, Germany}\\
Anatoly Sorokin & \emph{Institute of Cell Biophysics RAS, RU}\\
Alice Vill\'{e}ger & \emph{Freelance IT Consultant, UK}
\end{tabular}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hua...@us...> - 2016-06-09 04:23:58
|
Revision: 948
http://sourceforge.net/p/sbgn/code/948
Author: huaiyumi
Date: 2016-06-09 04:23:56 +0000 (Thu, 09 Jun 2016)
Log Message:
-----------
Update author list for PD spec
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sources/front-page.tex
Modified: ProcessDiagram/trunk/Specification/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/front-page.tex 2016-06-09 04:04:18 UTC (rev 947)
+++ ProcessDiagram/trunk/Specification/sources/front-page.tex 2016-06-09 04:23:56 UTC (rev 948)
@@ -38,6 +38,7 @@
Emek Demir & \emph{Memorial Sloan-Kettering Institute, USA}\\
Robin Haw & \emph{Ontario Institute for Cancer Research, Canada}\\
Augustin Luna & \emph{Memorial Sloan-Kettering Institute, USA}\\
+Alexander Mazein & \emph(European Institute for Systems Biology and Medicine, Lyon, France)\\
Huaiyu Mi & \emph{University of Southern California, USA}\\
Nicolas \lenov & \emph{Babraham Institute, UK}\\
Falk Schreiber & \emph{Monash University, Australia \& MLU Halle, Germany}\\
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hua...@us...> - 2016-06-09 04:04:20
|
Revision: 947
http://sourceforge.net/p/sbgn/code/947
Author: huaiyumi
Date: 2016-06-09 04:04:18 +0000 (Thu, 09 Jun 2016)
Log Message:
-----------
Update text in the submap section.
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sources/glyphs.tex
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2016-03-10 15:42:30 UTC (rev 946)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2016-06-09 04:04:18 UTC (rev 947)
@@ -1942,7 +1942,7 @@
\begin{attributes}
\associtem{terminals}{SubmapTerminal}{1..*} The terminals show how the
-EPNs in the Map link to those in the collapsed submap,
+EPNs in the Main Map link to those in the collapsed submap,
which are identified by a \sbgnclass{Tag}.
\end{attributes}
@@ -1999,7 +1999,7 @@
\subsubsection{Changes from Previous Version}
The semantics of the Submap have been clarified and the ability of
-submaps to be independent of a map has been removed\footnote{This
+submaps to be independent of the main map has been removed\footnote{This
change was agreed at SBGN 10 in Los Angeles, 2014.}.
\umlclasshead{LogicalOperator}
@@ -2184,7 +2184,7 @@
\begin{tabular}[c]{l p{10cm}}
\\\toprule
generic & A generic stoichiometric process that transforms a set of entity pools into another set of entity pools.\\
-omitted & Omitted processes are processes that are known to exist, but are omitted from the map for the sake of clarity or parsimony. A single \glyph{omitted process} can represent any number of actual processes. The \glyph{omitted process} is different from a \glyph{submap}. While a \glyph{submap} references to an explicit content, that is hidden in the map, the \glyph{omitted process} does not ``hide'' anything within the context of the map, and cannot be ``unfolded''.\\
+omitted & Omitted processes are processes that are known to exist, but are omitted from the map for the sake of clarity or parsimony. A single \glyph{omitted process} can represent any number of actual processes. The \glyph{omitted process} is different from a \glyph{submap}. While a \glyph{submap} references to an explicit content, that is hidden in the main map, the \glyph{omitted process} does not ``hide'' anything within the context of the map, and cannot be ``unfolded''.\\
uncertain & Uncertain processes are processes that may not exist. A single \glyph{uncertain process} can represent any number of actual processes.\\
association & The association between one or more \glyph{EPNs} represents the non-covalent binding of the biological objects represented by those \glyph{EPNs} into a larger complex.\\
dissociation & The dissociation of an \glyph{EPN} into one or more \glyph{EPNs} represents the rupture of a non-covalent binding between the biological entities represented by those \glyph{EPNs}.\\
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2016-03-10 15:42:32
|
Revision: 946
http://sourceforge.net/p/sbgn/code/946
Author: lenov
Date: 2016-03-10 15:42:30 +0000 (Thu, 10 Mar 2016)
Log Message:
-----------
Modified Paths:
--------------
EntityRelationship/trunk/images/refcard.eps
EntityRelationship/trunk/images/refcard.pdf
EntityRelationship/trunk/images/refcard.png
EntityRelationship/trunk/images/refcard.svg
Added Paths:
-----------
EntityRelationship/tags/Level1-Version2/templates/ER_L1V2-Inkscape.svg
EntityRelationship/tags/Level1-Version2/templates/ER_L1V2.eps
EntityRelationship/tags/Level1-Version2/templates/ER_L1V2.pdf
EntityRelationship/tags/Level1-Version2/templates/ER_L1V2.png
EntityRelationship/tags/Level1-Version2/templates/ER_L1V2.svg
EntityRelationship/trunk/templates/ER_L1V2-Inkscape.svg
EntityRelationship/trunk/templates/ER_L1V2.eps
EntityRelationship/trunk/templates/ER_L1V2.pdf
EntityRelationship/trunk/templates/ER_L1V2.png
EntityRelationship/trunk/templates/ER_L1V2.svg
Added: EntityRelationship/tags/Level1-Version2/templates/ER_L1V2-Inkscape.svg
===================================================================
--- EntityRelationship/tags/Level1-Version2/templates/ER_L1V2-Inkscape.svg (rev 0)
+++ EntityRelationship/tags/Level1-Version2/templates/ER_L1V2-Inkscape.svg 2016-03-10 15:42:30 UTC (rev 946)
@@ -0,0 +1,1189 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
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+ 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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+ id="svg2"
+ sodipodi:version="0.32"
+ inkscape:version="0.91 r13725"
+ version="1.0"
+ sodipodi:docname="refcard.svg"
+ inkscape:output_extension="org.inkscape.output.svg.inkscape"
+ inkscape:export-filename="/home/lenov/SBGN/svn/sbgn-code/EntityRelationship/trunk/images/refcard.png"
+ inkscape:export-xdpi="150"
+ inkscape:export-ydpi="150">
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+ <marker
+ inkscape:stockid="Arrow1Lstart"
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+ refX="0.0"
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+ <marker
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|
From: <le...@us...> - 2016-03-10 15:23:41
|
Revision: 945
http://sourceforge.net/p/sbgn/code/945
Author: lenov
Date: 2016-03-10 15:23:37 +0000 (Thu, 10 Mar 2016)
Log Message:
-----------
Modified Paths:
--------------
EntityRelationship/trunk/images/refcard.eps
EntityRelationship/trunk/images/refcard.pdf
EntityRelationship/trunk/images/refcard.png
EntityRelationship/trunk/images/refcard.svg
Modified: EntityRelationship/trunk/images/refcard.eps
===================================================================
--- EntityRelationship/trunk/images/refcard.eps 2016-01-13 22:39:11 UTC (rev 944)
+++ EntityRelationship/trunk/images/refcard.eps 2016-03-10 15:23:37 UTC (rev 945)
@@ -1,16 +1,14 @@
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-%%Creator: cairo 1.10.2 (http://cairographics.org)
-%%CreationDate: Wed May 11 13:28:48 2011
+%%Creator: cairo 1.14.2 (http://cairographics.org)
+%%CreationDate: Thu Mar 10 15:22:34 2016
%%Pages: 1
-%%BoundingBox: 0 -1 774 552
%%DocumentData: Clean7Bit
%%LanguageLevel: 2
+%%BoundingBox: 32 29 807 582
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[truncated message content] |
|
From: <tcz...@us...> - 2016-01-13 22:39:14
|
Revision: 944
http://sourceforge.net/p/sbgn/code/944
Author: tczauderna
Date: 2016-01-13 22:39:11 +0000 (Wed, 13 Jan 2016)
Log Message:
-----------
fixed some typos and some images in PD spec L1V2 draft
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/examples/process-translocation.svg
ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg
ProcessDiagram/trunk/Specification/le_images/process-translocation.pdf
ProcessDiagram/trunk/Specification/le_images/process-translocation.svg
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/glyphs.tex
Modified: ProcessDiagram/trunk/Specification/examples/process-translocation.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/process-translocation.svg 2016-01-08 06:53:11 UTC (rev 943)
+++ ProcessDiagram/trunk/Specification/examples/process-translocation.svg 2016-01-13 22:39:11 UTC (rev 944)
@@ -1,8 +1,9 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
<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"
@@ -12,10 +13,9 @@
height="744.09448"
id="svg2"
sodipodi:version="0.32"
- inkscape:version="0.44.1"
+ inkscape:version="0.91 r13725"
version="1.0"
- sodipodi:docbase="/home/lenov/SBGN/cvs/documents/specifications/Level1/images"
- sodipodi:docname="transition-example4.svg">
+ sodipodi:docname="process-translocation.svg">
<defs
id="defs4">
<marker
@@ -56,7 +56,7 @@
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
inkscape:zoom="1.4"
- inkscape:cx="500.18714"
+ inkscape:cx="393.40143"
inkscape:cy="438.94195"
inkscape:document-units="px"
inkscape:current-layer="layer2"
@@ -67,7 +67,9 @@
inkscape:window-x="0"
inkscape:window-y="0"
showguides="true"
- inkscape:guide-bbox="true">
+ inkscape:guide-bbox="true"
+ showgrid="false"
+ inkscape:window-maximized="0">
<sodipodi:guide
orientation="vertical"
position="192.85714"
@@ -100,7 +102,7 @@
style="opacity:1;fill:none;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:6;stroke-miterlimit:4;stroke-dasharray:none;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"
+ style="font-style:normal;font-weight:normal;font-size:12px;font-family:'Bitstream Vera Sans';fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
x="435.65817"
y="199.53555"
id="text2890"><tspan
@@ -108,7 +110,7 @@
id="tspan2892"
x="435.65817"
y="199.53555"
- style="font-size:48px">RE</tspan></text>
+ style="font-size:48px">ER</tspan></text>
<path
transform="matrix(-1,0,0,1,664.8622,23.39817)"
d="M 363.65492 267.30249 A 58.588848 58.588848 0 1 1 246.47722,267.30249 A 58.588848 58.588848 0 1 1 363.65492 267.30249 z"
Modified: ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg 2016-01-08 06:53:11 UTC (rev 943)
+++ ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg 2016-01-13 22:39:11 UTC (rev 944)
@@ -13,7 +13,7 @@
height="748.77167"
id="svg2"
version="1.1"
- inkscape:version="0.48.4 r9939"
+ inkscape:version="0.91 r13725"
sodipodi:docname="cloningrules-eg.svg">
<defs
id="defs4">
@@ -79,17 +79,17 @@
borderopacity="1.0"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
- inkscape:zoom="1.0780152"
- inkscape:cx="1015.429"
- inkscape:cy="594.67682"
+ inkscape:zoom="1.5245437"
+ inkscape:cx="378.82376"
+ inkscape:cy="360.11005"
inkscape:document-units="px"
inkscape:current-layer="g3801"
showgrid="false"
- inkscape:window-width="1280"
- inkscape:window-height="707"
- inkscape:window-x="0"
- inkscape:window-y="0"
- inkscape:window-maximized="0"
+ inkscape:window-width="2234"
+ inkscape:window-height="1235"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
+ inkscape:window-maximized="1"
showguides="true"
inkscape:guide-bbox="true"
inkscape:snap-grids="false"
@@ -360,8 +360,8 @@
sodipodi:nodetypes="cc"
inkscape:connector-curvature="0"
id="path3179"
- d="m 331.68907,253.91818 100,0"
- style="fill:none;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1" />
+ d="m 331.68907,253.91818 90.53743,0"
+ style="fill:none;stroke:#000000;stroke-width:0.95151162px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#TriangleOutL)" />
<path
inkscape:connector-curvature="0"
id="path3940"
@@ -630,7 +630,7 @@
sodipodi:cy="445.86218"
sodipodi:rx="20.5"
sodipodi:ry="20.5"
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+ d="m 156.7299,442.54536 a 20.5,20.5 0 0 1 -16.91078,23.54634 20.5,20.5 0 0 1 -23.54826,-16.90811 20.5,20.5 0 0 1 16.90544,-23.55017 20.5,20.5 0 0 1 23.55209,16.90278"
sodipodi:start="6.1206745"
sodipodi:end="12.403407"
sodipodi:open="true"
@@ -649,7 +649,7 @@
sodipodi:open="true"
sodipodi:end="12.403407"
sodipodi:start="6.1206745"
- d="m 616.33622,-25.643531 c 1.76919,10.790607 -5.54411,20.972336 -16.33472,22.7415283 -10.7906,1.7691924 -20.97233,-5.544109 -22.74153,-16.3347153 -1.76919,-10.790607 5.54411,-20.972336 16.33472,-22.741528 10.78715,-1.768626 20.96656,5.539519 22.74007,16.325869"
+ d="m 616.33622,-25.643531 a 19.79899,19.79899 0 0 1 -16.33251,22.7411655 19.79899,19.79899 0 0 1 -22.74301,-16.3299295 19.79899,19.79899 0 0 1 16.32735,-22.744862 19.79899,19.79899 0 0 1 22.74671,16.32478"
sodipodi:ry="19.79899"
sodipodi:rx="19.79899"
sodipodi:cy="-22.440125"
@@ -662,7 +662,7 @@
sodipodi:open="true"
sodipodi:end="12.403407"
sodipodi:start="6.1206745"
- d="m 422.66353,-82.711029 c 1.26371,7.707576 -3.96007,14.980239 -11.66765,16.243948 -7.70758,1.263709 -14.98024,-3.960078 -16.24395,-11.667654 -1.26371,-7.707576 3.96008,-14.980239 11.66766,-16.243948 7.7051,-1.263304 14.97611,3.956799 16.24291,11.661335"
+ d="m 422.66353,-82.711029 a 14.142136,14.142136 0 0 1 -11.66607,16.243689 14.142136,14.142136 0 0 1 -16.24501,-11.664235 14.142136,14.142136 0 0 1 11.6624,-16.24633 14.142136,14.142136 0 0 1 16.24765,11.660557"
sodipodi:ry="14.142136"
sodipodi:rx="14.142136"
sodipodi:cy="-80.422882"
@@ -864,21 +864,21 @@
id="rect6623" /></flowRegion><flowPara
style="font-size:20px"
id="flowPara6625">P</flowPara></flowRoot> <path
- style="fill:none;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-start:none;marker-end:none;display:inline"
+ style="display:inline;fill:none;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-start:none;marker-end:none"
d="m 856.07607,660.42654 -79.07607,0"
id="path6630"
inkscape:connector-type="polyline"
inkscape:connector-curvature="0"
sodipodi:nodetypes="cc" />
<path
- style="fill:none;stroke:#000000;stroke-width:0.99999994px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#TriangleOutL);display:inline"
+ style="display:inline;fill:none;stroke:#000000;stroke-width:0.99999994px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#TriangleOutL)"
d="m 690,660.36218 -88.89281,-44"
id="path6638"
inkscape:connector-type="polyline"
inkscape:connector-curvature="0"
sodipodi:nodetypes="cc" />
<path
- style="fill:none;stroke:#000000;stroke-width:1;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;marker-start:url(#TriangleInL);marker-end:none"
+ style="fill:none;stroke:#000000;stroke-width:1;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#TriangleInL);marker-end:none"
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inkscape:connector-type="polyline"
@@ -958,7 +958,7 @@
sodipodi:open="true"
sodipodi:end="12.403407"
sodipodi:start="6.1206745"
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+ d="m 156.7299,442.54536 a 20.5,20.5 0 0 1 -16.91078,23.54634 20.5,20.5 0 0 1 -23.54826,-16.90811 20.5,20.5 0 0 1 16.90544,-23.55017 20.5,20.5 0 0 1 23.55209,16.90278"
sodipodi:ry="20.5"
sodipodi:rx="20.5"
sodipodi:cy="445.86218"
Modified: ProcessDiagram/trunk/Specification/le_images/process-translocation.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/le_images/process-translocation.svg
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2016-01-08 06:53:11 UTC (rev 943)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2016-01-13 22:39:11 UTC (rev 944)
@@ -18,7 +18,7 @@
achieve this we took our lead from other successful standards: the
Unified Modelling Language (UML) \cite{umlspec} (a graphical
language that has been used by tens of thousands of software
-developers for almost two decades to describe and software system); and the
+developers for almost two decades to describe software system); and the
Systems Biology Markup Language \cite{sbmll3core} (SBML; the ``daddy'' of computational systems
biological standards and almost 15 years after its inception it is firmly
embedded in the scientific community it serves). Both languages
@@ -140,7 +140,7 @@
exists independently of C.
\item[navigability (black diamond anchor arrowhead)] If the
association ends in an arrow, this indicates the direction of the
- association. This means that only one aside of the association (G)
+ association. This means that only one side of the association (G)
is `aware' of the relationship.
\item[dependency] Indicates that the dependent class (E) requires the
other class adjacent to the arrow head (F) to satisfy its
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2016-01-08 06:53:14
|
Revision: 943
http://sourceforge.net/p/sbgn/code/943
Author: tczauderna
Date: 2016-01-08 06:53:11 +0000 (Fri, 08 Jan 2016)
Log Message:
-----------
fixed problems with SVGs: some processes and some units of information were shown as rounded rectangles because attribute rx or ry was set on rectangle shapes
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/examples/IFNGeneRef.svg
ProcessDiagram/trunk/Specification/examples/cloning.svg
ProcessDiagram/trunk/Specification/examples/glycolysis.svg
ProcessDiagram/trunk/Specification/examples/insulin.svg
ProcessDiagram/trunk/Specification/examples/macromolecule-CaMKII.svg
ProcessDiagram/trunk/Specification/examples/macromolecule-GluR.svg
ProcessDiagram/trunk/Specification/examples/modulation-VOC.svg
ProcessDiagram/trunk/Specification/examples/modulation-nAChR.svg
ProcessDiagram/trunk/Specification/examples/stimulation-example1.svg
ProcessDiagram/trunk/Specification/examples/submap-dissociated.svg
ProcessDiagram/trunk/Specification/examples/submap-folded.svg
ProcessDiagram/trunk/Specification/examples/submap-unfolded.svg
ProcessDiagram/trunk/Specification/examples/toto.svg
ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg
ProcessDiagram/trunk/Specification/images/complexGlyph.svg
ProcessDiagram/trunk/Specification/images/complexMultimer.svg
ProcessDiagram/trunk/Specification/images/complexMultimerGlyph.svg
ProcessDiagram/trunk/Specification/images/layout-branching.svg
ProcessDiagram/trunk/Specification/images/macromolMultimer.svg
ProcessDiagram/trunk/Specification/images/multimer.svg
ProcessDiagram/trunk/Specification/images/refcard.svg
ProcessDiagram/trunk/Specification/images/simpleChemical.svg
ProcessDiagram/trunk/Specification/images/simpleChemicalMultimer.svg
ProcessDiagram/trunk/Specification/images/submap-unfolded.svg
ProcessDiagram/trunk/Specification/images/unitInformation.svg
ProcessDiagram/trunk/Specification/le_images/Fig12.pdf
ProcessDiagram/trunk/Specification/le_images/Fig13.pdf
ProcessDiagram/trunk/Specification/le_images/Fig14.pdf
ProcessDiagram/trunk/Specification/le_images/Fig15.pdf
ProcessDiagram/trunk/Specification/le_images/MAPK-NoVar.pdf
ProcessDiagram/trunk/Specification/le_images/MAPK-OneVar.pdf
ProcessDiagram/trunk/Specification/le_images/MAPK-TwoVar.pdf
ProcessDiagram/trunk/Specification/le_images/MAPK-only.pdf
ProcessDiagram/trunk/Specification/le_images/NucAcidFeat-examples.pdf
ProcessDiagram/trunk/Specification/le_images/and.pdf
ProcessDiagram/trunk/Specification/le_images/association-MPF.pdf
ProcessDiagram/trunk/Specification/le_images/association-multimerisation.pdf
ProcessDiagram/trunk/Specification/le_images/association-unamed.pdf
ProcessDiagram/trunk/Specification/le_images/association.pdf
ProcessDiagram/trunk/Specification/le_images/catalysis-MAPK.pdf
ProcessDiagram/trunk/Specification/le_images/catalysis.pdf
ProcessDiagram/trunk/Specification/le_images/compartment.pdf
ProcessDiagram/trunk/Specification/le_images/complex-examples.pdf
ProcessDiagram/trunk/Specification/le_images/complex.pdf
ProcessDiagram/trunk/Specification/le_images/consumption.pdf
ProcessDiagram/trunk/Specification/le_images/dissociation-ribosome.pdf
ProcessDiagram/trunk/Specification/le_images/equivalence.pdf
ProcessDiagram/trunk/Specification/le_images/genetic-plain.pdf
ProcessDiagram/trunk/Specification/le_images/genetic.pdf
ProcessDiagram/trunk/Specification/le_images/hemoglobin-complex.pdf
ProcessDiagram/trunk/Specification/le_images/hemoglobin-macromolecule.pdf
ProcessDiagram/trunk/Specification/le_images/hemoglobin-multimer.pdf
ProcessDiagram/trunk/Specification/le_images/inhibition.pdf
ProcessDiagram/trunk/Specification/le_images/labeledCloneMarker.pdf
ProcessDiagram/trunk/Specification/le_images/logicArc.pdf
ProcessDiagram/trunk/Specification/le_images/macromolecule-examples.pdf
ProcessDiagram/trunk/Specification/le_images/macromolecule-plain.pdf
ProcessDiagram/trunk/Specification/le_images/modulation-VOC.pdf
ProcessDiagram/trunk/Specification/le_images/modulation-VOC.svg
ProcessDiagram/trunk/Specification/le_images/modulation-nAChR.pdf
ProcessDiagram/trunk/Specification/le_images/modulation-nAChR.svg
ProcessDiagram/trunk/Specification/le_images/modulation.pdf
ProcessDiagram/trunk/Specification/le_images/multimer-examples.pdf
ProcessDiagram/trunk/Specification/le_images/multimer.pdf
ProcessDiagram/trunk/Specification/le_images/multimer.svg
ProcessDiagram/trunk/Specification/le_images/necessary_stim-genetic.pdf
ProcessDiagram/trunk/Specification/le_images/necessary_stim-transport.pdf
ProcessDiagram/trunk/Specification/le_images/necessary_stim.pdf
ProcessDiagram/trunk/Specification/le_images/not.pdf
ProcessDiagram/trunk/Specification/le_images/omitted.pdf
ProcessDiagram/trunk/Specification/le_images/or.pdf
ProcessDiagram/trunk/Specification/le_images/perturbing_agent.pdf
ProcessDiagram/trunk/Specification/le_images/phenotype.pdf
ProcessDiagram/trunk/Specification/le_images/process-dimerisation.pdf
ProcessDiagram/trunk/Specification/le_images/process-modulated.pdf
ProcessDiagram/trunk/Specification/le_images/process-phosphorylation.pdf
ProcessDiagram/trunk/Specification/le_images/process-reaction.pdf
ProcessDiagram/trunk/Specification/le_images/process-reversible.pdf
ProcessDiagram/trunk/Specification/le_images/process-translocation.pdf
ProcessDiagram/trunk/Specification/le_images/process.pdf
ProcessDiagram/trunk/Specification/le_images/production.pdf
ProcessDiagram/trunk/Specification/le_images/refcard.pdf
ProcessDiagram/trunk/Specification/le_images/refcard.svg
ProcessDiagram/trunk/Specification/le_images/simpleChemical-examples.pdf
ProcessDiagram/trunk/Specification/le_images/simpleChemical.pdf
ProcessDiagram/trunk/Specification/le_images/simpleCloneMarker.pdf
ProcessDiagram/trunk/Specification/le_images/sourceSink.pdf
ProcessDiagram/trunk/Specification/le_images/stateVariable.pdf
ProcessDiagram/trunk/Specification/le_images/stimulation-reversible.pdf
ProcessDiagram/trunk/Specification/le_images/stimulation.pdf
ProcessDiagram/trunk/Specification/le_images/submap-dissociated.pdf
ProcessDiagram/trunk/Specification/le_images/submap-dissociated.svg
ProcessDiagram/trunk/Specification/le_images/submap-folded.pdf
ProcessDiagram/trunk/Specification/le_images/submap-folded.svg
ProcessDiagram/trunk/Specification/le_images/submap-unfolded.pdf
ProcessDiagram/trunk/Specification/le_images/submap-unfolded.svg
ProcessDiagram/trunk/Specification/le_images/submap.pdf
ProcessDiagram/trunk/Specification/le_images/unitInformation.pdf
ProcessDiagram/trunk/Specification/le_images/unspecified.pdf
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
Modified: ProcessDiagram/trunk/Specification/examples/IFNGeneRef.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/IFNGeneRef.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/IFNGeneRef.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -225,7 +225,7 @@
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style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.865;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" />
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- ry="12.606059"
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@@ -304,7 +304,7 @@
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- ry="12.606059"
+ ry="0"
rx="0"
y="682.80524"
x="619.74988"
Modified: ProcessDiagram/trunk/Specification/examples/cloning.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/cloning.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/cloning.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -114,7 +114,7 @@
d="M 279.40025,231.12146 L 279.40025,302.48913"
id="path13266" />
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- ry="12.606061"
+ ry="0"
rx="0"
y="254.59448"
x="266.5"
@@ -299,7 +299,7 @@
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- ry="12.606061"
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rx="0"
y="-338.58957"
x="776.5"
Modified: ProcessDiagram/trunk/Specification/examples/glycolysis.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/glycolysis.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/glycolysis.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -169,7 +169,7 @@
x="144.32758"
y="225.66823"
rx="0"
- ry="12.606059" />
+ ry="0" />
<path
sodipodi:type="arc"
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@@ -357,7 +357,7 @@
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style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:2;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" />
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- ry="12.606059"
+ ry="0"
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x="350.32758"
@@ -463,7 +463,7 @@
x="557.59235"
y="225.66823"
rx="0"
- ry="12.606059" />
+ ry="0" />
<path
style="fill:none;fill-opacity:0.75;fill-rule:evenodd;stroke:#000000;stroke-width:2;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
d="M 563.48183,160.76206 L 563.48183,211.02545"
@@ -519,7 +519,7 @@
id="path5846"
sodipodi:nodetypes="cc" />
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- ry="12.606059"
+ ry="0"
rx="0"
y="225.66823"
x="761.59235"
@@ -646,7 +646,7 @@
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y="225.66823"
rx="0"
- ry="12.606059" />
+ ry="0" />
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@@ -707,7 +707,7 @@
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sodipodi:nodetypes="cccc" />
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- ry="12.606059"
+ ry="0"
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x="868.22473"
@@ -949,7 +949,7 @@
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- ry="12.606059"
+ ry="0"
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@@ -1031,7 +1031,7 @@
x="-573.27423"
y="-520.60028"
rx="0"
- ry="12.606059" />
+ ry="0" />
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d="M 567.38475,585.50646 L 567.38475,535.24307"
@@ -1129,7 +1129,7 @@
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- ry="12.606059"
+ ry="0"
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@@ -1252,7 +1252,7 @@
x="-161.27423"
y="-520.60028"
rx="0"
- ry="12.606059" />
+ ry="0" />
<path
style="fill:none;fill-opacity:0.75;fill-rule:evenodd;stroke:#000000;stroke-width:2;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
d="M 155.38475,585.50646 L 155.38475,535.24307"
Modified: ProcessDiagram/trunk/Specification/examples/insulin.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/insulin.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/insulin.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -180,7 +180,7 @@
x="774.74652"
y="630.66241"
rx="0"
- ry="11.372863" />
+ ry="0" />
<text
xml:space="preserve"
style="font-size:5.01682329px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;font-family:Bitstream Vera Sans"
@@ -390,7 +390,7 @@
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inkscape:connector-curvature="0" />
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- ry="11.372863"
+ ry="0"
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@@ -557,7 +557,7 @@
x="213.92969"
y="571.12079"
rx="0"
- ry="11.372863" />
+ ry="0" />
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style="fill:none;stroke:#000000;stroke-width:1.86454642;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
d="m 219.60349,512.56414 0,45.34634"
@@ -805,7 +805,7 @@
inkscape:connector-curvature="0" />
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- ry="11.372863"
+ ry="0"
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@@ -1080,7 +1080,7 @@
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inkscape:connector-curvature="0" />
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- ry="11.372863"
+ ry="0"
rx="0"
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Modified: ProcessDiagram/trunk/Specification/examples/macromolecule-CaMKII.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/macromolecule-CaMKII.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/macromolecule-CaMKII.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -189,7 +189,7 @@
y="253.27139"
style="font-size:30.98366356px;font-weight:bold">P@286</tspan></text>
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- ry="27.857147"
+ ry="0"
rx="0"
y="432.34055"
x="418.26379"
Modified: ProcessDiagram/trunk/Specification/examples/macromolecule-GluR.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/macromolecule-GluR.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/macromolecule-GluR.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -229,7 +229,7 @@
sodipodi:role="line"
id="tspan3173">op@pore</tspan></text>
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- ry="22.857141"
+ ry="0"
rx="0"
y="222.45454"
x="341.21466"
Modified: ProcessDiagram/trunk/Specification/examples/modulation-VOC.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/modulation-VOC.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/modulation-VOC.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -201,7 +201,7 @@
x="354.22635"
y="309.94516"
rx="0"
- ry="12.606061"
+ ry="0"
transform="matrix(0,1,1,0,0,0)" />
<path
style="opacity:1;fill:none;fill-opacity:0.75;fill-rule:evenodd;stroke:#000000;stroke-width:3;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
Modified: ProcessDiagram/trunk/Specification/examples/modulation-nAChR.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/modulation-nAChR.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/modulation-nAChR.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -144,7 +144,7 @@
x="477.5"
y="310.59448"
rx="0"
- ry="12.606061" />
+ ry="0" />
<path
style="opacity:1;fill:black;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:2.49212766;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
d="M 490.13985,422.47057 L 478.92529,398.26133 L 501.44344,398.26133 L 490.13985,422.47057 z "
Modified: ProcessDiagram/trunk/Specification/examples/stimulation-example1.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/stimulation-example1.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/stimulation-example1.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -193,7 +193,7 @@
x="477.5"
y="310.59448"
rx="0"
- ry="12.606061" />
+ ry="0" />
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transform="translate(57.78014,55.9867)"
d="M 319.8143 267.30249 A 14.748228 14.748228 0 1 1 290.31784,267.30249 A 14.748228 14.748228 0 1 1 319.8143 267.30249 z"
Modified: ProcessDiagram/trunk/Specification/examples/submap-dissociated.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/submap-dissociated.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/submap-dissociated.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -193,7 +193,7 @@
inkscape:connector-curvature="0" />
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- ry="12.606061"
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@@ -314,7 +314,7 @@
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inkscape:connector-curvature="0" />
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@@ -336,7 +336,7 @@
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inkscape:connector-curvature="0" />
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- ry="12.606061"
+ ry="0"
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Modified: ProcessDiagram/trunk/Specification/examples/submap-folded.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/submap-folded.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/submap-folded.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -210,7 +210,7 @@
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inkscape:connector-curvature="0" />
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- ry="12.606061"
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y="149.41919"
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Modified: ProcessDiagram/trunk/Specification/examples/submap-unfolded.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/submap-unfolded.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/submap-unfolded.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -239,7 +239,7 @@
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inkscape:connector-curvature="0" />
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+ ry="0"
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@@ -376,7 +376,7 @@
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@@ -398,7 +398,7 @@
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@@ -478,7 +478,7 @@
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y="495.31659"
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+ ry="0" />
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id="path3549"
Modified: ProcessDiagram/trunk/Specification/examples/toto.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/toto.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/examples/toto.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -387,7 +387,7 @@
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- ry="12.606059"
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@@ -487,7 +487,7 @@
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- ry="12.606059"
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Modified: ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -55,7 +55,7 @@
height="66.025291"
x="28.296553"
y="453.94247"
- rx="12.914037"
+ rx="0"
ry="0" />
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@@ -157,11 +157,11 @@
height="372.38083"
x="-57.310925"
y="106.14651"
- rx="29.69622"
+ rx="0"
ry="0" />
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ry="0"
- rx="29.687727"
+ rx="0"
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x="-57.310925"
height="373.80505"
@@ -766,7 +766,7 @@
x="899.55273"
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- ry="14.614285" />
+ ry="0" />
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sodipodi:nodetypes="cc"
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@@ -790,7 +790,7 @@
x="661.13983"
y="683.68396"
rx="0"
- ry="14.614285" />
+ ry="0" />
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id="g6597"
Modified: ProcessDiagram/trunk/Specification/images/complexGlyph.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/complexGlyph.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/complexGlyph.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -44,7 +44,7 @@
x="-240.41631"
y="724.29547"
rx="0"
- ry="27.345144" />
+ ry="0" />
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inkscape:collect="always"
Modified: ProcessDiagram/trunk/Specification/images/complexMultimer.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/complexMultimer.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/complexMultimer.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -153,7 +153,7 @@
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@@ -180,7 +180,7 @@
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+ ry="0" />
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Modified: ProcessDiagram/trunk/Specification/images/complexMultimerGlyph.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/complexMultimerGlyph.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/complexMultimerGlyph.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -44,7 +44,7 @@
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Modified: ProcessDiagram/trunk/Specification/images/layout-branching.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/layout-branching.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/layout-branching.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -85,7 +85,7 @@
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Modified: ProcessDiagram/trunk/Specification/images/macromolMultimer.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/macromolMultimer.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/macromolMultimer.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -163,7 +163,7 @@
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Modified: ProcessDiagram/trunk/Specification/images/multimer.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/multimer.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/multimer.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -179,7 +179,7 @@
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@@ -218,7 +218,7 @@
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Modified: ProcessDiagram/trunk/Specification/images/refcard.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/refcard.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/refcard.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -433,7 +433,7 @@
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Modified: ProcessDiagram/trunk/Specification/images/simpleChemical.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/simpleChemical.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/simpleChemical.svg 2016-01-08 06:53:11 UTC (rev 943)
@@ -128,7 +128,7 @@
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Modified: ProcessDiagram/trunk/Specification/images/simpleChemicalMultimer.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/simpleChemicalMultimer.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/simpleChemicalMultimer.svg 2016-01-08 06:53:11 UTC (rev 943)
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Modified: ProcessDiagram/trunk/Specification/images/submap-unfolded.svg
===================================================================
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Modified: ProcessDiagram/trunk/Specification/images/unitInformation.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/unitInformation.svg 2015-12-24 12:36:39 UTC (rev 942)
+++ ProcessDiagram/trunk/Specification/images/unitInformation.svg 2016-01-08 06:53:11 UTC (rev 943)
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Modified: ProcessDiagram/trunk/Specification/le_images/Fig12.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/association-MPF.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/association-multimerisation.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/association.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/catalysis-MAPK.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/compartment.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/complex-examples.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/complex.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/consumption.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/dissociation-ribosome.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/equivalence.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/genetic-plain.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/genetic.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/hemoglobin-complex.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/hemoglobin-macromolecule.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/hemoglobin-multimer.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/inhibition.pdf
===================================================================
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Modified: ProcessDiagram/trunk/Specification/le_images/labeledCloneMarker.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/logicArc.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/macromolecule-examples.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/macromolecule-plain.pdf
===================================================================
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Modified: ProcessDiagram/trunk/Specification/le_images/modulation-VOC.pdf
===================================================================
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Modified: ProcessDiagram/trunk/Specification/le_images/modulation-VOC.svg
===================================================================
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Modified: ProcessDiagram/trunk/Specification/le_images/modulation-nAChR.pdf
===================================================================
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Modified: ProcessDiagram/trunk/Specification/le_images/modulation-nAChR.svg
===================================================================
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Modified: ProcessDiagram/trunk/Specification/le_images/modulation.pdf
===================================================================
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Modified: ProcessDiagram/trunk/Specification/le_images/multimer-examples.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/multimer.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/multimer.svg
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Modified: ProcessDiagram/trunk/Specification/le_images/necessary_stim-genetic.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/necessary_stim-transport.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/necessary_stim.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/omitted.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/or.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/perturbing_agent.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/phenotype.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/process-dimerisation.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/process-modulated.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/process-phosphorylation.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/process-reaction.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/process-reversible.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/process.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/production.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/refcard.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/refcard.svg
===================================================================
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Modified: ProcessDiagram/trunk/Specification/le_images/simpleChemical-examples.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/simpleChemical.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/simpleCloneMarker.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/stateVariable.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/stimulation.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/submap-dissociated.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/submap-dissociated.svg
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Modified: ProcessDiagram/trunk/Specification/le_images/submap-folded.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/submap-folded.svg
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Modified: ProcessDiagram/trunk/Specification/le_images/submap-unfolded.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/submap.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/unitInformation.pdf
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Modified: ProcessDiagram/trunk/Specification/le_images/unspecified.pdf
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Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <stu...@us...> - 2015-12-24 12:36:40
|
Revision: 942
http://sourceforge.net/p/sbgn/code/942
Author: stumoodie
Date: 2015-12-24 12:36:39 +0000 (Thu, 24 Dec 2015)
Log Message:
-----------
Review copy of PD V2 spec.
Added Paths:
-----------
ProcessDiagram/tags/L1V2DraftForReview2/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <stu...@us...> - 2015-12-24 12:30:35
|
Revision: 941
http://sourceforge.net/p/sbgn/code/941
Author: stumoodie
Date: 2015-12-24 12:30:33 +0000 (Thu, 24 Dec 2015)
Log Message:
-----------
Fixed minor issues. Ready for release.
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/examples/MAPK.svg
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/examples.tex
ProcessDiagram/trunk/Specification/sources/glyphs.tex
Modified: ProcessDiagram/trunk/Specification/examples/MAPK.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/MAPK.svg 2015-11-16 23:45:25 UTC (rev 940)
+++ ProcessDiagram/trunk/Specification/examples/MAPK.svg 2015-12-24 12:30:33 UTC (rev 941)
@@ -47,17 +47,17 @@
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- id="tspan6613"
+ d="m 113.56495,147.3423 140.26338,0"
+ style="fill:none;stroke:#000000;stroke-width:1.99999988;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ inkscape:connector-curvature="0" />
+ <g
+ id="g5041"
+ transform="translate(20,0)">
+ <path
+ sodipodi:nodetypes="cccccccc"
+ id="path6609"
+ d="m 721.13115,632.44063 0,38.4697 -68.2356,0 -0.007,0 -28.96885,-18.97913 28.97549,-19.43611 0.11955,-10e-4 68.11605,-0.0531 z"
+ style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:2;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ inkscape:connector-curvature="0" />
+ <text
+ id="text6611"
+ y="657.47894"
x="671.86853"
- y="657.47894"
- style="font-size:14.28316784px">ERK</tspan></text>
+ style="font-style:normal;font-weight:normal;font-size:3.57079196px;font-family:'Bitstream Vera Sans';fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ xml:space="preserve"><tspan
+ style="font-size:14.28316784px"
+ y="657.47894"
+ x="671.86853"
+ id="tspan6613"
+ sodipodi:role="line">ERK</tspan></text>
+ </g>
<path
id="path6615"
- d="M 574.58295,651.74865 L 624.84634,651.74865"
- style="fill:none;fill-opacity:0.75;fill-rule:evenodd;stroke:#000000;stroke-width:2;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
+ d="m 574.58293,651.74864 68.76339,0"
+ style="fill:none;fill-opacity:0.75;fill-rule:evenodd;stroke:#000000;stroke-width:2;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ inkscape:connector-curvature="0" />
<rect
rx="6.7917018"
ry="6.2293868"
@@ -993,5 +1005,12 @@
id="path3946"
d="m 419.75183,629.50802 0,-17.4247"
style="fill:none;stroke:#000000;stroke-width:1.80510938;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;overflow:visible" />
+ <rect
+ style="opacity:1;fill:none;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:3.54330707;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ id="rect5034"
+ width="729"
+ height="775"
+ x="14"
+ y="49.362183" />
</g>
</svg>
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sources/examples.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/examples.tex 2015-11-16 23:45:25 UTC (rev 940)
+++ ProcessDiagram/trunk/Specification/sources/examples.tex 2015-12-24 12:30:33 UTC (rev 941)
@@ -6,26 +6,26 @@
\begin{figure}[htb]
\begin{center}
-\scalebox{0.5}{\includegraphics{examples/glycolysis}}
+\scalebox{0.4}{\includegraphics{examples/glycolysis}}
\caption{Glycolysis. This example illustrates how SBGN can be used to describe metabolic pathways.}\label{fig:glycolysis}
\end{center}
\end{figure}
\fig{insulin} presents an example of signalling pathway, that exemplifies in addition the use of the \glyph{EPN} \glyph{complex}, the \glyph{state variable}, the \glyph{container} \glyph{compartment}, the \glyph{submap}, the \glyph{PNs} \glyph{association} and \glyph{phenotype}, and the \glyph{connecting arc} \glyph{stimulation}. Note the complex IGF and IGF receptor, located on the boundary of the compartment. This position is only for user convenience. The complex has to belong to a given compartment in \SBGNPDLone.
-\begin{figure}[t]
+\begin{figure}[htb]
\begin{center}
-\scalebox{0.5}{\includegraphics{examples/insulin}}
+\scalebox{0.4}{\includegraphics{examples/insulin}}
\caption{Insulin-like Growth Factor (IGF) signalling. This example shows the use of compartments and how details can be hidden by using a submap. The submap is shown on \fig{mapk}.}\label{fig:insulin}
\end{center}
\end{figure}
\fig{mapk} is an expanded version of the submap present on the map present in \fig{insulin}. It shows the use of \glyph{tag}.
-\begin{figure}[b]
+\begin{figure}[htb]
\begin{center}
-\scalebox{0.5}{\includegraphics{examples/MAPK}}
-\caption{A submap of the previous map showing the MAPK cascade.}\label{fig:mapk}
+\scalebox{0.3}{\includegraphics{examples/MAPK}}
+\caption{The expanded submap of the previous map showing the MAPK cascade.}\label{fig:mapk}
\end{center}
\end{figure}
@@ -42,7 +42,7 @@
\begin{figure}[htb]
\begin{center}
-\scalebox{0.5}{\includegraphics{examples/IFNGeneRef}}
+\scalebox{0.4}{\includegraphics{examples/IFNGeneRef}}
\caption{Activated STAT1$\alpha$ induction of the IRF1 gene. An example of gene regulation using logical operators.}\label{fig:IFN}
\end{center}
\end{figure}
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-11-16 23:45:25 UTC (rev 940)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-12-24 12:30:33 UTC (rev 941)
@@ -1941,8 +1941,8 @@
\subsubsection{Associations}
\begin{attributes}
-\associtem{terminals}{SubmapTerminal}{1..*} The terminals provide a
-reference between the EPNs in the Main Map and those in the submap,
+\associtem{terminals}{SubmapTerminal}{1..*} The terminals show how the
+EPNs in the Map link to those in the collapsed submap,
which are identified by a \sbgnclass{Tag}.
\end{attributes}
@@ -1998,9 +1998,9 @@
\subsubsection{Changes from Previous Version}
-This glyph was called \glyph{Submap} in previous version of the \PD
-specification. The semantics of the Submap have been clarified and the
-ability of submaps to be independent of the main map has been removed.
+The semantics of the Submap have been clarified and the ability of
+submaps to be independent of a map has been removed\footnote{This
+ change was agreed at SBGN 10 in Los Angeles, 2014.}.
\umlclasshead{LogicalOperator}
\label{sec:techref:logic}
@@ -2184,7 +2184,7 @@
\begin{tabular}[c]{l p{10cm}}
\\\toprule
generic & A generic stoichiometric process that transforms a set of entity pools into another set of entity pools.\\
-omitted & Omitted processes are processes that are known to exist, but are omitted from the map for the sake of clarity or parsimony. A single \glyph{omitted process} can represent any number of actual processes. The \glyph{omitted process} is different from a \glyph{submap}. While a \glyph{submap} references to an explicit content, that is hidden in the main map, the \glyph{omitted process} does not ``hide'' anything within the context of the map, and cannot be ``unfolded''.\\
+omitted & Omitted processes are processes that are known to exist, but are omitted from the map for the sake of clarity or parsimony. A single \glyph{omitted process} can represent any number of actual processes. The \glyph{omitted process} is different from a \glyph{submap}. While a \glyph{submap} references to an explicit content, that is hidden in the map, the \glyph{omitted process} does not ``hide'' anything within the context of the map, and cannot be ``unfolded''.\\
uncertain & Uncertain processes are processes that may not exist. A single \glyph{uncertain process} can represent any number of actual processes.\\
association & The association between one or more \glyph{EPNs} represents the non-covalent binding of the biological objects represented by those \glyph{EPNs} into a larger complex.\\
dissociation & The dissociation of an \glyph{EPN} into one or more \glyph{EPNs} represents the rupture of a non-covalent binding between the biological entities represented by those \glyph{EPNs}.\\
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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|
From: <tcz...@us...> - 2015-11-16 23:45:27
|
Revision: 940
http://sourceforge.net/p/sbgn/code/940
Author: tczauderna
Date: 2015-11-16 23:45:25 +0000 (Mon, 16 Nov 2015)
Log Message:
-----------
fixed some overfull boxes
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
ProcessDiagram/trunk/Specification/sources/glyphs.tex
ProcessDiagram/trunk/Specification/sources/introduction.tex
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-11-16 23:05:15 UTC (rev 939)
+++ ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-11-16 23:45:25 UTC (rev 940)
@@ -18,7 +18,7 @@
\section{Level 1 Release 1.1}
-The specification of SBGN PD Level 1 Release 1.1 was written by Stuart Moodie and Nicolas \lenov{}, with contributions from (in alphabetical order) Frank Bergmann, Sarah Boyd, Emek Demir, Sarala Wimalaratne, Yukiko Matsuoka, Huaiyu Mi, Falk Schreiber, Anatoly Sorokin, and Alice Vill\'{e}ger.
+The specification of SBGN PD Level 1 Release 1.1 was written by Stuart Moodie and Nicolas Le Nov\`{e}re, with contributions from (in alphabetical order) Frank Bergmann, Sarah Boyd, Emek Demir, Sarala Wimalaratne, Yukiko Matsuoka, Huaiyu Mi, Falk Schreiber, Anatoly Sorokin, and Alice Vill\'{e}ger.
\section{Level 1 Release 1.2}
@@ -54,8 +54,8 @@
Ontario Genomics Institute (OGI, \url{http://www.ontariogenomics.ca}),
National Science Foundation (NSF, \url{http://www.nsf.gov}),
USC Norris Comprehensive Cancer Center (\url{http://uscnorriscancer.usc.edu}),
-Martin Luther University Halle-Wittenberg (\url{http://www.uni-halle.de}),
-Monash University (\url{http://www.monash.edu}),
+Martin Luther University Halle-Witten\-berg (\url{http://www.uni-halle.de}),
+Monash University (\url{http://www.monash.edu}), \\
IPK Gatersleben (\url{http://www.ipk-gatersleben.de/en}),
University of Rostock (\url{http://www.uni-rostock.de}) and
German Federal Ministry of Research and Education (\url{http://www.bmbf.de}) provided additional support for SBGN workshops.
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-11-16 23:05:15 UTC (rev 939)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-11-16 23:45:25 UTC (rev 940)
@@ -1425,8 +1425,7 @@
\label{defn:Complex}
A \sbgnclass{Complex} represents a biochemical entity composed of
-other biochemical entities, whether macromolecules, simple chemicals,
-multimers, or other complexes (figure
+other biochemical entities, whether simple chemicals, macromolecules, multimers, or other complexes (figure
\ref{fig:techref:complexsubunituml}). The \sbgnclass{Complex} can described
its composition by the set of \sbgnclass{Subunit}s it contains (see
figure \ref{sec:techref:subunits}). This description is entirely optional and
@@ -2811,7 +2810,7 @@
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
+conformations as in the closed/open/de\-sen\-si\-tized conformations of a
transmembrane channel, and the active/inactive forms of an enzyme.
In the \PDl these states are defined by the
@@ -3874,8 +3873,8 @@
\sbgnclass{EquivalenceArc} (figure \ref{fig:techref:equivalencearcuml}) is the arc used to link a cross-reference
-to an EPN in another \PDm (represented by \classref{CrossReference})
-with an EPN (\classref{EntityPoolNode}) in this map.
+to an \classref{EntityPoolNode} in another \PDm (represented by \classref{CrossReference})
+with an \classref{EntityPoolNode} in this map.
\subsubsection{Generalisation}
Modified: ProcessDiagram/trunk/Specification/sources/introduction.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/introduction.tex 2015-11-16 23:05:15 UTC (rev 939)
+++ ProcessDiagram/trunk/Specification/sources/introduction.tex 2015-11-16 23:45:25 UTC (rev 940)
@@ -18,7 +18,7 @@
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
+standardize the graphical/vis\-ual 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
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2015-11-16 23:05:16
|
Revision: 939
http://sourceforge.net/p/sbgn/code/939
Author: tczauderna
Date: 2015-11-16 23:05:15 +0000 (Mon, 16 Nov 2015)
Log Message:
-----------
fixed a typo
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sources/glyphs.tex
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-08-08 15:00:29 UTC (rev 938)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-11-16 23:05:15 UTC (rev 939)
@@ -1322,7 +1322,7 @@
\label{fig:techref:example-camkii}
\end{figure}
-\fig{techref:example-glur} represents the glutamate receptor in the open state, with both phosphorylation and glycosylation. The entity carries two functional domains, the ligand-binding domain and the ion pore, and its chemical nature is precided.
+\fig{techref:example-glur} represents the glutamate receptor in the open state, with both phosphorylation and glycosylation. The entity carries two functional domains, the ligand-binding domain and the ion pore, and its chemical nature is preceded.
\begin{figure}[htb]
\centering
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <ca...@us...> - 2015-08-08 15:00:31
|
Revision: 938
http://sourceforge.net/p/sbgn/code/938
Author: cannin
Date: 2015-08-08 15:00:29 +0000 (Sat, 08 Aug 2015)
Log Message:
-----------
Added ER L1V2 PDF
Added Paths:
-----------
EntityRelationship/trunk/sbgn_ER-level1.pdf
Added: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Index: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
--- EntityRelationship/trunk/sbgn_ER-level1.pdf 2015-08-08 14:59:15 UTC (rev 937)
+++ EntityRelationship/trunk/sbgn_ER-level1.pdf 2015-08-08 15:00:29 UTC (rev 938)
Property changes on: EntityRelationship/trunk/sbgn_ER-level1.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/pdf
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <ca...@us...> - 2015-08-08 14:59:16
|
Revision: 937
http://sourceforge.net/p/sbgn/code/937
Author: cannin
Date: 2015-08-08 14:59:15 +0000 (Sat, 08 Aug 2015)
Log Message:
-----------
Removed unneeded files
Removed Paths:
-------------
EntityRelationship/tags/tagsB/
EntityRelationship/trunk/sbgn_ER-level1.pdf
Deleted: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <ca...@us...> - 2015-08-08 14:38:25
|
Revision: 936
http://sourceforge.net/p/sbgn/code/936
Author: cannin
Date: 2015-08-08 14:38:23 +0000 (Sat, 08 Aug 2015)
Log Message:
-----------
Added reference card templates
Added Paths:
-----------
EntityRelationship/trunk/templates/
EntityRelationship/trunk/templates/ER_L1V1.2-Inkscape.svg
EntityRelationship/trunk/templates/ER_L1V1.2.eps
EntityRelationship/trunk/templates/ER_L1V1.2.pdf
EntityRelationship/trunk/templates/ER_L1V1.2.png
EntityRelationship/trunk/templates/ER_L1V1.2.svg
Added: EntityRelationship/trunk/templates/ER_L1V1.2-Inkscape.svg
===================================================================
(Binary files differ)
Index: EntityRelationship/trunk/templates/ER_L1V1.2-Inkscape.svg
===================================================================
--- EntityRelationship/trunk/templates/ER_L1V1.2-Inkscape.svg 2015-08-08 14:21:13 UTC (rev 935)
+++ EntityRelationship/trunk/templates/ER_L1V1.2-Inkscape.svg 2015-08-08 14:38:23 UTC (rev 936)
Property changes on: EntityRelationship/trunk/templates/ER_L1V1.2-Inkscape.svg
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Added: svn:mime-type
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+image/svg+xml
\ No newline at end of property
Added: EntityRelationship/trunk/templates/ER_L1V1.2.eps
===================================================================
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Index: EntityRelationship/trunk/templates/ER_L1V1.2.eps
===================================================================
--- EntityRelationship/trunk/templates/ER_L1V1.2.eps 2015-08-08 14:21:13 UTC (rev 935)
+++ EntityRelationship/trunk/templates/ER_L1V1.2.eps 2015-08-08 14:38:23 UTC (rev 936)
Property changes on: EntityRelationship/trunk/templates/ER_L1V1.2.eps
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+application/postscript
\ No newline at end of property
Added: EntityRelationship/trunk/templates/ER_L1V1.2.pdf
===================================================================
(Binary files differ)
Index: EntityRelationship/trunk/templates/ER_L1V1.2.pdf
===================================================================
--- EntityRelationship/trunk/templates/ER_L1V1.2.pdf 2015-08-08 14:21:13 UTC (rev 935)
+++ EntityRelationship/trunk/templates/ER_L1V1.2.pdf 2015-08-08 14:38:23 UTC (rev 936)
Property changes on: EntityRelationship/trunk/templates/ER_L1V1.2.pdf
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Added: svn:mime-type
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+application/pdf
\ No newline at end of property
Added: EntityRelationship/trunk/templates/ER_L1V1.2.png
===================================================================
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Index: EntityRelationship/trunk/templates/ER_L1V1.2.png
===================================================================
--- EntityRelationship/trunk/templates/ER_L1V1.2.png 2015-08-08 14:21:13 UTC (rev 935)
+++ EntityRelationship/trunk/templates/ER_L1V1.2.png 2015-08-08 14:38:23 UTC (rev 936)
Property changes on: EntityRelationship/trunk/templates/ER_L1V1.2.png
___________________________________________________________________
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+*
\ No newline at end of property
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+image/png
\ No newline at end of property
Added: EntityRelationship/trunk/templates/ER_L1V1.2.svg
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Index: EntityRelationship/trunk/templates/ER_L1V1.2.svg
===================================================================
--- EntityRelationship/trunk/templates/ER_L1V1.2.svg 2015-08-08 14:21:13 UTC (rev 935)
+++ EntityRelationship/trunk/templates/ER_L1V1.2.svg 2015-08-08 14:38:23 UTC (rev 936)
Property changes on: EntityRelationship/trunk/templates/ER_L1V1.2.svg
___________________________________________________________________
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## -0,0 +1 ##
+*
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+image/svg+xml
\ No newline at end of property
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From: <ca...@us...> - 2015-08-08 14:21:19
|
Revision: 935
http://sourceforge.net/p/sbgn/code/935
Author: cannin
Date: 2015-08-08 14:21:13 +0000 (Sat, 08 Aug 2015)
Log Message:
-----------
Added Makefile goal to clear out temporary files
Removed draft notice
Added tagged version
Modified Paths:
--------------
EntityRelationship/trunk/Makefile
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/front-page.tex
Added Paths:
-----------
EntityRelationship/tags/Level1-Version2/
EntityRelationship/tags/Level1-Version2/Makefile
EntityRelationship/tags/Level1-Version2/README.txt
EntityRelationship/tags/Level1-Version2/examples/
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro-new-2.eps
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro-new-2.pdf
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro-new-2.png
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro-new-2.svg
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro-new.eps
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro-new.pdf
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro-new.png
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro-new.svg
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro.eps
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro.pdf
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro.png
EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro.svg
EntityRelationship/tags/Level1-Version2/examples/HelloWorld.pdf
EntityRelationship/tags/Level1-Version2/examples/PCR.eps
EntityRelationship/tags/Level1-Version2/examples/PCR.pdf
EntityRelationship/tags/Level1-Version2/examples/PCR.png
EntityRelationship/tags/Level1-Version2/examples/PCR.svg
EntityRelationship/tags/Level1-Version2/examples/ex-absoluteInhibition.eps
EntityRelationship/tags/Level1-Version2/examples/ex-absoluteInhibition.pdf
EntityRelationship/tags/Level1-Version2/examples/ex-absoluteInhibition.png
EntityRelationship/tags/Level1-Version2/examples/ex-absoluteInhibition.svg
EntityRelationship/tags/Level1-Version2/examples/ex-annotation.eps
EntityRelationship/tags/Level1-Version2/examples/ex-annotation.pdf
EntityRelationship/tags/Level1-Version2/examples/ex-annotation.png
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EntityRelationship/tags/Level1-Version2/examples/ex-assignement.png
EntityRelationship/tags/Level1-Version2/examples/ex-assignment.eps
EntityRelationship/tags/Level1-Version2/examples/ex-assignment.pdf
EntityRelationship/tags/Level1-Version2/examples/ex-assignment.svg
EntityRelationship/tags/Level1-Version2/examples/ex-delay.eps
EntityRelationship/tags/Level1-Version2/examples/ex-delay.pdf
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EntityRelationship/tags/Level1-Version2/examples/ex-domain.eps
EntityRelationship/tags/Level1-Version2/examples/ex-domain.pdf
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EntityRelationship/tags/Level1-Version2/examples/ex-domain.svg
EntityRelationship/tags/Level1-Version2/examples/ex-entity.eps
EntityRelationship/tags/Level1-Version2/examples/ex-entity.pdf
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EntityRelationship/tags/Level1-Version2/examples/ex-existence.eps
EntityRelationship/tags/Level1-Version2/examples/ex-existence.pdf
EntityRelationship/tags/Level1-Version2/examples/ex-existence.png
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EntityRelationship/tags/Level1-Version2/examples/ex-inhibition.eps
EntityRelationship/tags/Level1-Version2/examples/ex-inhibition.pdf
EntityRelationship/tags/Level1-Version2/examples/ex-inhibition.png
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EntityRelationship/tags/Level1-Version2/examples/ex-interaction-influences.eps
EntityRelationship/tags/Level1-Version2/examples/ex-interaction-influences.pdf
EntityRelationship/tags/Level1-Version2/examples/ex-interaction-influences.png
EntityRelationship/tags/Level1-Version2/examples/ex-interaction-influences.svg
EntityRelationship/tags/Level1-Version2/examples/ex-interaction.eps
EntityRelationship/tags/Level1-Version2/examples/ex-interaction.pdf
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EntityRelationship/tags/Level1-Version2/sources/necessaryStimulation.tex
EntityRelationship/tags/Level1-Version2/sources/non-interaction.tex
EntityRelationship/tags/Level1-Version2/sources/not.tex
EntityRelationship/tags/Level1-Version2/sources/or.tex
EntityRelationship/tags/Level1-Version2/sources/outcome.tex
EntityRelationship/tags/Level1-Version2/sources/perturbation.tex
EntityRelationship/tags/Level1-Version2/sources/phenotype.tex
EntityRelationship/tags/Level1-Version2/sources/preface.tex
EntityRelationship/tags/Level1-Version2/sources/refcard.aux
EntityRelationship/tags/Level1-Version2/sources/refcard.tex
EntityRelationship/tags/Level1-Version2/sources/relationships.tex
EntityRelationship/tags/Level1-Version2/sources/revision_history.aux
EntityRelationship/tags/Level1-Version2/sources/revision_history.tex
EntityRelationship/tags/Level1-Version2/sources/semantics.tex
EntityRelationship/tags/Level1-Version2/sources/stateVariable.tex
EntityRelationship/tags/Level1-Version2/sources/stimulation.tex
EntityRelationship/tags/Level1-Version2/sources/submap.tex
EntityRelationship/tags/Level1-Version2/sources/syncEv.tex
EntityRelationship/tags/Level1-Version2/sources/syntax.tex
EntityRelationship/tags/Level1-Version2/sources/toc.tex
EntityRelationship/tags/Level1-Version2/sources/typography.tex
EntityRelationship/tags/Level1-Version2/sources/unitInformation.tex
EntityRelationship/tags/Level1-Version2/sources/usermanual.tex
EntityRelationship/tags/Level1-Version2/sources/usermanual.tex.backup
EntityRelationship/tags/Level1-Version2/sources/variableValue.tex
EntityRelationship/tags/Level1-Version2/sources/versioning.tex
EntityRelationship/tags/Level1-Version2/sources/working.aux
EntityRelationship/tags/Level1-Version2/sources/working.tex
EntityRelationship/tags/Level1-Version2/templates/
EntityRelationship/tags/Level1-Version2/templates/ER_L1V1.2-Inkscape.svg
EntityRelationship/tags/Level1-Version2/templates/ER_L1V1.2.eps
EntityRelationship/tags/Level1-Version2/templates/ER_L1V1.2.pdf
EntityRelationship/tags/Level1-Version2/templates/ER_L1V1.2.png
EntityRelationship/tags/Level1-Version2/templates/ER_L1V1.2.svg
Property Changed:
----------------
/
Index:
===================================================================
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+*.idea
Added: EntityRelationship/tags/Level1-Version2/Makefile
===================================================================
--- EntityRelationship/tags/Level1-Version2/Makefile (rev 0)
+++ EntityRelationship/tags/Level1-Version2/Makefile 2015-08-08 14:21:13 UTC (rev 935)
@@ -0,0 +1,37 @@
+# =============================================================================
+# Top-level Makefile for the SBGN Entity Relationship specification.
+#
+# $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/trunk/documents/specifications/EntityRelationship/Level1/Makefile $
+# =============================================================================
+
+MAIN = sbgn_ER-level1
+
+LATEX = pdflatex
+BIBTEX = bibtex
+
+all default:
+ $(LATEX) $(MAIN).tex
+ $(LATEX) $(MAIN).tex
+ $(BIBTEX) $(MAIN)
+ $(LATEX) $(MAIN).tex
+
+# Clean up temporary files
+clean:
+ rm -f *.aux
+ rm -f *.bbl
+ rm -f *.blg
+ rm -f *.log
+ rm -f *.lox
+ rm -f *.out
+ rm -f *.toc
+
+# Clean up temporary files and PDF output
+distclean:
+ rm -f *.aux
+ rm -f *.bbl
+ rm -f *.blg
+ rm -f *.log
+ rm -f *.lox
+ rm -f *.out
+ rm -f *.toc
+ rm -f *.pdf
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===================================================================
--- EntityRelationship/tags/Level1-Version2/README.txt (rev 0)
+++ EntityRelationship/tags/Level1-Version2/README.txt 2015-08-08 14:21:13 UTC (rev 935)
@@ -0,0 +1,13 @@
+
+ Specification for the
+
+ ----------------------------------------
+ Systems Biology Graphical Notation (SBGN)
+ Entity Relationship Level 1
+ ----------------------------------------
+
+ For more information about SBGN, visit:
+ http://sbgn.org
+
+ Please join the sbgn-discuss mailing list by visiting
+ http://www.sbgn.org/Forums
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--- EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro-new-2.svg 2015-08-08 13:50:26 UTC (rev 934)
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===================================================================
--- EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro-new.pdf 2015-08-08 13:50:26 UTC (rev 934)
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--- EntityRelationship/tags/Level1-Version2/examples/CaMKII-intro.pdf 2015-08-08 13:50:26 UTC (rev 934)
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Property changes on: EntityRelationship/tags/Level1-Version2/examples/ex-assignment.eps
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+application/postscript
\ No newline at end of property
Added: EntityRelationship/tags/Level1-Version2/examples/ex-assignment.pdf
===================================================================
(Binary files differ)
Index: EntityRelationship/tags/Level1-Version2/examples/ex-assignment.pdf
===================================================================
--- EntityRelationship/tags/Level1-Version2/examples/ex-assignment.pdf 2015-08-08 13:50:26 UTC (rev 934)
+++ EntityRelationship/tags/Level1-Version2/examples/ex-assignment.pdf 2015-08-08 14:21:13 UTC (rev 935)
Property changes on: EntityRelationship/tags/Level1-Version2/examples/ex-assignment.pdf
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+application/pdf
\ No newline at end of property
Added: EntityRelationship/tags/Level1-Version2/examples/ex-assignment.svg
===================================================================
(Binary files differ)
Index: EntityRelationship/tags/Level1-Version2/examples/ex-assignment.svg
===================================================================
--- EntityRelationship/tags/Level1-Version2/examples/ex-assignment.svg 2015-08-08 13:50:26 UTC (rev 934)
+++ EntityRelationship/tags/Level1-Version2/examples/ex-assignment.svg 2015-08-08 14:21:13 UTC (rev 935)
Property changes on: EntityRelationship/tags/Level1-Version2/examples/ex-assignment.svg
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+image/svg+xml
\ No newline at end of property
Added: EntityRelationship/tags/Level1-Version2/examples/ex-delay.eps
===================================================================
(Binary files differ)
Index: EntityRelationship/tags/Level1-Version2/examples/ex-delay.eps
===================================================================
--- EntityRelationship/tags/Level1-Version2/examples/ex-delay.eps 2015-08-08 13:50:26 UTC (rev 934)
+++ EntityRelationship/tags/Level1-Version2/examples/ex-delay.eps 2015-08-08 14:21:13 UTC (rev 935)
Property changes on: EntityRelationship/tags/Level1-Version2/examples/ex-delay.eps
___________________________________________________________________
Added: svn:execut...
[truncated message content] |
|
From: <ca...@us...> - 2015-08-08 13:50:29
|
Revision: 934
http://sourceforge.net/p/sbgn/code/934
Author: cannin
Date: 2015-08-08 13:50:26 +0000 (Sat, 08 Aug 2015)
Log Message:
-----------
Modified Paths:
--------------
EntityRelationship/tags/tagsB/Makefile
EntityRelationship/tags/tagsB/sbgn_ER-level1.pdf
EntityRelationship/tags/tagsB/sources/front-page.tex
Added Paths:
-----------
EntityRelationship/tags/tagsB/
Modified: EntityRelationship/tags/tagsB/Makefile
===================================================================
--- EntityRelationship/trunk/Makefile 2015-08-05 06:37:28 UTC (rev 932)
+++ EntityRelationship/tags/tagsB/Makefile 2015-08-08 13:50:26 UTC (rev 934)
@@ -14,3 +14,24 @@
$(LATEX) $(MAIN).tex
$(BIBTEX) $(MAIN)
$(LATEX) $(MAIN).tex
+
+# Clean up temporary files
+clean:
+ rm -f *.aux
+ rm -f *.bbl
+ rm -f *.blg
+ rm -f *.log
+ rm -f *.lox
+ rm -f *.out
+ rm -f *.toc
+
+# Clean up temporary files and PDF output
+distclean:
+ rm -f *.aux
+ rm -f *.bbl
+ rm -f *.blg
+ rm -f *.log
+ rm -f *.lox
+ rm -f *.out
+ rm -f *.toc
+ rm -f *.pdf
Modified: EntityRelationship/tags/tagsB/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/tags/tagsB/sources/front-page.tex
===================================================================
--- EntityRelationship/trunk/sources/front-page.tex 2015-08-05 06:37:28 UTC (rev 932)
+++ EntityRelationship/tags/tagsB/sources/front-page.tex 2015-08-08 13:50:26 UTC (rev 934)
@@ -21,10 +21,10 @@
%Date: \sbgndate\\[0.25in]
Date: \today\\[0.25in]
- \cornersize{0.3}\ovalbox{\begin{minipage}{4.9in}\color{DarkRed}
- Disclaimer: This is a working draft of the SBGN Entity Relationship
- Level~1 Version 2 specification. It is not a normative document.
- \end{minipage}}
+% \cornersize{0.3}\ovalbox{\begin{minipage}{4.9in}\color{DarkRed}
+ %Disclaimer: This is a working draft of the SBGN Entity Relationship
+ %Level~1 Version 2 specification. It is not a normative document.
+ %\end{minipage}}
\vspace{0.5in}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ca...@us...> - 2015-08-08 13:44:35
|
Revision: 933
http://sourceforge.net/p/sbgn/code/933
Author: cannin
Date: 2015-08-08 13:44:33 +0000 (Sat, 08 Aug 2015)
Log Message:
-----------
Modified Paths:
--------------
EntityRelationship/tags/Level1-Version1.2/trunk/Makefile
EntityRelationship/tags/Level1-Version1.2/trunk/sbgn_ER-level1.pdf
EntityRelationship/tags/Level1-Version1.2/trunk/sources/front-page.tex
Added Paths:
-----------
EntityRelationship/tags/Level1-Version1.2/trunk/
Modified: EntityRelationship/tags/Level1-Version1.2/trunk/Makefile
===================================================================
--- EntityRelationship/trunk/Makefile 2015-08-05 06:37:28 UTC (rev 932)
+++ EntityRelationship/tags/Level1-Version1.2/trunk/Makefile 2015-08-08 13:44:33 UTC (rev 933)
@@ -14,3 +14,24 @@
$(LATEX) $(MAIN).tex
$(BIBTEX) $(MAIN)
$(LATEX) $(MAIN).tex
+
+# Clean up temporary files
+clean:
+ rm -f *.aux
+ rm -f *.bbl
+ rm -f *.blg
+ rm -f *.log
+ rm -f *.lox
+ rm -f *.out
+ rm -f *.toc
+
+# Clean up temporary files and PDF output
+distclean:
+ rm -f *.aux
+ rm -f *.bbl
+ rm -f *.blg
+ rm -f *.log
+ rm -f *.lox
+ rm -f *.out
+ rm -f *.toc
+ rm -f *.pdf
Modified: EntityRelationship/tags/Level1-Version1.2/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/tags/Level1-Version1.2/trunk/sources/front-page.tex
===================================================================
--- EntityRelationship/trunk/sources/front-page.tex 2015-08-05 06:37:28 UTC (rev 932)
+++ EntityRelationship/tags/Level1-Version1.2/trunk/sources/front-page.tex 2015-08-08 13:44:33 UTC (rev 933)
@@ -21,10 +21,10 @@
%Date: \sbgndate\\[0.25in]
Date: \today\\[0.25in]
- \cornersize{0.3}\ovalbox{\begin{minipage}{4.9in}\color{DarkRed}
- Disclaimer: This is a working draft of the SBGN Entity Relationship
- Level~1 Version 2 specification. It is not a normative document.
- \end{minipage}}
+% \cornersize{0.3}\ovalbox{\begin{minipage}{4.9in}\color{DarkRed}
+ %Disclaimer: This is a working draft of the SBGN Entity Relationship
+ %Level~1 Version 2 specification. It is not a normative document.
+ %\end{minipage}}
\vspace{0.5in}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2015-08-05 06:37:30
|
Revision: 932
http://sourceforge.net/p/sbgn/code/932
Author: tczauderna
Date: 2015-08-05 06:37:28 +0000 (Wed, 05 Aug 2015)
Log Message:
-----------
fixed warnings;
fixed issues;
fixed some overfull boxes;
made bibliography more consistent
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.bib
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sbgn_ER-level1.tex
EntityRelationship/trunk/sources/CVs.tex
EntityRelationship/trunk/sources/acknowledgments.tex
EntityRelationship/trunk/sources/latex-style.tex
EntityRelationship/trunk/sources/revision_history.tex
Modified: EntityRelationship/trunk/sbgn_ER-level1.bib
===================================================================
--- EntityRelationship/trunk/sbgn_ER-level1.bib 2015-08-05 03:57:06 UTC (rev 931)
+++ EntityRelationship/trunk/sbgn_ER-level1.bib 2015-08-05 06:37:28 UTC (rev 932)
@@ -29,7 +29,7 @@
}
@Book{DiBattista:1998,
- author = {{D}i {B}attista, G. and Eades, P. and Tamassia, R. and Tollis, I.~G.},
+ author = {{D}i {B}attista, Giuseppe and Eades, Peter and Tamassia, Roberto and Tollis, Ioannis~G.},
title = {Graph Drawing: Algorithms for the Visualization of Graphs},
year = {1998},
publisher = {Prentice Hall},
@@ -37,11 +37,11 @@
}
@Book{Kaufmann:2001,
- author = {Kaufmann, M. and Wagner, D.},
+ author = {Kaufmann, Michael and Wagner, Dorothea},
title = {Drawing Graphs: Methods and Models},
year = {2001},
volume = {2025},
- series = {Lecture Notes in Computer Science Tutorial},
+ series = {Lecture Notes in Computer Science},
publisher = {Springer},
}
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/trunk/sbgn_ER-level1.tex
===================================================================
--- EntityRelationship/trunk/sbgn_ER-level1.tex 2015-08-05 03:57:06 UTC (rev 931)
+++ EntityRelationship/trunk/sbgn_ER-level1.tex 2015-08-05 06:37:28 UTC (rev 932)
@@ -43,7 +43,7 @@
\bibliographystyle{unsrt}
\bibliography{sbgn_ER-level1}
\clearpage
-\listoffixmes
+%\listoffixmes
%% ----------------------------------------------------------------------------
\end{document}
Modified: EntityRelationship/trunk/sources/CVs.tex
===================================================================
--- EntityRelationship/trunk/sources/CVs.tex 2015-08-05 03:57:06 UTC (rev 931)
+++ EntityRelationship/trunk/sources/CVs.tex 2015-08-05 06:37:28 UTC (rev 932)
@@ -15,7 +15,7 @@
The material type of an \glyph{Entity} indicates its chemical structure. A list of common material types is shown in \tab{material-types-cv}, but others are possible. The values are to be taken from the \sbo (\sbourl), specifically from the branch having identifier \sboid{SBO:0000240} (\emph{material entity}). The labels are defined by \SBGNERLone.
-\begin{table}[h]
+\begin{table}[ht]
\centering
\begin{tabular}{l>{\ttfamily}ll}
\toprule
@@ -68,9 +68,9 @@
A common reason for the introduction of state variables on an entity is to allow access to the configuration of possible covalent modification sites on that entity. For instance, a macromolecule may have one or more sites where a phosphate group may be attached; this change in the site's configuration (\ie being either phosphorylated or not) may factor into whether, and how, the entity can participate in different processes. Being able to describe such modifications in a consistent fashion is the motivation for the existence of SBGN's covalent modifications controlled vocabulary.
-\tab{covalent-mod-cv} lists a number of common types of covalent modifications. The most common values are defined by the \sbo in the branch having identifier \sboid{SBO:0000210} (\emph{addition} under \emph{events}$\rightarrow$\emph{reaction}$\rightarrow$\emph{biochemical reaction}$\rightarrow$\emph{conversion}$\rightarrow$\emph{addition}). The labels shown in \tab{covalent-mod-cv} are defined by \SBGNERLone; for all other kinds of modifications not listed here, the author of an \ERm must create a new label (and should also describe the meaning of the label in a legend or text accompanying the map).
+\tab{covalent-mod-cv} lists a number of common types of covalent modifications. The most common values are defined by the \sbo in the branch having identifier \sboid{SBO:0000210} (\emph{addition} under \emph{events} $\rightarrow$ \emph{reaction} $\rightarrow$ \emph{biochemical reaction} $\rightarrow$ \emph{conversion} $\rightarrow$ \emph{addition}). The labels shown in \tab{covalent-mod-cv} are defined by \SBGNERLone; for all other kinds of modifications not listed here, the author of an \ERm must create a new label (and should also describe the meaning of the label in a legend or text accompanying the map).
-\begin{table}[h]
+\begin{table}[ht]
\centering
\begin{tabular}{l>{\ttfamily}ll}
\toprule
Modified: EntityRelationship/trunk/sources/acknowledgments.tex
===================================================================
--- EntityRelationship/trunk/sources/acknowledgments.tex 2015-08-05 03:57:06 UTC (rev 931)
+++ EntityRelationship/trunk/sources/acknowledgments.tex 2015-08-05 06:37:28 UTC (rev 932)
@@ -17,20 +17,20 @@
\section{Financial support}
-The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, \url{http://www.nedo.go.jp/}).
-The Okinawa Institute of Science and Technology (OIST, \url{http://www.oist.jp/}),
+The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, \url{http://www.nedo.go.jp}).
+The Okinawa Institute of Science and Technology (OIST, \url{http://www.oist.jp}),
the AIST Computational Biology Research Center (AIST CBRC, \url{http://www.cbrc.jp/index.eng.html}),
-the British Biotechnology and Biological Sciences Research Council (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award,
-the European Media Laboratory (EML Research gGmbH, \url{http://www.eml.org/english/}),
+the British Biotechnology and Biological Sciences Research Council (BBSRC, \url{http://www.bbsrc.ac.uk}) through a Japan Partnering Award,
+the European Media Laboratory (EML Research gGmbH, \url{http://www.eml.org/english}),
the Beckman Institute at the California Institute of Technology (\url{http://bnmc.caltech.edu}),
-Ontario Institute for Cancer Research (OICR, \url{http://oicr.on.ca/}),
-Ontario Genomics Institute (OGI, \url{http://www.ontariogenomics.ca/}),
-National Science Foundation (NSF, \url{http://www.nsf.gov/}),
-USC Norris Comprehensive Cancer Center (\url{http://uscnorriscancer.usc.edu/}),
-Martin Luther University Halle-Wittenberg (\url{http://www.uni-halle.de/}),
-Monash University (\url{http://www.monash.edu.au/}),
-IPK Gatersleben (\url{http://www.ipk-gatersleben.de/en/}),
-University of Rostock (\url{http://www.uni-rostock.de/}) and
-German Federal Ministry of Research and Education (\url{http://www.bmbf.de/}) provided additional support for SBGN workshops.
-Some help was provided by the Japan Science and Technology Agency (JST, \url{http://www.jst.go.jp/}) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp/}) for the development of the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
+Ontario Institute for Cancer Research (OICR, \url{http://oicr.on.ca}),
+Ontario Genomics Institute (OGI, \url{http://www.ontariogenomics.ca}),
+National Science Foundation (NSF, \url{http://www.nsf.gov}),
+USC Norris Comprehensive Cancer Center (\url{http://uscnorriscancer.usc.edu}),
+Martin Luther University Halle-Wittenberg (\url{http://www.uni-halle.de}),
+Monash University (\url{http://www.monash.edu}),
+IPK Gatersleben (\url{http://www.ipk-gatersleben.de/en}),
+University of Rostock (\url{http://www.uni-rostock.de}) and
+German Federal Ministry of Research and Education (\url{http://www.bmbf.de}) provided additional support for SBGN workshops.
+Some help was provided by the Japan Science and Technology Agency (JST, \url{http://www.jst.go.jp}) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp}) for the development of the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
Modified: EntityRelationship/trunk/sources/latex-style.tex
===================================================================
--- EntityRelationship/trunk/sources/latex-style.tex 2015-08-05 03:57:06 UTC (rev 931)
+++ EntityRelationship/trunk/sources/latex-style.tex 2015-08-05 06:37:28 UTC (rev 932)
@@ -7,6 +7,10 @@
% Warning: more \usepackage commands are used later in this file.
\usepackage{ifpdf}
+% loading package float before package hyperref avoids these warnings
+% "destination with the same identifier ... has been already used, duplicate ignored"
+\usepackage{float}
+
\ifpdf
% Case: using pdflatex
@@ -49,7 +53,7 @@
\usepackage{array}
\usepackage{fancybox}
\usepackage{xspace}
-\usepackage{float}
+%\usepackage{float}
\usepackage[american]{varioref}
\usepackage[normalem]{ulem}
\usepackage{eso-pic}
@@ -76,6 +80,11 @@
%% Special customizations
%% ----------------------------------------------------------------------------
+% this option avoids these warnings "PDF inclusion: multiple pdfs with page group included in a single page"
+% pdftex 1.40.15 and higher
+% see also https://tex.stackexchange.com/questions/183149/cant-silence-a-pdftex-pdf-inclusion-multiple-pdfs-with-page-group-error
+\pdfsuppresswarningpagegroup=1
+
\makeatletter
% Adjust bottom-of-page behavior and page line spacing.
Modified: EntityRelationship/trunk/sources/revision_history.tex
===================================================================
--- EntityRelationship/trunk/sources/revision_history.tex 2015-08-05 03:57:06 UTC (rev 931)
+++ EntityRelationship/trunk/sources/revision_history.tex 2015-08-05 06:37:28 UTC (rev 932)
@@ -7,7 +7,7 @@
\begin{center}
%\tablecaption{Namespace scope definitions.}
-\label{tab:revision history 1.2}
+\label{tab:revision history 2}
\tablefirsthead{\hline
Description & Message or Tracker ID\\\hline}
\tablehead{\hline
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2015-08-05 03:57:08
|
Revision: 931
http://sourceforge.net/p/sbgn/code/931
Author: tczauderna
Date: 2015-08-05 03:57:06 +0000 (Wed, 05 Aug 2015)
Log Message:
-----------
added catalysis to table on page 64
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/glyphs.tex
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-08-04 05:22:15 UTC (rev 930)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-08-05 03:57:06 UTC (rev 931)
@@ -3657,6 +3657,7 @@
\\\midrule
modulation & \glyph{Modulation}\\
stimulation & \glyph{Stimulation}\\
+catalysis & \glyph{Catalysis}\\
inhibition & \glyph{Inhibition}\\
necessary\_stim & \glyph{Necessary Stimulation}\\
\bottomrule\\
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2015-08-04 05:22:18
|
Revision: 930
http://sourceforge.net/p/sbgn/code/930
Author: tczauderna
Date: 2015-08-04 05:22:15 +0000 (Tue, 04 Aug 2015)
Log Message:
-----------
fixed misspellings according to Augustin's list;
fixed warnings;
made bibliography more consistent;
fixed a typo on front page
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
ProcessDiagram/trunk/Specification/sources/front-page.tex
ProcessDiagram/trunk/Specification/sources/glyphs.tex
ProcessDiagram/trunk/Specification/sources/grammar.tex
ProcessDiagram/trunk/Specification/sources/language_overview.tex
ProcessDiagram/trunk/Specification/sources/latex-style.tex
ProcessDiagram/trunk/Specification/sources/layout.tex
ProcessDiagram/trunk/Specification/sources/revision_history.tex
ProcessDiagram/trunk/Specification/sources/whatsnew.tex
ProcessDiagram/trunk/Specification/sources/working.tex
Added Paths:
-----------
ProcessDiagram/trunk/Specification/readme!.txt
Added: ProcessDiagram/trunk/Specification/readme!.txt
===================================================================
--- ProcessDiagram/trunk/Specification/readme!.txt (rev 0)
+++ ProcessDiagram/trunk/Specification/readme!.txt 2015-08-04 05:22:15 UTC (rev 930)
@@ -0,0 +1,16 @@
+If compiling the pdf from an environment like TeXnicCenter make sure to
+
+* create PDFs from the SVG images using Inkscape
+
+ call make in these folders
+ /examples
+ /images
+ /le_images
+
+* create the glossaries for the rules
+
+ with Perl
+ makeglossaries sbgn_PD-level1
+
+ without Perl
+ makeindex -s sbgn_PD-level1.ist -t sbgn_PD-level1.glg -o sbgn_PD-level1.gls sbgn_PD-level1.glo
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib 2015-08-04 05:22:15 UTC (rev 930)
@@ -40,7 +40,7 @@
}
@Book{DiBattista:1998,
- author = {{D}i {B}attista, G. and Eades, P. and Tamassia, R. and Tollis, I.G.},
+ author = {{D}i {B}attista, Giuseppe and Eades, Peter and Tamassia, Roberto and Tollis, Ioannis G.},
title = {Graph Drawing: Algorithms for the Visualization of Graphs},
year = {1998},
publisher = {Prentice Hall},
@@ -48,11 +48,11 @@
}
@Book{Kaufmann:2001,
- author = {Kaufmann, M. and Wagner, D.},
+ editor = {Kaufmann, Michael and Wagner, Dorothea},
title = {Drawing Graphs: Methods and Models},
year = {2001},
volume = {2025},
- series = {Lecture Notes in Computer Science Tutorial},
+ series = {Lecture Notes in Computer Science},
publisher = {Springer},
}
@@ -126,7 +126,7 @@
year = {2012},
volume = {30},
number = {11},
- pages = {555-557},
+ pages = {555--557},
}
@InProceedings{Maimon:2001,
@@ -193,18 +193,11 @@
@article{LeNovere:2009p1,
author = {Nicolas Le Nov\`{e}re and Michael Hucka and Huaiyu Mi and Stuart Moodie and Falk Schreiber and Anatoly Sorokin and Emek Demir and Katja Wegner and Mirit Aladjem and Sarala Wimalaratne and Frank Bergman and Ralph Gauges and Peter Ghazal and Hideya Kawaji and Lu Li and Yukiko Matsuoka and Alice Vill\'{e}ger and Sarah Boyd and Laurence Calzone and Melanie Courtot and Ugur Dogrus{\"o}z and Tom Freeman and Akira Funahashi and Samik Ghosh and Akiya Jouraku and Sohyoung Kim and Fedor Kolpakov and Augustin Luna and Sven Sahle and Esther Schmidt and Steven Watterson and Guanming Wu and Igor Goryanin and Douglas Kell and Chris Sander and Herbert Sauro and Jacky Snoep and Kurt Kohn and Hiroaki Kitano},
journal = {Nature Biotechnology},
-title = {The Systems Biology Graphical Notation},
-note = {10.1038/nbt.1558},
+title = {The {S}ystems {B}iology {G}raphical {N}otation},
number = {8},
pages = {735--741},
volume = {27},
year = {2009},
-date-added = {2009-08-26 14:04:26 +0100},
-date-modified = {2009-08-26 14:04:26 +0100},
-doi = {10.1038/nbt.1558},
-URL = {http://dx.doi.org/10.1038/nbt.1558},
-uri = {papers://77A5F866-15B8-4DD4-868D-FB8B6E3E7794/Paper/p1},
-rating = {0}
}
@misc{sbmll3core,
@@ -217,8 +210,7 @@
@misc{umlspec,
title = {{OMG Unified Modeling Language (OMG UML), Superstructure, V2.1.2}},
-author = {Object management Group},
+author = {Object Management Group},
year = 2010,
howpublished = {Available via the World Wide Web at \url{http://www.omg.org/spec/UML/2.1.2/Superstructure/PDF/}},
}
-
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -32,7 +32,7 @@
\usepackage[olditem,oldenum]{paralist}
\usepackage{fourier}
\usepackage{multicol}
-\usepackage[toc,section=chapter,numberedsection]{glossaries}
+%\usepackage[toc,section=chapter,numberedsection]{glossaries}
%\usepackage{layouts}
\usepackage[pdftex]{graphicx}
@@ -42,6 +42,16 @@
\usepackage{rotating}
+% glossaries must be loaded after hyperref
+% to avoid warnings "pdfTeX warning (dest): name{glo:...} has been referenced but does not exist, replaced by a fixed one"
+% use the following three lines or [noredefwarn} as an option for the glossaries package
+% to avoid warnings "Package glossaries Warning: Overriding \printglossary on input line ..." and "Package glossaries Warning: Overriding 'theglossary' environment on input line ..."
+%\let\printglossary\relax
+%\let\theglossary\relax
+%\let\endtheglossary\relax
+%\usepackage[toc,section=chapter,numberedsection]{glossaries}
+\usepackage[toc,section=chapter,numberedsection,noredefwarn]{glossaries}
+
% Booktabs for sharp-looking \toprule, \midrule, \bottomrule in tables.
\usepackage{booktabs}
@@ -66,6 +76,12 @@
%% ----------------------------------------------------------------------------
%\input{sources/latex-style}
+
+% this option avoids these warnings "PDF inclusion: multiple pdfs with page group included in a single page"
+% pdftex 1.40.15 and higher
+% see also https://tex.stackexchange.com/questions/183149/cant-silence-a-pdftex-pdf-inclusion-multiple-pdfs-with-page-group-error
+\pdfsuppresswarningpagegroup=1
+
\input{sources/latex-macros}
\makeglossaries
Modified: ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -1,6 +1,6 @@
\chapter{Acknowledgments}\label{sec:acknowledgments}
-Here we acknowledge those people and organisations the assisted in the develeopment of this and previous releases of the SBGN \PDl specification. First we specifically acknowledge those who contributed directly to each revision of the specification document, followed by a comprehensive acknowledgement of contributors that attended workshops and forum meetings or in some other way provided input to the standard. Finally, we acknowledge the bodies that provided financial support for the development of the standard.
+Here we acknowledge those people and organisations the assisted in the development of this and previous releases of the SBGN \PDl specification. First we specifically acknowledge those who contributed directly to each revision of the specification document, followed by a comprehensive acknowledgement of contributors that attended workshops and forum meetings or in some other way provided input to the standard. Finally, we acknowledge the bodies that provided financial support for the development of the standard.
% Here is a more comprehensive list of person who have been actively involved in SBGN development, either by their help designing the languages, their comments on the specification, help with development infrastructure or any other useful input.\\[\baselineskip]
@@ -14,7 +14,7 @@
the specification benefited much from the help of (in alphabetical order) Frank Bergmann, Sarala
Dissanayake, Ralph Gauges, Peter Ghazal, Lu Li, and Steven Watterson.
-% Mirit Aladjemm, Frank Bergmann, Emek Demir, Sarala Dissanayake, Ugur Dogrusoz, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Igor Goryanin, Michael Hucka, Akiya Jouraku, Sohyoung Kim, Hiroaki Kitano, Kurt Kohn, Fedor Kolpakov , Nicolas Le Nov\`{e}re, Lu Li, Yukiko Matsuoka, Huaiyu Mi, Stuart Moodie, Sven Sahle, Falk Schreiber, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Steven Watterson, Alice Villeger, Katja Wegner.\\[\baselineskip]
+% Mirit Aladjem, Frank Bergmann, Emek Demir, Sarala Dissanayake, Ugur Dogrusoz, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Igor Goryanin, Michael Hucka, Akiya Jouraku, Sohyoung Kim, Hiroaki Kitano, Kurt Kohn, Fedor Kolpakov , Nicolas Le Nov\`{e}re, Lu Li, Yukiko Matsuoka, Huaiyu Mi, Stuart Moodie, Sven Sahle, Falk Schreiber, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Steven Watterson, Alice Villeger, Katja Wegner.\\[\baselineskip]
\section{Level 1 Release 1.1}
@@ -44,22 +44,22 @@
\section{Financial Support}
-The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, \url{http://www.nedo.go.jp/}).
-The Okinawa Institute of Science and Technology (OIST, \url{http://www.oist.jp/}),
+The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, \url{http://www.nedo.go.jp}).
+The Okinawa Institute of Science and Technology (OIST, \url{http://www.oist.jp}),
the AIST Computational Biology Research Center (AIST CBRC, \url{http://www.cbrc.jp/index.eng.html}),
-the British Biotechnology and Biological Sciences Research Council (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award,
-the European Media Laboratory (EML Research gGmbH, \url{http://www.eml.org/english/}),
+the British Biotechnology and Biological Sciences Research Council (BBSRC, \url{http://www.bbsrc.ac.uk}) through a Japan Partnering Award,
+the European Media Laboratory (EML Research gGmbH, \url{http://www.eml.org/english}),
the Beckman Institute at the California Institute of Technology (\url{http://bnmc.caltech.edu}),
-Ontario Institute for Cancer Research (OICR, \url{http://oicr.on.ca/}),
-Ontario Genomics Institute (OGI, \url{http://www.ontariogenomics.ca/}),
-National Science Foundation (NSF, \url{http://www.nsf.gov/}),
-USC Norris Comprehensive Cancer Center (\url{http://uscnorriscancer.usc.edu/}),
-Martin Luther University Halle-Wittenberg (\url{http://www.uni-halle.de/}),
-Monash University (\url{http://www.monash.edu.au/}),
-IPK Gatersleben (\url{http://www.ipk-gatersleben.de/en/}),
-University of Rostock (\url{http://www.uni-rostock.de/}) and
-German Federal Ministry of Research and Education (\url{http://www.bmbf.de/}) provided additional support for SBGN workshops.
-Some help was provided by the Japan Science and Technology Agency (JST, \url{http://www.jst.go.jp/}) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp/}) for the development of the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
+Ontario Institute for Cancer Research (OICR, \url{http://oicr.on.ca}),
+Ontario Genomics Institute (OGI, \url{http://www.ontariogenomics.ca}),
+National Science Foundation (NSF, \url{http://www.nsf.gov}),
+USC Norris Comprehensive Cancer Center (\url{http://uscnorriscancer.usc.edu}),
+Martin Luther University Halle-Wittenberg (\url{http://www.uni-halle.de}),
+Monash University (\url{http://www.monash.edu}),
+IPK Gatersleben (\url{http://www.ipk-gatersleben.de/en}),
+University of Rostock (\url{http://www.uni-rostock.de}) and
+German Federal Ministry of Research and Education (\url{http://www.bmbf.de}) provided additional support for SBGN workshops.
+Some help was provided by the Japan Science and Technology Agency (JST, \url{http://www.jst.go.jp}) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp}) for the development of the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
%The development of SBGN was mainly supported by a grant from the Japanese \emph{New Energy and Industrial Technology Development Organization} (NEDO, \url{http://www.nedo.go.jp/}). The \emph{Okinawa Institute of Science and Technology} (OIST, \url{http://www.oist.jp/}), the \emph{AIST Computational Biology Research Center} (AIST CBRC, \url{http://www.cbrc.jp/index.eng.html}) the British \emph{Biotechnology and Biological Sciences Research Council} (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award, the European Media Laboratory (EML Research gGmbH, \url{http://www.eml-r.org/}), and the Beckman Institute at the California Institute of Technology (\url{http://bnmc.caltech.edu}) provided additional support for SBGN workshops. Some help was provided by the \emph{Japan Science and Technology Agency} (JST, \url{http://www.jst.go.jp/}) and the \emph{Genome Network Project} of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp/}) for the development of the gene regulation network aspect of SBGN, and from the \emph{Engineering and Physical Sciences Research Council} (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
Modified: ProcessDiagram/trunk/Specification/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/front-page.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sources/front-page.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -36,7 +36,7 @@
Stuart Moodie & \emph{Eight Pillars Ltd, UK}\\
Tobias Czauderna & \emph{Monash University, Australia}\\
Emek Demir & \emph{Memorial Sloan-Kettering Institute, USA}\\
-Robin Haw & \emph{Othario Institute for Cancer Research, Canada}\\
+Robin Haw & \emph{Ontario Institute for Cancer Research, Canada}\\
Augustin Luna & \emph{Memorial Sloan-Kettering Institute, USA}\\
Huaiyu Mi & \emph{University of Southern California, USA}\\
Nicolas \lenov & \emph{Babraham Institute, UK}\\
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -98,7 +98,7 @@
\item[R] Required (attributes only).
\item[O] Optional (attributes only).
\item[1] required - only one instance is permitted (association only).
- \item[0..1] optional - zero or one instance ir permitted (association only).
+ \item[0..1] optional - zero or one instance is permitted (association only).
\item[1..*] at least 1 instance is required.
\item[*] any number of instances are permitted.
\end{description}
@@ -176,7 +176,7 @@
superclasses are not included here, but are part of this classes
definition.
\item[Unique Key] The attributes that together uniquely identify the
- \PD element or concept. If this is ommited then there is no unique
+ \PD element or concept. If this is omitted then there is no unique
key. See section~\ref{sec:techref:uniquenessdefinition} for more
information about identity and uniqueness.
\item[Rules and Constraints] The semantics of the class are defined
@@ -317,9 +317,9 @@
\subsubsection{Rules and Constraints}
\begin{valrules}
-\defrule{PD1}{A map is valid if it is empty (although not very
+\defrule{PD01}{A map is valid if it is empty (although not very
useful).}
-\defrule{PD2}{All instances of \classref{SBGNGlyph} must be unique (see
+\defrule{PD02}{All instances of \classref{SBGNGlyph} must be unique (see
section \ref{sec:techref:uniquenessdefinition}).}
\end{valrules}
@@ -452,7 +452,7 @@
\subsubsection{Rules and Constraints}
\begin{valrules}
-\defrule{PD3}{The set of \sbgnclass{SBGNNode}s linked to this node via a
+\defrule{PD03}{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}).}
\end{valrules}
@@ -739,18 +739,18 @@
\subsubsection{Rules and Constraints}
\begin{valrules}
-\defrule{PD4}{If \attrib{cardinality} $>1$ then the descendant glyph must be displayed
+\defrule{PD04}{If \attrib{cardinality} $>1$ then the descendant glyph must be displayed
as a multimer.}
-\defrule{PD5}{If the EPN is drawn directly on a \glyph{Map} then
+\defrule{PD05}{If the EPN is drawn directly on a \glyph{Map} then
\attrib{owning\_compartment} is not set. We interpret this as
belonging to an invisible default compartment.}
-\defrule{PD6}{\attrib{natures} can only use the material type
+\defrule{PD06}{\attrib{natures} can only use the material type
(section~\ref{sec:techref:material-types-cv}), conceptual type
(section \ref{sec:techref:conceptual-types-cv}) or physical
characteristics (section \ref{sec:techref:physical-characteristics-cv}) controlled vocabularies.}
-\defrule{PD7}{The appropriate subclass of \sbgnclass{CloneMarker} must be used
+\defrule{PD07}{The appropriate subclass of \sbgnclass{CloneMarker} must be used
to distinguish logically identical instances of this class.}
-\defrule{PD8}{All \sbgnclass{StateVariableDefinition}s associated with the
+\defrule{PD08}{All \sbgnclass{StateVariableDefinition}s associated with the
\sbgnclass{EntityType} must have an associated
\sbgnclass{StateVariable}.}
\end{valrules}
@@ -869,7 +869,7 @@
\subsubsection{Rules and Constraints}
\begin{valrules}
-\defrule{PD9}{All instances of \glyph{Empty Set} can be regarded as identical
+\defrule{PD09}{All instances of \glyph{Empty Set} can be regarded as identical
therefore no special decoration is used to indicate replication on
the map.}
\defrule{PD10}{The \sbgnclass{EmptySet} must be associated with at least
@@ -1174,13 +1174,13 @@
\subsubsection{Changes from Previous Version}
-No changes from pervious version.
+No changes from previous version.
\umlclasshead{StatefulEPN}
\label{defn:StatefulEPN}
Stateful entity pools can undergo physical changes, for example
-chemical modifcation or conformational change, which we wish to record
+chemical modification or conformational change, which we wish to record
in a \PDm. This information is captured via the
\sbgnclass{StateVariable} (as can be seen in figure
\ref{fig:techref:statefulepnuml}). The \sbgnclass{LabellecCloneMarker} must be
@@ -1612,7 +1612,7 @@
below apply.}
\defrule{PD24}{The subunit defines a namespace for its state variables, e.g.\,
subunit ``A'' assigned a state variable ``P@Ser202'' and a subunit
- ``B'' assigned the same state variable can be distinguised as
+ ``B'' assigned the same state variable can be distinguished as
A:P@Ser202 and B:P@Ser202.}
\defrule{PD25}{If the subunit is of type Complex then \attrib{children} can contain one or
more \sbgnclass{Subunit} instances.}
@@ -1655,7 +1655,7 @@
\begin{tabular}[c]{l l l}\toprule\\
SimpleChemical & \glyph{Simple Chemical Monomer} & \glyph{Simple
Chemical Multimer}\\
-UnspecifiedEntity & \glyph{Unspecificed Entity} & None\\
+UnspecifiedEntity & \glyph{Unspecified Entity} & None\\
PerturbingAgent & \glyph{Perturbing Agent} & None\\
Macromolecule & \glyph{Macromolecule Monomer} &
\glyph{Macromolecule Multimer}\\
@@ -1687,7 +1687,7 @@
% \begin{supertabular}{ l l l}
% SimpleChemical & \glyph{Simple Chemical Monomer} & \glyph{Simple
% Chemical Multimer}\\
-% UnspecifiedEntity & \glyph{Unspecificed Entity} & None\\
+% UnspecifiedEntity & \glyph{Unspecified Entity} & None\\
% PerturbingAgent & \glyph{Perturbing Agent} & None\\
% Macromolecule & \glyph{Macromolecule Monomer} &
% \glyph{Macromolecule Multimer}\\
@@ -1698,7 +1698,7 @@
% \end{center}
The example in figure \ref{fig:techref:complexSubunits} illustrates the use of
-subunits in a complex. It also shows an equivalent compex without
+subunits in a complex. It also shows an equivalent complex without
subunits.
% This is an import point. For every \glyph{Complex} drawn
% with subunits it will always be possible to drawn an equivalent
@@ -2878,7 +2878,7 @@
\glyphSboTerm Not applicable.
\glyphContainer A \glyph{state variable} is represented by a
-``stadium'' container, that is two hemicercles of same radius joined
+``stadium'' container, that is two hemicircles of same radius joined
by parallel segments, as shown in \fig{techref:state-var}. The parallel
segment axis should be tangent to the border of the glyph of the
\glyph{EPN} being modified by the \glyph{state variable}. The center
@@ -3020,7 +3020,7 @@
description of the trans-phosphorylation of CaMKII. Note that
three different types of links are used between annotation nodes
and annotated elements. However, it is recommended to use a
- consistent scheme whithin a map.}
+ consistent scheme within a map.}
\label{fig:techref:ex-annotation}
\end{figure}
@@ -3045,8 +3045,8 @@
\sbgnclass{CrossReference}\query{A new concept required for
consistency between tags ans submap terminals.} handles links or relationships between elements of a
map and submap. At present there is only one reference glyph,
-\glyph{tag}, which can be used in a map refered to by a \glyph{submap}
-(\sect{techref:submap}) or as an auxilary unit on the \glyph{submap}. The
+\glyph{tag}, which can be used in a map referred to by a \glyph{submap}
+(\sect{techref:submap}) or as an auxiliary unit on the \glyph{submap}. The
\glyph{clone marker} can also provide additional reference mechanisms
and is discussed below (\sect{techref:cloneMarker}).
@@ -4133,7 +4133,7 @@
taken from controlled vocabularies defined below. When displayed in
some cases it is mandatory to prefix a code indicating the type of
controlled vocabulary used. This is in order to make it clear what
-the information is that the value referes to: for example 'mt'
+the information is that the value refers to: for example 'mt'
indicates that a value 'rna' is describing the material RNA.
In the rest of this section, we describe the controlled vocabularies
@@ -4144,7 +4144,7 @@
the sense that only the values defined for each CV can be used in a
valid \PDm and also closed because only the controlled vocabularies
defined in this specification can be used in a valid \PDm\query{The
- previous version was a bit vaque but implied that the CVs were
+ previous version was a bit vague but implied that the CVs were
open. This has been changed after discussion on the list.}. We
understand that this is of necessity restrictive, but in closing these
definitions it means we can be clear about the meaning of all CV terms
@@ -4173,7 +4173,7 @@
Non-macromolecular ion & mt:ion & SBO:0000327\\
Non-macromolecular radical & mt:rad & SBO:0000328\\
Ribonucleic acid & mt:rna & SBO:0000250\\
- Deoxribonucleic acid & mt:dna & SBO:0000251\\
+ Deoxyribonucleic acid & mt:dna & SBO:0000251\\
Protein & mt:prot & SBO:0000297\\
Polysaccharide & mt:psac & SBO:0000249\\
\bottomrule
Modified: ProcessDiagram/trunk/Specification/sources/grammar.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/grammar.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sources/grammar.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -203,14 +203,14 @@
% \subsection{Entity Pool Nodes}
% \begin{description}
-% \item[PD1] The identity of an EPN is defined by a combination of its compartment, entity type (e.g. complex or macromolecule), name and state variables (if any).
-% \item[PD2] A Complex’s identity consists of the identity of its subunits and a name is optional. All complexes with the same name should have the same subunits.
-% \item[PD3] An EPN may belong to only one compartment.
-% \item[PD4] An EPN belongs to only one compartment. If no compartment is draw it is assumed to belong to a “default” compartment.
-% \item[PD5] An EPN can overlap more than one compartment and in this case it is deferred to the drawing tool or author to assign the owning compartment. Note this rule need not apply in cases where SBGN is draw by hand.
-% \item[PD6] A Complex may contain subunits that belong to different compartments (the complex itself will belong to only one, however).
-% \item[PD7] The layout or organisation of a compartment does not imply anything about its topology.
-% \item[PD8] The layout or organisation of the EPNs in a complex does not imply any information about topology.
+% \item[PD01] The identity of an EPN is defined by a combination of its compartment, entity type (e.g. complex or macromolecule), name and state variables (if any).
+% \item[PD02] A Complex’s identity consists of the identity of its subunits and a name is optional. All complexes with the same name should have the same subunits.
+% \item[PD03] An EPN may belong to only one compartment.
+% \item[PD04] An EPN belongs to only one compartment. If no compartment is draw it is assumed to belong to a “default” compartment.
+% \item[PD05] An EPN can overlap more than one compartment and in this case it is deferred to the drawing tool or author to assign the owning compartment. Note this rule need not apply in cases where SBGN is draw by hand.
+% \item[PD06] A Complex may contain subunits that belong to different compartments (the complex itself will belong to only one, however).
+% \item[PD07] The layout or organisation of a compartment does not imply anything about its topology.
+% \item[PD08] The layout or organisation of the EPNs in a complex does not imply any information about topology.
% \item[PD10] Complexes can be nested. This does imply information about the complex’s topology.
% \item[PD11] A complex should consist of different EPNs. If two or more elements of the complex are identical then they should be replaced by a multimer.
% \item[PD12] Source and sink nodes must have no name and be attached to only one consumption or production arc.
Modified: ProcessDiagram/trunk/Specification/sources/language_overview.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/language_overview.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sources/language_overview.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -275,7 +275,7 @@
Non-macromolecular ion & mt:ion & SBO:0000327\\
Non-macromolecular radical & mt:rad & SBO:0000328\\
Ribonucleic acid & mt:rna & SBO:0000250\\
- Deoxribonucleic acid & mt:dna & SBO:0000251\\
+ Deoxyribonucleic acid & mt:dna & SBO:0000251\\
Protein & mt:prot & SBO:0000297\\
Polysaccharide & mt:psac & SBO:0000249\\
\bottomrule
@@ -896,7 +896,7 @@
% \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}).
+% 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 referred to by a \glyph{submap} (\sect{submap}) or as an auxiliary 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/Specification/sources/latex-style.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/latex-style.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sources/latex-style.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -8,6 +8,10 @@
\usepackage{ifpdf}
+% loading package float before package hyperref avoids these warnings
+% "destination with the same identifier ... has been already used, duplicate ignored"
+\usepackage{float}
+
% Pass options to xcolor. This is called by other packages so an
% explicit call later leads to an error.
\ifpdf
@@ -30,7 +34,7 @@
\usepackage{array}
\usepackage{fancybox}
\usepackage{xspace}
-\usepackage{float}
+%\usepackage{float}
\usepackage{framed}
\usepackage{eso-pic}
\usepackage{ifthen}
@@ -95,6 +99,11 @@
%% Special customizations
%% ----------------------------------------------------------------------------
+% this option avoids these warnings "PDF inclusion: multiple pdfs with page group included in a single page"
+% pdftex 1.40.15 and higher
+% see also https://tex.stackexchange.com/questions/183149/cant-silence-a-pdftex-pdf-inclusion-multiple-pdfs-with-page-group-error
+\pdfsuppresswarningpagegroup=1
+
\makeatletter
% Adjust bottom-of-page behavior and page line spacing.
Modified: ProcessDiagram/trunk/Specification/sources/layout.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/layout.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sources/layout.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -5,7 +5,7 @@
The previous chapters describe the appearance and meaning of
\SBGNPDLone components. Here we describe rules governing the visual
-appearence and asthetics of the \PDl. The components of a \PD have to
+appearance and aesthetics of the \PDl. The components of a \PD have to
be placed in a meaningful way -- a random distribution with
spaghetti-like connections will most likely hide the information
encoded in the underlying model, whereas an elegant placement of the
@@ -195,7 +195,7 @@
\section{Additional suggestions}
-Here is a list of additional layout suggestions which may help improve the asthetics and clarity of \PD maps.
+Here is a list of additional layout suggestions which may help improve the aesthetics and clarity of \PD maps.
\begin{itemize}
\item Angle of edge crossings: If edge crossing cannot be avoided then the edges should cross with an angle close to 90 degrees.
Modified: ProcessDiagram/trunk/Specification/sources/revision_history.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/revision_history.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sources/revision_history.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -22,15 +22,15 @@
Removed ``The connectors and the box move as a rigid entity'' in the definition of \glyph{process} & \\\hline
Changed the definition of process node to ``represent processes that transform one or several EPNs into \emph{one or several EPNs, identical or different}''& \\\hline
Changed SBO term of \glyph{compartment} From SBO:0000289 (functional compartment) to SBO:0000290 (physical compartment) & \\\hline
-Reoganised classification of glyphs & \\\hline
-Reoganised glyph section to reflect the above changes & \\\hline
+Reorganised classification of glyphs & \\\hline
+Reorganised glyph section to reflect the above changes & \\\hline
Revised reference card to reflect changes in glyph organisation &
\\\hline
Revised logic operators throughout spec to make sure input and output
arcs meet before attaching to the glyph - as with processes. &
\\\hline
Added enumerated rules to grammar section. This is probably not
-complete, but should help the implementation of semantc validation by
+complete, but should help the implementation of semantic validation by
software tools. The hope is this will be refined as tools start
validating maps. & \\\hline
Updated UML maps and data dictionary to be consistent with rest
@@ -41,7 +41,7 @@
\glyph{Compartment} description is confusing and contradictory. & 2841122
\\\hline
\glyph{Clone marker} fill percentages unhelpful. & 2841114 \\\hline
-Use of CV for physical charactetistic not clear. & 2841085 \\\hline
+Use of CV for physical characteristic not clear. & 2841085 \\\hline
Definition of Cardinality is ambiguous. & 2840996 \\\hline
input to AND on IFN example. & 2804326 \\\hline
more SBO terms for \glyph{multimers} & 2803593 \\\hline
Modified: ProcessDiagram/trunk/Specification/sources/whatsnew.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/whatsnew.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sources/whatsnew.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -23,7 +23,7 @@
\begin{description}
\item[Annotation (New)] This version sees the introduction of the annotation glyph. This makes the \PDl consistent with the other SBGN languages. The glyph provides a mechanisms to annotate parts of an SBGN map and does not affect the meaning of the map. See section~\ref{defn:Annotation}.
-\item[State Variable] The symbol used for this glyph has been modified to use the stadium (or capsule) glyph. This replaces the elipse although the circle is preserved (it can be though of as a special form of the stadium symbol with no straight edges). More details can be found in section~\ref{defn:StateVariable}.
+\item[State Variable] The symbol used for this glyph has been modified to use the stadium (or capsule) glyph. This replaces the ellipse although the circle is preserved (it can be though of as a special form of the stadium symbol with no straight edges). More details can be found in section~\ref{defn:StateVariable}.
\item[Small Molecule] The small molecule glyph has been changed from a circle to a stadium symbol. The circle had the drawback of taking up a lot of space if the author wanted to draw the label inside the shape. Also if the circle was deformed it became an oval, which is the symbol of a Unspecified Entity. The new glyph does not have either of these problems and can also adopt a circle shape if the straight lined have zero length. See section~\ref{sec:techref:simpleChemical}.
\item[Empty Set] The empty set glyph is a rationalisation of the source and sink glyphs, which both have the same symbol. They are now represented by the same glyph and the usage rules have been relaxed. More details can be found in section~\ref{defn:emptySet}.
\end{description}
Modified: ProcessDiagram/trunk/Specification/sources/working.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/working.tex 2015-07-27 02:29:57 UTC (rev 929)
+++ ProcessDiagram/trunk/Specification/sources/working.tex 2015-08-04 05:22:15 UTC (rev 930)
@@ -25,4 +25,4 @@
\section{State and transformation of compartments}
-In \SBGNPDLone a \glyph{compartment} is a stateless entity. It cannot carry \glyph{state variables}, and cannot be subjected to process modifying a state. As a recult, a \glyph{compartment} cannot be transformed, moved, split or merged with another. If one want to represent the transformation of a compartment, one has to create the start and end compartments, and represent the transport of all the \glyph{EPNs} from one to the other. This is not satisfactory, and should be addressed in the future.
\ No newline at end of file
+In \SBGNPDLone a \glyph{compartment} is a stateless entity. It cannot carry \glyph{state variables}, and cannot be subjected to process modifying a state. As a result, a \glyph{compartment} cannot be transformed, moved, split or merged with another. If one want to represent the transformation of a compartment, one has to create the start and end compartments, and represent the transport of all the \glyph{EPNs} from one to the other. This is not satisfactory, and should be addressed in the future.
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2015-07-27 02:29:59
|
Revision: 929
http://sourceforge.net/p/sbgn/code/929
Author: tczauderna
Date: 2015-07-27 02:29:57 +0000 (Mon, 27 Jul 2015)
Log Message:
-----------
tag for release of specification level 1 version 1.2
Added Paths:
-----------
ActivityFlow/tags/L1R1.2/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2015-07-27 02:28:08
|
Revision: 928
http://sourceforge.net/p/sbgn/code/928
Author: tczauderna
Date: 2015-07-27 02:28:07 +0000 (Mon, 27 Jul 2015)
Log Message:
-----------
deleted old L1R1.2 tag
Removed Paths:
-------------
ActivityFlow/tags/L1R1.2/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2015-07-27 02:25:47
|
Revision: 927
http://sourceforge.net/p/sbgn/code/927
Author: tczauderna
Date: 2015-07-27 02:25:43 +0000 (Mon, 27 Jul 2015)
Log Message:
-----------
resynchronised repository after Sourceforge service restoration
update authors list, correct typos, update acknowledgements
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/acknowledgments.tex
ActivityFlow/trunk/sources/front-page.tex
ActivityFlow/trunk/sources/revision_history.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2015-05-05 18:53:18 UTC (rev 926)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2015-07-27 02:25:43 UTC (rev 927)
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From: <tcz...@us...> - 2015-07-16 04:15:32
|
Revision: 935
http://sourceforge.net/p/sbgn/code/935
Author: tczauderna
Date: 2015-07-16 04:15:30 +0000 (Thu, 16 Jul 2015)
Log Message:
-----------
tag for release specification level 1 version 1.2
Added Paths:
-----------
ActivityFlow/tags/L1R1.2/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
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