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From: <tcz...@us...> - 2015-04-22 08:57:06
|
Revision: 909
http://sourceforge.net/p/sbgn/code/909
Author: tczauderna
Date: 2015-04-22 08:57:03 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
fixed figures for modulating arcs
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/images/catalysis.svg
ProcessDiagram/trunk/Specification/images/inhibition.svg
ProcessDiagram/trunk/Specification/images/modulation.svg
ProcessDiagram/trunk/Specification/images/necessary_stim.svg
ProcessDiagram/trunk/Specification/images/stimulation.svg
Modified: ProcessDiagram/trunk/Specification/images/catalysis.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/catalysis.svg 2015-04-22 08:04:25 UTC (rev 908)
+++ ProcessDiagram/trunk/Specification/images/catalysis.svg 2015-04-22 08:57:03 UTC (rev 909)
@@ -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"
@@ -12,9 +13,8 @@
height="744.09448"
id="svg2"
sodipodi:version="0.32"
- inkscape:version="0.45.1"
+ inkscape:version="0.91 r13725"
version="1.0"
- sodipodi:docbase="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/images"
sodipodi:docname="catalysis.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape">
<defs
@@ -115,12 +115,14 @@
inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
- inkscape:window-width="1392"
- inkscape:window-height="1022"
+ inkscape:window-width="1192"
+ inkscape:window-height="670"
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="301.42857"
@@ -169,17 +171,17 @@
id="text5256"
y="284.09448"
x="823.71429"
- style="font-size:12px;font-style:normal;font-weight:normal;opacity:1;fill:#000000;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';opacity:1;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:24px;font-weight:normal;text-align:center;text-anchor:middle"
+ style="font-weight:normal;font-size:24px;text-align:center;text-anchor:middle"
y="284.09448"
x="823.71429"
id="tspan5258"
sodipodi:role="line">Target</tspan><tspan
id="tspan5260"
- style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
+ style="font-weight:normal;font-size:24px;text-align:center;text-anchor:middle"
y="314.09448"
x="823.71429"
- sodipodi:role="line">TRN</tspan></text>
+ sodipodi:role="line">PN</tspan></text>
</g>
</svg>
Modified: ProcessDiagram/trunk/Specification/images/inhibition.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/inhibition.svg 2015-04-22 08:04:25 UTC (rev 908)
+++ ProcessDiagram/trunk/Specification/images/inhibition.svg 2015-04-22 08:57:03 UTC (rev 909)
@@ -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"
@@ -12,9 +13,8 @@
height="744.09448"
id="svg2"
sodipodi:version="0.32"
- inkscape:version="0.45.1"
+ inkscape:version="0.91 r13725"
version="1.0"
- sodipodi:docbase="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/images"
sodipodi:docname="inhibition.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape">
<defs
@@ -115,12 +115,14 @@
inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
- inkscape:window-width="1392"
- inkscape:window-height="1022"
- inkscape:window-x="280"
- inkscape:window-y="0"
+ inkscape:window-width="1192"
+ inkscape:window-height="609"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
showguides="true"
- inkscape:guide-bbox="true">
+ inkscape:guide-bbox="true"
+ showgrid="false"
+ inkscape:window-maximized="1">
<sodipodi:guide
orientation="vertical"
position="301.42857"
@@ -164,17 +166,17 @@
id="text5256"
y="282.66592"
x="826.28571"
- style="font-size:12px;font-style:normal;font-weight:normal;opacity:1;fill:#000000;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';opacity:1;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:24px;font-weight:normal;text-align:center;text-anchor:middle"
+ style="font-weight:normal;font-size:24px;text-align:center;text-anchor:middle"
y="282.66592"
x="826.28571"
id="tspan5258"
sodipodi:role="line">Target</tspan><tspan
id="tspan5260"
- style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
+ style="font-weight:normal;font-size:24px;text-align:center;text-anchor:middle"
y="312.66592"
x="826.28571"
- sodipodi:role="line">TRN</tspan></text>
+ sodipodi:role="line">PN</tspan></text>
</g>
</svg>
Modified: ProcessDiagram/trunk/Specification/images/modulation.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/modulation.svg 2015-04-22 08:04:25 UTC (rev 908)
+++ ProcessDiagram/trunk/Specification/images/modulation.svg 2015-04-22 08:57:03 UTC (rev 909)
@@ -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"
@@ -12,9 +13,8 @@
height="744.09448"
id="svg2"
sodipodi:version="0.32"
- inkscape:version="0.45.1"
+ inkscape:version="0.91 r13725"
version="1.0"
- sodipodi:docbase="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/images"
sodipodi:docname="modulation.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape">
<defs
@@ -115,13 +115,14 @@
inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
- inkscape:window-width="1392"
- inkscape:window-height="1022"
- inkscape:window-x="280"
- inkscape:window-y="0"
+ inkscape:window-width="1192"
+ inkscape:window-height="609"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
showguides="true"
inkscape:guide-bbox="true"
- showgrid="true">
+ showgrid="true"
+ inkscape:window-maximized="1">
<sodipodi:guide
orientation="vertical"
position="301.42857"
@@ -160,18 +161,18 @@
id="text2859"
y="282.09448"
x="832.28571"
- style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;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"
xml:space="preserve"><tspan
- style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
+ style="font-weight:normal;font-size:24px;text-align:center;text-anchor:middle"
y="282.09448"
x="832.28571"
id="tspan2861"
sodipodi:role="line">Target</tspan><tspan
id="tspan2863"
- style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
+ style="font-weight:normal;font-size:24px;text-align:center;text-anchor:middle"
y="312.09448"
x="832.28571"
- sodipodi:role="line">TRN</tspan></text>
+ sodipodi:role="line">PN</tspan></text>
<rect
style="opacity:1;fill:none;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5.00000014;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect2197"
Modified: ProcessDiagram/trunk/Specification/images/necessary_stim.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/necessary_stim.svg 2015-04-22 08:04:25 UTC (rev 908)
+++ ProcessDiagram/trunk/Specification/images/necessary_stim.svg 2015-04-22 08:57:03 UTC (rev 909)
@@ -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="0.45.1"
+ inkscape:version="0.91 r13725"
version="1.0"
- sodipodi:docbase="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/images"
- sodipodi:docname="trigger.svg"
+ sodipodi:docname="necessary_stim.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape">
<defs
id="defs4">
@@ -115,12 +115,14 @@
inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
- inkscape:window-width="1345"
- inkscape:window-height="1022"
+ inkscape:window-width="1192"
+ inkscape:window-height="670"
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="301.42857"
@@ -169,17 +171,17 @@
id="text5256"
y="283.23734"
x="822.35712"
- style="font-size:12px;font-style:normal;font-weight:normal;opacity:1;fill:#000000;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';opacity:1;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:24px;font-weight:normal;text-align:center;text-anchor:middle"
+ style="font-weight:normal;font-size:24px;text-align:center;text-anchor:middle"
y="283.23734"
x="822.35712"
id="tspan5258"
sodipodi:role="line">Target</tspan><tspan
id="tspan5260"
- style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
+ style="font-weight:normal;font-size:24px;text-align:center;text-anchor:middle"
y="313.23734"
x="822.35712"
- sodipodi:role="line">TRN</tspan></text>
+ sodipodi:role="line">PN</tspan></text>
</g>
</svg>
Modified: ProcessDiagram/trunk/Specification/images/stimulation.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/stimulation.svg 2015-04-22 08:04:25 UTC (rev 908)
+++ ProcessDiagram/trunk/Specification/images/stimulation.svg 2015-04-22 08:57:03 UTC (rev 909)
@@ -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"
@@ -12,9 +13,8 @@
height="744.09448"
id="svg2"
sodipodi:version="0.32"
- inkscape:version="0.45.1"
+ inkscape:version="0.91 r13725"
version="1.0"
- sodipodi:docbase="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/images"
sodipodi:docname="stimulation.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape">
<defs
@@ -115,12 +115,14 @@
inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
- inkscape:window-width="1392"
- inkscape:window-height="1022"
+ inkscape:window-width="1192"
+ inkscape:window-height="670"
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="301.42857"
@@ -164,17 +166,17 @@
id="text2859"
y="283.54617"
x="831.12604"
- style="font-size:12px;font-style:normal;font-weight:normal;opacity:1;fill:#000000;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';opacity:1;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:24px;font-weight:normal;text-align:center;text-anchor:middle"
+ style="font-weight:normal;font-size:24px;text-align:center;text-anchor:middle"
y="283.54617"
x="831.12604"
id="tspan2861"
sodipodi:role="line">Target</tspan><tspan
id="tspan2863"
- style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
+ style="font-weight:normal;font-size:24px;text-align:center;text-anchor:middle"
y="313.54617"
x="831.12604"
- sodipodi:role="line">TRN</tspan></text>
+ sodipodi:role="line">PN</tspan></text>
</g>
</svg>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2015-04-22 08:04:33
|
Revision: 908
http://sourceforge.net/p/sbgn/code/908
Author: tczauderna
Date: 2015-04-22 08:04:25 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
fixed some figures
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/examples/MAPK.svg
ProcessDiagram/trunk/Specification/examples/compartment_overlapping_wrong.svg
ProcessDiagram/trunk/Specification/examples/muscle.svg
ProcessDiagram/trunk/Specification/images/MAPK-only.svg
Modified: ProcessDiagram/trunk/Specification/examples/MAPK.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/MAPK.svg 2015-04-22 07:44:54 UTC (rev 907)
+++ ProcessDiagram/trunk/Specification/examples/MAPK.svg 2015-04-22 08:04:25 UTC (rev 908)
@@ -13,7 +13,7 @@
height="1052.3622"
id="svg2"
sodipodi:version="0.32"
- inkscape:version="0.48.0 r9654"
+ inkscape:version="0.91 r13725"
version="1.0"
sodipodi:docname="MAPK.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape"
@@ -47,17 +47,17 @@
objecttolerance="10"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
- inkscape:zoom="3.8356634"
+ inkscape:zoom="2.7122236"
inkscape:cx="378.64456"
- inkscape:cy="835.53591"
+ inkscape:cy="859.52133"
inkscape:document-units="px"
inkscape:current-layer="layer1"
width="744.09448px"
height="1052.3622px"
- inkscape:window-width="1280"
- inkscape:window-height="1002"
- inkscape:window-x="0"
- inkscape:window-y="0"
+ inkscape:window-width="1192"
+ inkscape:window-height="609"
+ inkscape:window-x="-8"
+ inkscape:window-y="-8"
showguides="true"
inkscape:guide-bbox="true"
showgrid="false"
@@ -158,11 +158,12 @@
x="286.75604"
y="235.86102"
rx="0"
- ry="12.606059" />
+ ry="0" />
<path
- style="fill:none;stroke:#000000;stroke-width:2;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
- d="m 292.64552,174.95486 0,50.26339"
- id="path5814" />
+ style="fill:none;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 292.64552,167.05518 0,55.263"
+ id="path5814"
+ inkscape:connector-curvature="0" />
<path
sodipodi:type="arc"
style="fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:2.18048453;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
@@ -343,7 +344,7 @@
d="M 265.57327,449.66505 L 254.71688,454.69411 L 254.71688,444.59607 L 265.57327,449.66505 z "
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" />
<rect
- ry="12.606059"
+ ry="0"
rx="0"
y="443.86102"
x="186.23462"
@@ -504,7 +505,7 @@
x="414.23462"
y="443.86102"
rx="0"
- ry="12.606059" />
+ ry="0" />
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Modified: ProcessDiagram/trunk/Specification/examples/compartment_overlapping_wrong.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/compartment_overlapping_wrong.svg 2015-04-22 07:44:54 UTC (rev 907)
+++ ProcessDiagram/trunk/Specification/examples/compartment_overlapping_wrong.svg 2015-04-22 08:04:25 UTC (rev 908)
@@ -1,8 +1,9 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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+
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xmlns:dc="http://purl.org/dc/elements/1.1/"
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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"
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sodipodi:version="0.32"
- inkscape:version="0.45.1"
- sodipodi:docbase="D:\workspace-doc\SBGN_trunk\documents\specifications\ProcessDiagram\Level1\examples"
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sodipodi:docname="compartment_overlapping_wrong.svg"
- inkscape:output_extension="org.inkscape.output.svg.inkscape">
+ inkscape:output_extension="org.inkscape.output.svg.inkscape"
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Modified: ProcessDiagram/trunk/Specification/examples/muscle.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/muscle.svg 2015-04-22 07:44:54 UTC (rev 907)
+++ ProcessDiagram/trunk/Specification/examples/muscle.svg 2015-04-22 08:04:25 UTC (rev 908)
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Modified: ProcessDiagram/trunk/Specification/images/MAPK-only.svg
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2015-04-22 07:45:02
|
Revision: 907
http://sourceforge.net/p/sbgn/code/907
Author: lptolik
Date: 2015-04-22 07:44:54 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
resolving an issues with spec
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/grammar.tex
EntityRelationship/trunk/sources/semantics.tex
EntityRelationship/trunk/sources/syncEv.tex
EntityRelationship/trunk/sources/syntax.tex
Property Changed:
----------------
EntityRelationship/trunk/
EntityRelationship/trunk/sources/
Index: EntityRelationship/trunk
===================================================================
--- EntityRelationship/trunk 2015-04-21 12:38:27 UTC (rev 906)
+++ EntityRelationship/trunk 2015-04-22 07:44:54 UTC (rev 907)
Property changes on: EntityRelationship/trunk
___________________________________________________________________
Modified: svn:ignore
## -1,47 +1,20 ##
-.git
-.gitignore
-
-# TeX files #
-######################
*.aux
-*.glo
-*.idx
-*.log
-*.toc
-*.ist
-*.acn
-*.acr
-*.alg
*.bbl
*.blg
-*.dvi
-*.glg
-*.gls
-*.ilg
-*.ind
+*.lox
+*.aux
*.lof
*.lot
-*.maf
-*.mtc
-*.mtc1
+*.fls
*.out
+*.toc
+*.bcf
+*-blx.aux
+*-blx.bib
+*.brf
+*.fdb_latexmk
+*.synctex
*.synctex.gz
-
-# FixMe files #
-######################
-*.lox
-
-# FixMe files #
-######################
-*.xdy
-
-# OS generated files #
-######################
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-Icon?
-ehthumbs.db
-Thumbs.db
+*.synctex.gz(busy)
+*.pdfsync
+*.log
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Index: EntityRelationship/trunk/sources
===================================================================
--- EntityRelationship/trunk/sources 2015-04-21 12:38:27 UTC (rev 906)
+++ EntityRelationship/trunk/sources 2015-04-22 07:44:54 UTC (rev 907)
Property changes on: EntityRelationship/trunk/sources
___________________________________________________________________
Modified: svn:ignore
## -1 +1,20 ##
*.aux
+*.bbl
+*.blg
+*.lox
+*.aux
+*.lof
+*.lot
+*.fls
+*.out
+*.toc
+*.bcf
+*-blx.aux
+*-blx.bib
+*.brf
+*.fdb_latexmk
+*.synctex
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+*.log
Modified: EntityRelationship/trunk/sources/grammar.tex
===================================================================
--- EntityRelationship/trunk/sources/grammar.tex 2015-04-21 12:38:27 UTC (rev 906)
+++ EntityRelationship/trunk/sources/grammar.tex 2015-04-22 07:44:54 UTC (rev 907)
@@ -20,9 +20,9 @@
of the symbols and syntax of the language. We first need to define the
abstractions we are using.
-SBGN \ERs{} describe biological interactions involving biological entities. An \glyph{entity node} (\sect{ENs}), such as a molecule, influences the behaviour of other \glyph{entity nodes} via a relationship.
+SBGN \ERs{} describe biological interactions involving biological entities. An \glyph{entity node} (\sect{ENs}), such as a molecule, influences the behaviour of other \glyph{entities} via a relationship.
-It may be convenient to think of a SBGN \ERs{} as listing independent rules that describe influences between \glyph{entity nodes}. A map can then be analysed with ``what if?'' queries.
+It may be convenient to think of a SBGN \ERs{} as listing independent rules that describe influences between \glyph{entities}. A map can then be analysed with ``what if?'' queries.
\input{sources/syntax.tex}
\input{sources/semantics.tex}
Modified: EntityRelationship/trunk/sources/semantics.tex
===================================================================
--- EntityRelationship/trunk/sources/semantics.tex 2015-04-21 12:38:27 UTC (rev 906)
+++ EntityRelationship/trunk/sources/semantics.tex 2015-04-22 07:44:54 UTC (rev 907)
@@ -15,48 +15,48 @@
\noindent
An \glyph{assignment} (\sect{assignment}) linking a \glyph{variable value} $v$ to a \glyph{state variable} $V$ of an \glyph{entity} $E$ means: ``$v$ is assigned to $V$ of $E$'' or ``$V$ of $E$ takes the value $v$''. An \glyph{outcome} on an \glyph{assignment} represents the cases when the statement is true, that is all instances of $E$ (free or as a complex subunint) on which the variable effectively displays the value. It is used as follows: ``when (or if) $V$ of $E$ takes the value $v$ then \ldots'' or more succintly ``when (or if) $E\{V => v\}$ then \ldots''.\\[\baselineskip]
-\noindent
-A \glyph{phenotype} (\sect{phenotype}) $P$ means: ``$P$ exists''.\\[\baselineskip]
+%\noindent
+%A \glyph{phenotype} (\sect{phenotype}) $P$ means: ``$P$ exists''.\\[\baselineskip]
\subsection{Influences}
-A \glyph{modulation} (\sect{modulation}) linking an \glyph{entity node} $E$ and a relationship $R$ means: ``If $E$ exists then $R$ is either reinforced or weakened''.
+A \glyph{modulation} (\sect{modulation}) linking an \glyph{entity node} (\sect{ENs}) $E$ and a relationship $R$ means: ``If $E$ exists then $R$ is either reinforced or weakened''.
%An \glyph{outcome} on a \glyph{modulation} represents the cases when the modulation effectively takes place. It is used as follow: ``when (or if) $I$ modulates $R$ then \ldots''.
\\[\baselineskip]
\noindent
-A \glyph{stimulation} (\sect{stimulation}) linking an \glyph{entity node} $E$ and a relationship $R$ means: ``If $E$ exists then $R$ is reinforced'' or ``If $E$ exists then the probability of $R$ is increased''.
+A \glyph{stimulation} (\sect{stimulation}) linking an \glyph{entity node} (\sect{ENs}) $E$ and a relationship $R$ means: ``If $E$ exists then $R$ is reinforced'' or ``If $E$ exists then the probability of $R$ is increased''.
%An \glyph{outcome} on a \glyph{stimulation} represents the cases when the stimulation effectively takes place. It is used as follow: ``when (or if) $I$ stimulates $R$ then \ldots''.
\\[\baselineskip]
\noindent
-An \glyph{absolute stimulation} (\sect{absoluteStimulation}) linking an \glyph{entity node} $E$ and a relationship $R$ means: ``If $E$ exists then $R$ always takes place with necessity''.
+An \glyph{absolute stimulation} (\sect{absoluteStimulation}) linking an \glyph{entity node} (\sect{ENs}) $E$ and a relationship $R$ means: ``If $E$ exists then $R$ always takes place with necessity''.
\\[\baselineskip]
\noindent
-A \glyph{necessary stimulation} (\sect{necessaryStimulation}) linking an \glyph{entity node} $E$ and a relationship $R$ means: ``$R$ only takes place if $E$ exists.
+A \glyph{necessary stimulation} (\sect{necessaryStimulation}) linking an \glyph{entity node} (\sect{ENs}) $E$ and a relationship $R$ means: ``$R$ only takes place if $E$ exists.
%An \glyph{outcome} on a \glyph{necessary stimulation} represents the cases when the stimulation effectively takes place. It is used as follow: ``when (or if) $I$ allows $R$ then \ldots''.
\\[\baselineskip]
\noindent
-An \glyph{inhibition} (\sect{inhibition}) linking an \glyph{entity node} $E$ and a relationship $R$ means: ``If $E$ exists then $R$ is weakened'' or ``If $E$ exists then the probability of $R$ is lowered''.
+An \glyph{inhibition} (\sect{inhibition}) linking an \glyph{entity node} (\sect{ENs}) $E$ and a relationship $R$ means: ``If $E$ exists then $R$ is weakened'' or ``If $E$ exists then the probability of $R$ is lowered''.
%An \glyph{outcome} on an \glyph{inhibition} represents the cases when the inhibition effectively takes place. It is used as follow: ``when (or if) $I$ inhibits $R$ then \ldots''.
\\[\baselineskip]
\noindent
-An \glyph{absolute inhibition} (\sect{absoluteInhibition}) linking an \glyph{entity node} $E$ and a relationship $R$ means: ``If $E$ exists then $R$ never takes place''.
+An \glyph{absolute inhibition} (\sect{absoluteInhibition}) linking an \glyph{entity node} (\sect{ENs}) $E$ and a relationship $R$ means: ``If $E$ exists then $R$ never takes place''.
%An \glyph{outcome} on an \glyph{absolute inhibition} represents the cases when the absolute inhibition effectively takes place. It is used as follow: ``when (or if) $I$ blocks $R$ then \ldots''.
\\[\baselineskip]
\subsection{Logical Operators}
-An \glyph{and} (\sect{and}) linking several \glyph{logic arcs} originating from \glyph{entity nodes} $E_i$ and an influence $F$ means: ``if for each $i$, $E_i$ exists, then $F$''.\\[\baselineskip]
+An \glyph{and} (\sect{and}) linking several \glyph{logic arcs} originating from \glyph{entity nodes} (\sect{ENs}) $E_i$ and an influence $F$ means: ``if for each $i$, $E_i$ exists, then $F$''.\\[\baselineskip]
\noindent
-An \glyph{or} (\sect{or}) linking several \glyph{logic arcs} originating from \glyph{entity nodes} $E_i$ and an influence $F$ means: ``if for any $i$, $E_i$ exists, then $F$''.\\[\baselineskip]
+An \glyph{or} (\sect{or}) linking several \glyph{logic arcs} originating from \glyph{entity nodes} (\sect{ENs}) $E_i$ and an influence $F$ means: ``if for any $i$, $E_i$ exists, then $F$''.\\[\baselineskip]
\noindent
-A \glyph{not} (\sect{not}) linking a \glyph{logic arc} originating from an \glyph{entity node} $E$ and an influence $F$ means: `` $F$ takes place only if $E$ does not exist''.\\[\baselineskip]
+A \glyph{not} (\sect{not}) linking a \glyph{logic arc} originating from an \glyph{entity node} (\sect{ENs}) $E$ and an influence $F$ means: `` $F$ takes place only if $E$ does not exist''.\\[\baselineskip]
%\noindent
%A \glyph{delay} (\sect{delay}) linking a \glyph{logic arc} originating from an \glyph{entity node} $E$ and an influence $F$ means: ``If $E$ exists then $F$ takes place, but not immediately''.\\[\baselineskip]
Modified: EntityRelationship/trunk/sources/syncEv.tex
===================================================================
--- EntityRelationship/trunk/sources/syncEv.tex 2015-04-21 12:38:27 UTC (rev 906)
+++ EntityRelationship/trunk/sources/syncEv.tex 2015-04-22 07:44:54 UTC (rev 907)
@@ -9,7 +9,7 @@
\label{fig:synchronousPD}
\end{figure}
-Use two outcomes or two stimulation links \fig{asynchronous} is not appropriate in this case as all statement in \ER are independent. According to the diagram in \fig{asynchronous} it is possible that \glyph{entity} $B$ is created, but \glyph{entity} $A$ is not deleted, because outcomes are independent and not guarantied to be in true state.
+Having two outcomes and two stimulation links (\fig{asynchronous}) does not work in this case because all statement on \ERm are independent. So it is possible that \glyph{entity} $B$ is created, but \glyph{entity} $A$ is not deleted.
\begin{figure}[H]
\centering
Modified: EntityRelationship/trunk/sources/syntax.tex
===================================================================
--- EntityRelationship/trunk/sources/syntax.tex 2015-04-21 12:38:27 UTC (rev 906)
+++ EntityRelationship/trunk/sources/syntax.tex 2015-04-22 07:44:54 UTC (rev 907)
@@ -58,13 +58,13 @@
%\item There can be any number of \glyph{perturbing agents} with the same label (name). All of them represent the same concept, such as a specific physical input.
%\item There can be any number of \glyph{phenotype} with the same label (name). All of them represent the same concept, producing identical readout.
\item Name of the \glyph{state variable} should be unique within the \glyph{entity} definition.
-\item From an \glyph{outcome} can only originate one relationship, whether influence or interaction. The relationships being seen as independent rules, separate consequences of an assignment or an interaction have to originate from different outcomes, that is assetion of truth of this assignment or interaction.
+\item From an \glyph{outcome} can only originate one relationship, whether influence or interaction. The relationships being seen as independent rules, separate consequences of an assignment or an interaction have to originate from different outcomes, that is assertion of truth of this assignment or interaction.
%\item A given \glyph{Influence} can only target one relationship. Influence arcs cannot be branched out.
%\item There cannot be both an \glyph{absolute stimulation} and an \glyph{absolute inhibition} targeting the same statement.
\item In the case of a non-binary interaction, the ``cis'' or ``trans'' \glyph{unit of information} must be carried by the circle representing the n-ary interaction, and not the arc connecting this circle and a given interactor.
\item If an \glyph{influence} targeting an \glyph{interaction} carries a ``cis'' or ``trans'' unit of information, at least one of the \glyph{interactors} must be the same \glyph{entity} as the origin of the influence.
\item If more than one instance of an \glyph{entity} is involved in an \glyph{interaction}, a \glyph{unit of information} \glyph{cardinality} (\sect{miscellaneous-cv}) must be associated with each entity involved in the statement.
-\item A \glyph{cis} or \glyph{trans} unit of information can only be carried by a relationship involving a single \glyph{entity} directly or by traceable set of \glyph{outcomes}.
+\item A \glyph{cis} or \glyph{trans} unit of information can only be carried by a relationship involving an instances of a single \glyph{entity} directly or by traceable set of \glyph{outcomes}.
\end{enumerate}
%\normalcolor
\ 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: <stu...@us...> - 2015-04-21 12:38:30
|
Revision: 906
http://sourceforge.net/p/sbgn/code/906
Author: stumoodie
Date: 2015-04-21 12:38:27 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
Fixed typos and added comments from COMBINE 2014
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/images/complex.svg
ProcessDiagram/trunk/Specification/images/sbgn_model_revised/45.session
ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
ProcessDiagram/trunk/Specification/sources/glyphs.tex
ProcessDiagram/trunk/Specification/sources/layout.tex
Added Paths:
-----------
ProcessDiagram/trunk/Specification/sources/whatsnew.tex
Modified: ProcessDiagram/trunk/Specification/images/complex.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/complex.svg 2015-04-21 12:24:10 UTC (rev 905)
+++ ProcessDiagram/trunk/Specification/images/complex.svg 2015-04-21 12:38:27 UTC (rev 906)
@@ -14,7 +14,7 @@
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<text
@@ -748,5 +514,16 @@
x="-422.7442"
id="tspan6602"
sodipodi:role="line">INFO</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;font-family:Bitstream Vera Sans"
+ x="192.93913"
+ y="593.90662"
+ id="text4641"><tspan
+ sodipodi:role="line"
+ id="tspan4643"
+ x="192.93913"
+ y="593.90662"
+ style="font-size:64px">A:(B:C)</tspan></text>
</g>
</svg>
Modified: ProcessDiagram/trunk/Specification/images/sbgn_model_revised/45.session
===================================================================
--- ProcessDiagram/trunk/Specification/images/sbgn_model_revised/45.session 2015-04-21 12:24:10 UTC (rev 905)
+++ ProcessDiagram/trunk/Specification/images/sbgn_model_revised/45.session 2015-04-21 12:38:27 UTC (rev 906)
@@ -1,4 +1,5 @@
-window_sizes 1551 1194 262 1283 1135 0
+window_sizes 1440 796 262 1172 744 0
+cleanlooks_style
diagrams
classdiagram_ref 134701 // MapView
1327 718 100 18 0 0
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2015-04-21 12:24:10 UTC (rev 905)
+++ ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2015-04-21 12:38:27 UTC (rev 906)
@@ -31,12 +31,12 @@
\usepackage[right,pagewise,modulo]{lineno}
\usepackage[olditem,oldenum]{paralist}
\usepackage{fourier}
+\usepackage{multicol}
%\usepackage{layouts}
\usepackage[pdftex]{graphicx}
\DeclareGraphicsExtensions{.pdf,.png}
-
\usepackage[pdftex]{hyperref}
\usepackage{rotating}
@@ -56,6 +56,10 @@
\setsecnumdepth{subsection}
+%\maxtocdepth{subsection}
+
+
+
%% ----------------------------------------------------------------------------
%% Layout customizations and macro definitions.
%% ----------------------------------------------------------------------------
@@ -63,11 +67,16 @@
%\input{sources/latex-style}
\input{sources/latex-macros}
+\makeindex
%% ----------------------------------------------------------------------------
\begin{document}
%% ----------------------------------------------------------------------------
+\newcommand{\umlclasshead}[1]{\subsection{\index{#1}#1}}
+
+\renewenvironment*{theindex}{\begin{itemize}[label={}]\tightlist\setlength{\itemindent}{-25pt}\nolinenumbers\begin{multicols}{2}}{\end{multicols}\end{itemize}}
+
\frontmatter
\input{sources/front-page}
@@ -75,6 +84,7 @@
\tableofcontents
+
\mainmatter
\linenumbers
@@ -82,6 +92,9 @@
\include{sources/introduction}
\include{sources/concepts}
+
+\include{sources/whatsnew}
+
%\include{sources/language_overview}
%\include{sources/primer}
@@ -110,6 +123,9 @@
\bibliographystyle{unsrt}
\bibliography{sbgn_PD-level1}
+\clearpage
+%\pagestyle{Index}
+%\printindex
%% ----------------------------------------------------------------------------
\end{document}
Modified: ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-04-21 12:24:10 UTC (rev 905)
+++ ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-04-21 12:38:27 UTC (rev 906)
@@ -28,6 +28,10 @@
The specification of SBGN PD Level 1.3 was modified by Stuart Moodie, with contributions from (in alphabetical order), Tobias Czauderna, Nicolas \lenov{}, and Anatoly Sorokin.
+\section{Level 1 Release 2.0}
+
+PUT SOME ACKNOWLEDGEMENTS HERE!
+
\section{Comprehensive list of acknowledgements}
Here is a more comprehensive list of people 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. We intend this list to be complete. We are very sorry if we forgot someone, and would be grateful if you could notify us of any omission.
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-04-21 12:24:10 UTC (rev 905)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-04-21 12:38:27 UTC (rev 906)
@@ -6,8 +6,8 @@
\chapter{Language Specification}
\label{chp:glyphs}
-
\section{Introduction}
+\label{sec:lang-intro}
In this chapter we aim to describe the \PDl by describing its elements
and underlying concepts in detail. The challenge in doing this is to
@@ -16,37 +16,32 @@
goal is to minimise duplication or rules as much as possible, which
makes the specification more difficult to update in the future. To
achieve this we took our lead from other successful standards: the
-Unified Modelling Language (UML) \cite{umlspec} which is a graphical
+Unified Modelling Language (UML) \cite{umlspec} (a graphical
language that has been used by tens of thousands of software
-developers for over a decade to describe and software system; and the
-Systems Biology Markup Language (SBML) Level 3 Core specification
-\cite{sbmll3core} which is the ``daddy'' of computational systems
-biological standards and over 10 years after its inception is firmly
-embedded in the scientific community it serves. In both these
-specifications the language is modelled in UML where each language
-element is described as an UML class. The specification defines each
-class in turn and in so doing describes how the language elements fit
-together (syntax) and how they are applied and their rules
-(semantics). Since UML is a graphical language, the class definition
-also includes, where applicable to the language element, a description
-of the symbols used and guidelines about how the
-symbols should be drawn or laid out.
+developers for almost two decades to describe and 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
+specifications have similar approaches. The concepts and elements of
+the language are defined as classes and their interaction is described
+as relationships of containment, association or inheritance. In the
+case of UML, being a graphical language, the class descriptions also
+include a description of the symbols used with guidelines about how
+the symbols should be drawn or laid out. In this document we will also
+follow these precedents and take the following approach:
-Based on these specifications we will follow the following conventions
-in this chapter:
-
\begin{itemize}
\item The language will be described by a UML class model:
\begin{itemize}
- \item each language element or concept being represented as a
+ \item each language element or concept is represented as a
class.
- \item the syntax being represented by the cardinality of
- associations between classes.
+ \item conceptual organisation is described by a generalisation relationship
+ \item syntax is defined by the cardinality of associations between classes.
\end{itemize}
\item Each class is defined in detail, including a description of the concept or
element represented, parent classes, attributes, interactions with
- other classes and any semantic rules not captured in UML.
-\item Where classes correspond to a glyph, the symbol representing it
+ other classes and any semantic rules that cannot be captured in UML.
+\item Where a class corresponds to a glyph, the symbol representing it
is described and appropriate illustrations are provided.
\end{itemize}
@@ -141,12 +136,13 @@
shown at the opposite end of the association to it.
\item[shared aggregation (open diamond)] The aggregating class (C) is
adjacent to the diamond and is connected to the other class (D) via
- a solid line. Here there is a whole/part relationship, but there the
- part (class D) can be shared with another class and can exists
- independently of C.
-\item[navigability (black diamond anchor arrowhead)] If the association ends in an arrow, this
- indicates the direction of the association. Here this should be
- taken to mean that only one aside of the association (G) is `aware' of the relationship.
+ a solid line. This represents a whole/part relationship (as above), but one
+ where the 'part' (class D) can be shared with another class and can
+ 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)
+ 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
specification or implementation.
@@ -167,7 +163,7 @@
\subsection{Definition format}
-To help you read the definitions each one follows a standard format
+ To help you read the definitions each one follows a standard format
which each section found in the same order. Sections that are not
relevant are omitted.
@@ -249,7 +245,11 @@
\section{Definitions}
\label{sec:techref:definitions}
-\subsection{SBGNElement}
+\subsection{Index of Classes}
+
+\printindex
+
+\umlclasshead{SBGNElement}
\label{defn:SBGNElement}
All the glyphs in \SBGNPDLone inherit from
@@ -280,13 +280,13 @@
Not defined in the previous version.
-\subsection{Map}
+\umlclasshead{Map}
\label{defn:Map}\label{sec:techref:map}
\begin{figure}[htb]
\centering
- \includegraphics[width=0.55\textwidth]{images/mapuml}
+ \includegraphics[width=0.6\textwidth]{images/mapuml}
\caption{UML definition of Map and \sbgnclass{SBGNElement}.}
\label{fig:techref:mapuml}
\end{figure}
@@ -336,12 +336,12 @@
Not defined explicitly in previous versions.
-\subsection{SBGNGlyph}
+\umlclasshead{SBGNGlyph}
\label{defn:SBGNGlyph}
\begin{figure}[htb]
\centering
- \includegraphics[width=0.9\textwidth]{images/glyphauxuml}
+ \includegraphics[width=\textwidth]{images/glyphauxuml}
\caption{UML definition of the \sbgnclass{SBGNGlyph} and its subclasses.}
\label{fig:techref:glyphauxuml}
\end{figure}
@@ -375,12 +375,12 @@
Not defined in previous version.
-\subsection{AuxiliaryUnit}
+\umlclasshead{AuxiliaryUnit}
\label{defn:AuxiliaryUnit}
\begin{figure}[htb]
\centering
- \includegraphics[width=0.75\textwidth]{images/auxiliaryunituml}
+ \includegraphics[width=\textwidth]{images/auxiliaryunituml}
\caption{UML definition of the Auxiliary Unit and its subclasses.}
\label{fig:techref:auxiliaryunituml}
\end{figure}
@@ -412,7 +412,7 @@
Not defined in previous version.
-\subsection{SBGNNode}
+\umlclasshead{SBGNNode}
\label{defn:SBGNNode}
The \sbgnclass{SBGNNode} (figure \ref{fig:techref:sbgnnodearcuml}) represents
@@ -422,7 +422,7 @@
\begin{figure}[htb]
\centering
- \includegraphics[width=0.55\textwidth]{images/sbgnnodearcuml}
+ \includegraphics[width=0.6\textwidth]{images/sbgnnodearcuml}
\caption{UML definition of the \sbgnclass{SBGNNode} and
\sbgnclass{SBGNArc} classes.}
\label{fig:techref:sbgnnodearcuml}
@@ -457,7 +457,7 @@
Not defined in the previous version.
-\subsection{SBGNArc}
+\umlclasshead{SBGNArc}
\label{defn:SBGNArc}
The \sbgnclass{SBGNArc} (figure \ref{fig:techref:sbgnnodearcuml}) represents
@@ -495,12 +495,12 @@
Not defined in the previous version.
-\subsection{EntityType}
+\umlclasshead{EntityType}
\label{defn:EntityType}
\begin{figure}[htb]
\centering
- \includegraphics[width=0.85\textwidth]{images/entitytypeuml}
+ \includegraphics[width=\textwidth]{images/entitytypeuml}
\caption{UML definition of the entity type and the state variable
definition. The diagram shows how these classes interact with the
entity pool, state variable and so influence
@@ -600,7 +600,7 @@
Although not defined explicitly in the previous version, this concept
and the associated rules did exist in the language.
-\subsection{StateVariableDefinition}
+\umlclasshead{StateVariableDefinition}
\label{defn:StateVariableDefinition}
The \sbgnclass{StateVariableDefinition}\query{As with EntityType this
@@ -642,7 +642,7 @@
Although not defined explicitly in the previous version, arguably this
concept did exist in the language.
-\subsection{EntityPoolNode}
+\umlclasshead{EntityPoolNode}
\label{sec:techref:EPNs}\label{defn:EntityPoolNode}\label{sec:techref:EPN}
An entity pool is a population of entities that cannot be
@@ -659,7 +659,7 @@
\begin{figure}[htb]
\centering
- \includegraphics[width=0.85\textwidth]{images/epnuml}
+ \includegraphics[width=0.95\textwidth]{images/epnuml}
\caption{UML definition of the entity pool node and its descendant glyphs.}
\label{fig:techref:epnuml}
\end{figure}
@@ -762,7 +762,7 @@
but which now must contain a unique set of controlled vocabularies and
is part of the logical key of the \sbgnclass{EntityPoolNode}.
-\subsection{Empty Set}
+\umlclasshead{EmptySet}
\label{sec:techref:sourceSink}
It is useful to have the ability to represent the creation of an entity or
@@ -797,7 +797,7 @@
\begin{figure}[htb]
\centering
- \includegraphics[width=0.75\textwidth]{images/emptysetuml}
+ \includegraphics[width=0.9\textwidth]{images/emptysetuml}
\caption{The UML definition of the \glyph{EmptySet} and its context
in relation to other elements of the \PDl.}
\label{fig:techref:emptysetuml}
@@ -863,7 +863,7 @@
\glyph{Sink} glyphs where types of EPN, representing single entity
pools, while the \sbgnclass{EmptySet} is not.
-\subsection{StatelessEPN}
+\umlclasshead{StatelessEPN}
\label{defn:StatelessEPN}
The \sbgnclass{StatelessEPN} (figure \ref{fig:techref:statelessepnuml})
@@ -874,7 +874,7 @@
\begin{figure}[htb]
\centering
- \includegraphics[width=0.75\textwidth]{images/statelessepnuml}
+ \includegraphics[width=0.9\textwidth]{images/statelessepnuml}
\caption{UML definition of the stateless entity pool node and its
descendant glyphs.}
\label{fig:techref:statelessepnuml}
@@ -904,7 +904,7 @@
Not defined in the previous version.
-\subsection{Simple chemical}
+\umlclasshead{SimpleChemical}
\label{sec:techref:simpleChemical}
A \sbgnclass{SimpleChemical} is the `opposite' of a macromolecule
@@ -989,7 +989,7 @@
compatibility with previous versions the stadium symbol can be drawn
without straight horizontal elements so that it becomes a circle.
-\subsection{UnspecifiedEntity}
+\umlclasshead{UnspecifiedEntity}
\label{sec:techref:unspecifiedEntity}
The simplest type of \sbgnclass{EntityPoolNode} is the
@@ -1053,7 +1053,7 @@
No changes from the previous version.
-\subsection{Perturbing Agent}
+\umlclasshead{PerturbingAgent}
\label{sec:techref:perturbing agent}
Biochemical networks can be affected by external influences. Those
@@ -1112,7 +1112,7 @@
No changes from pervious version.
-\subsection{StatefulEPN}
+\umlclasshead{StatefulEPN}
\label{defn:StatefulEPN}
Stateful entity pools can undergo physical changes, for example
@@ -1124,7 +1124,7 @@
\begin{figure}[htb]
\centering
- \includegraphics[width=0.75\textwidth]{images/statefulepnuml}
+ \includegraphics[width=\textwidth]{images/statefulepnuml}
\caption{UML definition of the stateful entity pool node: showing its
descendants and its association with state variables.}
\label{fig:techref:statefulepnuml}
@@ -1161,7 +1161,7 @@
Not defined explicitly in the previous version.
-\subsection{Macromolecule}
+\umlclasshead{Macromolecule}
\label{sec:techref:macromolecule}
Many biological processes involve \emph{macromolecules}: biochemical
@@ -1264,7 +1264,7 @@
No changes from the previous version.
-\subsection{NucleicAcidFeature}
+\umlclasshead{NucleicAcidFeature}
\label{sec:techref:genetic}
The \sbgnclass{NucleicAcidFeature} represents a fragment of a
@@ -1349,7 +1349,7 @@
%%%% Complex
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Complex}\label{sec:techref:complex}
+\umlclasshead{Complex}\label{sec:techref:complex}
\label{defn:Complex}
A \sbgnclass{Complex} represents a biochemical entity composed of
@@ -1363,7 +1363,7 @@
\begin{figure}[htb]
\centering
- \includegraphics[width = 0.75\textwidth]{images/complexsubunituml}
+ \includegraphics[width = 0.9\textwidth]{images/complexsubunituml}
\caption{The UML definition of the \sbgnclass{Complex} and its
associated \sbgnclass{subunit}s. In particular this describes organisation
of the state variables that belong to both the subunit, but also
@@ -1471,7 +1471,7 @@
Complex glyph.
\end{itemize}
-\subsection{Subunit}
+\umlclasshead{Subunit}
\label{defn:Subunit}\label{sec:techref:subunits}
The \sbgnclass{Subunit}\query{The principles of the subunit have been
@@ -1618,7 +1618,7 @@
paradigms of the \PDl. This is corrected in the current version and
subunits are now adornments of the \sbgnclass{Complex}.
-\subsection{ProcessNode}\label{sec:techref:PNs}
+\umlclasshead{ProcessNode}\label{sec:techref:PNs}
\label{defn:ProcessNode}
The \sbgnclass{Process} (figure \ref{fig:techref:processumlview}) represents a
@@ -1666,7 +1666,7 @@
been changed the current status where all processes are unique in a \PDm.
\end{itemize}
-\subsection{NonStoichiometricProcess}
+\umlclasshead{NonStoichiometricProcess}
\label{defn:NonStoichiometricProcess}
The \sbgnclass{NonStoichiometricProcess}\query{This has been discussed
@@ -1679,7 +1679,7 @@
\begin{figure}[htb]
\centering
- \includegraphics[width = 0.45\textwidth]{images/nonstoichprocessuml}
+ \includegraphics[width = 0.75\textwidth]{images/nonstoichprocessuml}
\caption{The UML definition of the \sbgnclass{NonStoichiometricProcess} and its
associated subclasses.}
\label{fig:techref:nonstoichprocessuml}
@@ -1707,7 +1707,7 @@
Not defined in the previous version.
-\subsection{Phenotype}
+\umlclasshead{Phenotype}
A biochemical network can generate phenotypes or affect biological
processes. Such processes can take place at different levels and are
@@ -1780,7 +1780,7 @@
unique.
-\subsection{SubmapNode}
+\umlclasshead{SubmapNode}
\label{sec:techref:submap}\label{defn:SubmapNode}
The \sbgnclass{SubmapNode}\query{This name change has not been
@@ -1791,14 +1791,14 @@
reader as a separate related map. The \sbgnclass{Submap} is not
equivalent to an \sbgnclass{OmittedProcess} (section
\ref{sec:techref:omitted}). The \sbgnclass{Submap} allows the detail of
-section of the \PDm to be exported to another \PDm and replaced by the
+the section of the \PDm to be exported to another \PDm and replaced by the
\sbgnclass{SubmapNode}, which acts as a place-holder. This is
described in section \ref{sec:techref:map} and the semantics of submap linking
is defined in section \ref{sec:techref:submaplinkingsemantics}.
\begin{figure}[htb]
\centering
- \includegraphics[width = 0.65\textwidth]{images/submapnodeuml}
+ \includegraphics[width = \textwidth]{images/submapnodeuml}
\caption{The UML definition of the \sbgnclass{SubmapNode} and its
relationship to its submap, tags etc.}
\label{fig:techref:submapnodeuml}
@@ -1838,7 +1838,7 @@
\begin{itemize}
\item All instances of \classref{SubmapTerminal} held by this class
must be logically unique.
-\item attrib{in\_arcs} and \attrib{out\_arcs} must be empty (\ie
+\item \attrib{in\_arcs} and \attrib{out\_arcs} must be empty (\ie
degree $=0$).
\end{itemize}
@@ -1874,13 +1874,13 @@
specification. This is confusing when talking about the Submap itself
so this glyph is now referred to as the SubmapNode to distinguish it.
-\subsection{LogicalOperator}
+\umlclasshead{LogicalOperator}
\label{sec:techref:logic}
\label{defn:LogicalOperator}
\begin{figure}[htb]
\centering
- \includegraphics[width = 0.5\textwidth]{images/logicaloperatoruml}
+ \includegraphics[width = 0.75\textwidth]{images/logicaloperatoruml}
\caption{The UML definition of the \sbgnclass{LogicalOperator}.}
\label{fig:techref:logicaloperatoruml}
\end{figure}
@@ -1993,12 +1993,12 @@
the previous version the semantics and glyphs are unchanged.
-\subsection{StoichiometricProcess}
+\umlclasshead{StoichiometricProcess}
\label{defn:StoichiometricProcess}\label{sec:techref:stoichiometricprocess}
\begin{figure}[htb]
\centering
- \includegraphics[width = 0.45\textwidth]{images/stoichprocessuml}
+ \includegraphics[width = 0.6\textwidth]{images/stoichprocessuml}
\caption{The UML definition of the
\sbgnclass{StiochiometricProcess}. The class interacts with
subclasses of \sbgnclass{FluxArc} and \sbgnclass{ModulationArc}.}
@@ -2373,13 +2373,13 @@
Although the \sbgnclass{NonStoichiometricProcess} was not explicitly defined in
the previous version the semantics and glyphs are unchanged.
-\subsection{Compartment}
+\umlclasshead{Compartment}
\label{sec:techrefcompartment}
\label{defn:Compartment}
\begin{figure}[htb]
\centering
- \includegraphics[width = 0.5\textwidth]{images/compartmentuml}
+ \includegraphics[width = 0.9\textwidth]{images/compartmentuml}
\caption{The UML definition of the \sbgnclass{Compartment} showing
how it containment of \sbgnclass{EntityPoolNode}.}
\label{fig:techref:compartmentuml}
@@ -2503,12 +2503,12 @@
text as annotation then maps containing these features will be invalid
according to the current specification.
-\subsection{AttributeValue}
+\umlclasshead{AttributeValue}
\label{defn:AttributeValue}
\begin{figure}[htb]
\centering
- \includegraphics[width = 0.5\textwidth]{images/attributevalueuml}
+ \includegraphics[width = 0.9\textwidth]{images/attributevalueuml}
\caption{The UML definition of the \...
[truncated message content] |
|
From: <lp...@us...> - 2015-04-21 12:24:17
|
Revision: 905
http://sourceforge.net/p/sbgn/code/905
Author: lptolik
Date: 2015-04-21 12:24:10 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
resolving an issues with spec
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/ENs.tex
EntityRelationship/trunk/sources/and.tex
EntityRelationship/trunk/sources/auxiliary.tex
EntityRelationship/trunk/sources/domain.tex
EntityRelationship/trunk/sources/entity.tex
EntityRelationship/trunk/sources/not.tex
EntityRelationship/trunk/sources/or.tex
EntityRelationship/trunk/sources/stateVariable.tex
Property Changed:
----------------
EntityRelationship/trunk/sources/
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Index: EntityRelationship/trunk/sources
===================================================================
--- EntityRelationship/trunk/sources 2015-04-21 11:31:12 UTC (rev 904)
+++ EntityRelationship/trunk/sources 2015-04-21 12:24:10 UTC (rev 905)
Property changes on: EntityRelationship/trunk/sources
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.aux
Modified: EntityRelationship/trunk/sources/ENs.tex
===================================================================
--- EntityRelationship/trunk/sources/ENs.tex 2015-04-21 11:31:12 UTC (rev 904)
+++ EntityRelationship/trunk/sources/ENs.tex 2015-04-21 12:24:10 UTC (rev 905)
@@ -12,7 +12,7 @@
\subsection{Interactors}\label{sec:interactors}
-Interactors are entity nodes that are able to participate in an interaction (\sect{interaction}). \SBGNERLone{} provides two interactors, the \glyph{entity} and the \glyph{outcome} of a statement.
+Interactors are nodes that are able to participate in an interaction (\sect{interaction}). \SBGNERLone{} provides two interactors, the \glyph{entity} and the \glyph{outcome} of a statement.
\input{sources/entity.tex}
\input{sources/outcome.tex}
Modified: EntityRelationship/trunk/sources/and.tex
===================================================================
--- EntityRelationship/trunk/sources/and.tex 2015-04-21 11:31:12 UTC (rev 904)
+++ EntityRelationship/trunk/sources/and.tex 2015-04-21 12:24:10 UTC (rev 905)
@@ -4,7 +4,7 @@
%\color{blue}
\subsubsection{Glyph: \glyph{And}}\label{sec:and}
-The glyph \glyph{and} is used to denote that all the \glyph{entity nodes} linked as input are necessary to produce the output influence.
+The glyph \glyph{and} is used to denote that all the \glyph{interactors} linked as input are necessary to produce the output influence.
\begin{glyphDescription}
Modified: EntityRelationship/trunk/sources/auxiliary.tex
===================================================================
--- EntityRelationship/trunk/sources/auxiliary.tex 2015-04-21 11:31:12 UTC (rev 904)
+++ EntityRelationship/trunk/sources/auxiliary.tex 2015-04-21 12:24:10 UTC (rev 905)
@@ -6,7 +6,7 @@
\section{Auxiliary units}\label{sec:aux}
-\glyph{Auxiliary units} are decorations used on \glyph{entities} (\sect{entity}) and \glyph{interactions} (\sect{interaction}) to further refine their semantics. \SBGNERLone{} provides two \glyph{auxiliary units}, the \glyph{unit of information} and the \glyph{state variable}.
+\glyph{Auxiliary units} are decorations used on \glyph{entities} (\sect{entity}), \glyph{interactions} (\sect{interaction}) and \glyph{influences} (\sect{influences}) to further refine their semantics. \SBGNERLone{} provides two \glyph{auxiliary units}, the \glyph{unit of information} and the \glyph{state variable}.
\input{sources/unitInformation.tex}
\input{sources/stateVariable.tex}
Modified: EntityRelationship/trunk/sources/domain.tex
===================================================================
--- EntityRelationship/trunk/sources/domain.tex 2015-04-21 11:31:12 UTC (rev 904)
+++ EntityRelationship/trunk/sources/domain.tex 2015-04-21 12:24:10 UTC (rev 905)
@@ -5,7 +5,7 @@
\section{\glyph{Entity} nesting }
\label{sec:domain}
-\SBGNERLone Version 2 allows \glyph{entities} to be nested. The relationships between the enclosed \glyph{entity} and the enclosing \glyph{entity} is partship. Note that this relation between \glyph{entities} of different levels does not imply anything about \glyph{entities} of the same level. In the \fig{domain}, A is part of X and B is part of X. However, nothing is said about A and B. A and B could be of different nature (transmembrane domain and transduction domain) or could be overlapping (binding domain and catalytic domain sharing some amino-acids).
+\SBGNERLone Version 2 allows \glyph{entities} to be nested. The enclosed \glyph{entity} represents a part of the enclosing \glyph{entity}, note that this relation between \glyph{entities} of different levels does not imply anything about \glyph{entities} of the same level. In the \fig{domain}, A is part of X and B is part of X. However, nothing is said about A and B. A and B could be of different nature (transmembrane domain and transduction domain) or could be overlapping (binding domain and catalytic domain sharing some amino-acids).
\begin{figure}[H]
\centering
Modified: EntityRelationship/trunk/sources/entity.tex
===================================================================
--- EntityRelationship/trunk/sources/entity.tex 2015-04-21 11:31:12 UTC (rev 904)
+++ EntityRelationship/trunk/sources/entity.tex 2015-04-21 12:24:10 UTC (rev 905)
@@ -36,7 +36,7 @@
\label{fig:ex-entity}
\end{figure}
-The granularity of the representation, that is what a given \glyph{entity} actually represents, is let to the person generating the map. For instance (\fig{entity-granularity}), one could choose to represent phosphorylated and non-phosphorylated forms of a protein using a single \glyph{entity}, carrying a \glyph{state variable} representing the phosphorylation. The phosphorylated form would be represented by the \glyph{outcome} located on the \glyph{assignment}. Alternatively one could use two separate entities, carrying the \glyph{existence} \glyph{state variable}. The phosphorylated form would be represented by the \glyph{entity}.
+The granularity of the representation, that is what a given \glyph{entity} actually represents, is let to the person generating the map. For instance (\fig{entity-granularity}), one could choose to represent phosphorylated and non-phosphorylated forms of a protein using a single \glyph{entity}, carrying a \glyph{state variable} representing the phosphorylation. The phosphorylated form would be represented by the \glyph{outcome} located on the \glyph{assignment}. Alternatively one could create separate entity for phosphorylated state, carrying the \glyph{existence} \glyph{state variable} and represent phosphorylation by assignment of the true value to the \glyph{existence} \glyph{state variable}.
\begin{figure}[H]
\centering
Modified: EntityRelationship/trunk/sources/not.tex
===================================================================
--- EntityRelationship/trunk/sources/not.tex 2015-04-21 11:31:12 UTC (rev 904)
+++ EntityRelationship/trunk/sources/not.tex 2015-04-21 12:24:10 UTC (rev 905)
@@ -4,7 +4,7 @@
%\color{blue}
\subsubsection{Glyph: \glyph{Not}}\label{sec:not}
-The glyph \glyph{not} is used to denote that the output influence only happens in the absence of the input \glyph{entity node}.
+The glyph \glyph{not} is used to denote that the output influence only happens in the absence of the input \glyph{interactor}.
\begin{glyphDescription}
Modified: EntityRelationship/trunk/sources/or.tex
===================================================================
--- EntityRelationship/trunk/sources/or.tex 2015-04-21 11:31:12 UTC (rev 904)
+++ EntityRelationship/trunk/sources/or.tex 2015-04-21 12:24:10 UTC (rev 905)
@@ -4,7 +4,7 @@
%\color{blue}
\subsubsection{Glyph: \glyph{Or}}\label{sec:or}
-The glyph \glyph{or} is used to denote that any of the \glyph{entity nodes} linked as input is sufficient to produce the output influence.
+The glyph \glyph{or} is used to denote that any of the \glyph{interactors} linked as input is sufficient to produce the output influence.
\begin{glyphDescription}
Modified: EntityRelationship/trunk/sources/stateVariable.tex
===================================================================
--- EntityRelationship/trunk/sources/stateVariable.tex 2015-04-21 11:31:12 UTC (rev 904)
+++ EntityRelationship/trunk/sources/stateVariable.tex 2015-04-21 12:24:10 UTC (rev 905)
@@ -9,9 +9,9 @@
Many biological entities such as molecules can exist in different \emph{states}, meaning different physical or informational configurations. These states can arise for a variety of reasons. For example, macromolecules can be subject to post-synthesis modifications, wherein residues of the macromolecules (amino acids, nucleosides, or glucid residues) are modified through covalent linkage to other chemicals. Other examples of states are alternative conformations as in the closed/open/desensitized conformations of a transmembrane channel, and the active/inactive forms of an enzyme.
SBGN provides a means of associating one or more \glyph{state variables} with an entity; each such variable can be used to represent a dimension along which the state of the overall entity can vary. When an entity can exist in different states, the state of the instance of the entity % (\ie the SBGN object)
-can be described by the current values of all its \glyph{state variables}, and the values of the \glyph{state variables} of all its possible components, recursively.
+can be described by the current values of all its \glyph{state variables}, and the values of the \glyph{state variables} of all its possible components (nested entities \sect{domain}), recursively.
-In \SBGNERLone, \glyph{state variables} are also used to describe the localisation in compartments (a transport is therefore described as a state variable assignment, see \sect{assignment}).
+In \SBGNERLone, \glyph{state variables} are also used to describe the localisation in compartments (a transport is therefore could be described as assignment of different values to the location state variable, see \sect{assignment}).
\begin{glyphDescription}
@@ -32,7 +32,7 @@
\label{fig:state-var}
\end{figure}
-Two state variables are predefined. The variable \glyph{existence} is used to represent the creation or destruction of entities, as seen on \fig{ex-existence}\label{sec:existence}. \glyph{Existence} can take two values, true (T) or false (F). The variable is represented by a circle vertically divided in two. One hemicircle is black, and the other white.
+Two state variables are predefined. The variable \glyph{existence} is used to represent the creation or destruction of instances of an entity, as seen on \fig{ex-existence}\label{sec:existence}. \glyph{Existence} can take two values, true (T) or false (F). The variable is represented by a circle vertically divided in two. One hemicircle is black, and the other white.
\begin{figure}[H]
\centering
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2015-04-21 11:31:15
|
Revision: 904
http://sourceforge.net/p/sbgn/code/904
Author: lptolik
Date: 2015-04-21 11:31:12 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
A7 figure capture fixed
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/usermanual.tex
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/trunk/sources/usermanual.tex
===================================================================
--- EntityRelationship/trunk/sources/usermanual.tex 2015-04-21 11:14:43 UTC (rev 903)
+++ EntityRelationship/trunk/sources/usermanual.tex 2015-04-21 11:31:12 UTC (rev 904)
@@ -79,7 +79,7 @@
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.75]{examples/rtk.png}
- \caption{Receptor tyrosine kinase activation: examples of active kinase complexes are shown. Black lines connect two complexes with outcomes, which definition is compatible with the complex status.}
+ \caption{The complete diagram of receptor tyrosine kinase activation.}
\label{fig:rtk-full}
\end{figure}
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|
|
From: <lp...@us...> - 2015-04-21 11:14:45
|
Revision: 903
http://sourceforge.net/p/sbgn/code/903
Author: lptolik
Date: 2015-04-21 11:14:43 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
missing images
Modified Paths:
--------------
EntityRelationship/trunk/sources/er-overview.tex
EntityRelationship/trunk/sources/introduction.tex
Added Paths:
-----------
EntityRelationship/trunk/images/asynchronous.pdf
EntityRelationship/trunk/images/asynchronous.png
EntityRelationship/trunk/images/asynchronous.svg
Added: EntityRelationship/trunk/images/asynchronous.pdf
===================================================================
(Binary files differ)
Index: EntityRelationship/trunk/images/asynchronous.pdf
===================================================================
--- EntityRelationship/trunk/images/asynchronous.pdf 2015-04-21 09:26:59 UTC (rev 902)
+++ EntityRelationship/trunk/images/asynchronous.pdf 2015-04-21 11:14:43 UTC (rev 903)
Property changes on: EntityRelationship/trunk/images/asynchronous.pdf
___________________________________________________________________
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Added: EntityRelationship/trunk/images/asynchronous.png
===================================================================
(Binary files differ)
Index: EntityRelationship/trunk/images/asynchronous.png
===================================================================
--- EntityRelationship/trunk/images/asynchronous.png 2015-04-21 09:26:59 UTC (rev 902)
+++ EntityRelationship/trunk/images/asynchronous.png 2015-04-21 11:14:43 UTC (rev 903)
Property changes on: EntityRelationship/trunk/images/asynchronous.png
___________________________________________________________________
Added: svn:mime-type
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+ style="display:inline;fill:none;stroke:#000000;stroke-width:2;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#EmptyTriangleOutL)"
+ sodipodi:nodetypes="ccc" />
+ <path
+ style="display:inline;fill:none;stroke:#000000;stroke-width:2;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#EmptyTriangleOutL)"
+ d="m 250.54669,127.93215 32.60539,0.0903 46.14529,0.0514"
+ id="path11820"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="ccc" />
+ <text
+ id="text11822"
+ x="241.35002"
+ y="155.05339"
+ style="font-size:15px;display:inline"
+ inkscape:transform-center-x="133.30401"
+ inkscape:transform-center-y="102.14203">
+ <tspan
+ id="tspan11824"
+ y="155.05339"
+ x="241.35002"
+ style="font-variant:normal;font-weight:normal;font-size:16px;font-family:'Bitstream Vera Sans';-inkscape-font-specification:BitstreamVeraSans-Roman;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none">T</tspan>
+ </text>
+ <g
+ transform="translate(151.08257,-50.980056)"
+ id="g5883">
+ <path
+ inkscape:connector-curvature="0"
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+ style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:3;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ id="path5885" />
+ <path
+ inkscape:connector-curvature="0"
+ d="m 178.17626,206.21512 c 7.7103,0 13.96486,6.1475 13.96486,13.73 0,7.5775 -6.25456,13.725 -13.96486,13.725 -0.0237,0 -0.0485,0 -0.0733,0 l 0.0733,-13.725 0,-13.73 z"
+ style="fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:3.07598758;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ id="path5887" />
+ </g>
+ <g
+ transform="matrix(1,0,0,-1,153.96794,388.50442)"
+ id="g5889">
+ <g
+ transform="matrix(1.25,0,0,1.25,1.80435,11.50262)"
+ id="g5891"
+ style="display:inline">
+ <path
+ id="path5893"
+ style="fill:none;stroke:#000000;stroke-width:2.04078007;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ d="m 140.715,211.039 0,-28.242"
+ inkscape:connector-curvature="0" />
+ </g>
+ <g
+ transform="matrix(0,1.25,-1.25,0,1.80435,11.50262)"
+ id="g5895"
+ style="display:inline">
+ <path
+ id="path5897"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.02039003;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ d="m 190.961,-140.715 4.078,-4.082 -14.285,4.082 14.285,4.082 -4.078,-4.082 z"
+ inkscape:connector-curvature="0" />
+ </g>
+ <g
+ transform="matrix(1.25,0,0,-1.25,1.80435,11.50262)"
+ id="g5899"
+ style="display:inline">
+ <path
+ id="path5901"
+ style="fill:none;stroke:#000000;stroke-width:2.4000001;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
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+ inkscape:connector-curvature="0" />
+ </g>
+ </g>
+ <ellipse
+ style="display:inline;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:2;stroke-miterlimit:10;stroke-dasharray:none;stroke-opacity:1"
+ id="ellipse3906"
+ cx="246.68504"
+ cy="115.7592"
+ rx="4.5104966"
+ ry="4.0594468" />
+ </g>
+</svg>
Modified: EntityRelationship/trunk/sources/er-overview.tex
===================================================================
--- EntityRelationship/trunk/sources/er-overview.tex 2015-04-21 09:26:59 UTC (rev 902)
+++ EntityRelationship/trunk/sources/er-overview.tex 2015-04-21 11:14:43 UTC (rev 903)
@@ -14,7 +14,7 @@
\label{fig:eg1}
\end{figure}
-The essence of the \ERs is to depict the influences of entities upon the behaviour of others. The entities are classes of things that exist, either on their own, or when statements (interactions and assignments) become true. For entity to be true at least one instance of it should exist otherwise entity will be false. For instance, an entity can exist (such as ``entity A'' in \fig{eg1}), instances of different entities can interact (such as ``entity A'' and ``entity B'' in \fig{eg1}), or a value can be assigned to a property of some instance of an entity (such as ``value 1'' to property ``var'' of ``entity A'' in \fig{eg1}). The influences can therefore be understood as logical consequences of existence of its instances. The stimulation of the interaction between ``entity A'' and ``entity B'' in \fig{eg1} takes place if `value 1'' is really assigned to property ``var'' of some instance of the ``entity A''. The existence of the assignment (set of instances where value is really assigned to the property) is represented by the black dot (called \glyph{outcome}). On the contrary to the \PDl, where the different processes affect each other in a way that the behaviour of the depicted system can only be understood taking into account the whole system, the relationships are essentially independent. One can imagine that each of the relationships represents a specific conclusion of a scientific experiment reported in an article. Their addition on a map represents the knowledge we have of the effects of the entities represented upon each other. In \fig{eg1}, we have three statements:
+The essence of the \ERs is to depict the influences of entities upon the behaviour of others. The entities are classes of things that can exist, either on their own, or when statements (interactions and assignments) become true, so existence is the key concept in \ERs. For entity to participate in relationship at least one instance of it should exist otherwise entity will be non-existent. Instances of different entities can interact (such as ``entity A'' and ``entity B'' in \fig{eg1}), or a value can be assigned to a property of some instance of an entity (such as ``value 1'' to property ``var'' of ``entity A'' in \fig{eg1}). The influences can therefore be understood as logical consequences of existence of its instances. The stimulation of the interaction between ``entity A'' and ``entity B'' in \fig{eg1} takes place if ``value 1'' is really assigned to property ``var'' of some instance of the ``entity A''. The existence of the assignment (set of instances where value is really assigned to the property) is represented by the black dot (called \glyph{outcome}). On the contrary to the \PDl, where the different processes affect each other in a way that the behaviour of the depicted system can only be understood taking into account the whole system, the relationships are essentially independent. One can imagine that each of the relationships represents a specific conclusion of a scientific experiment reported in an article. Their addition on a map represents the knowledge we have of the effects of the entities represented upon each other. In \fig{eg1}, we have three statements:
\begin{itemize}
\item ``entity A'' can interact with ``entity B''.
Modified: EntityRelationship/trunk/sources/introduction.tex
===================================================================
--- EntityRelationship/trunk/sources/introduction.tex 2015-04-21 09:26:59 UTC (rev 902)
+++ EntityRelationship/trunk/sources/introduction.tex 2015-04-21 11:14:43 UTC (rev 903)
@@ -10,7 +10,7 @@
Nicolas Le Nov\`{e}re, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit I Aladjem, Sarala M Wimalaratne, Frank T Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji, Lu Li, Yukiko Matsuoka, Alice Villéger, Sarah E Boyd, Laurence Calzone, Melanie Courtot, Ugur Dogrusoz, Tom C Freeman, Akira Funahashi, Samik Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin, Douglas B Kell, Chris Sander, Herbert Sauro, Jacky L Snoep, Kurt Kohn, Hiroaki Kitano. The Systems Biology Graphical Notation. Nature Biotechnology 27, 735 - 741 (2009). \url{http://dx.doi.org/10.1038/nbt.1558}
\end{quote}
-This document defines the \emph{\ER{}} visual language of SBGN. \ERs are one of three views of a biological process offered by SBGN, the others being \PDs and \AFs. SBGN \ERl{} allows to see all the relationships in which a given entity participates, regardless of the temporal aspects. Entities are defined here in a broad sense as something that exists. Relationships can be seen as rules describing the influences of entities nodes on other relationships. An overview of \ERs is given in \sect{overview}.
+This document defines the \emph{\ER{}} visual language of SBGN. \ERs are one of three views of a biological process offered by SBGN, the others being \PDs and \AFs. SBGN \ERl{} allows to see all the relationships in which a given entity participates, regardless of the temporal aspects. Entities are defined here in a broad sense as something that can exists. Relationships can be seen as rules describing the influences of entities on other relationships. An overview of \ERs is given in \sect{overview}.
\input{sources/er-overview.tex}
\input{sources/versioning.tex}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2015-04-21 09:27:08
|
Revision: 902
http://sourceforge.net/p/sbgn/code/902
Author: tczauderna
Date: 2015-04-21 09:26:59 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
fixed opacity in SVGs
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/examples/compartment-3comp.svg
ProcessDiagram/trunk/Specification/examples/compartment-cell-wrong.svg
ProcessDiagram/trunk/Specification/examples/compartment-cell.svg
ProcessDiagram/trunk/Specification/examples/compartment_overlapping_wrong.svg
ProcessDiagram/trunk/Specification/examples/muscle.svg
ProcessDiagram/trunk/Specification/examples/process-reversible.svg
ProcessDiagram/trunk/Specification/examples/stoichEx1.svg
ProcessDiagram/trunk/Specification/examples/wrongStateVariables.svg
ProcessDiagram/trunk/Specification/images/GluR.svg
ProcessDiagram/trunk/Specification/images/layout-branching.svg
ProcessDiagram/trunk/Specification/images/layout-unit-information.svg
ProcessDiagram/trunk/Specification/images/refcard.svg
ProcessDiagram/trunk/Specification/images/stateVariable.svg
ProcessDiagram/trunk/Specification/le_images/process-dimerisation.svg
ProcessDiagram/trunk/Specification/le_images/submap-dissociated.svg
ProcessDiagram/trunk/Specification/le_images/submap-folded.svg
ProcessDiagram/trunk/Specification/le_images/submap-unfolded.svg
ProcessDiagram/trunk/Specification/le_images/submap.svg
ProcessDiagram/trunk/UserManual/images/process-dimerisation.svg
ProcessDiagram/trunk/UserManual/images/submap-dissociated.svg
ProcessDiagram/trunk/UserManual/images/submap-folded.svg
ProcessDiagram/trunk/UserManual/images/submap-unfolded.svg
ProcessDiagram/trunk/UserManual/images/submap.svg
Modified: ProcessDiagram/trunk/Specification/examples/compartment-3comp.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/compartment-3comp.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/examples/compartment-3comp.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -64,9 +64,9 @@
height="480.77545"
width="537.34399"
id="rect4818"
- style="opacity:0.98800001;fill:#c8c8c8;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
+ style="opacity:1;fill:#c8c8c8;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
<rect
- style="opacity:0.98800001;fill:white;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:white;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect4816"
width="515.15289"
height="364.64017"
@@ -82,9 +82,9 @@
height="329.72101"
width="490.3353"
id="rect4814"
- style="opacity:0.98800001;fill:#c8c8c8;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
+ style="opacity:1;fill:#c8c8c8;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
<rect
- style="opacity:0.98800001;fill:white;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:white;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect4810"
width="464.71249"
height="272.78348"
@@ -115,7 +115,7 @@
y="273.23816"
style="font-size:24px">outer</tspan></text>
<rect
- style="opacity:0.98800001;fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect3262"
width="82.832512"
height="24.243662"
@@ -140,9 +140,9 @@
height="242.88527"
width="439.86505"
id="rect4812"
- style="opacity:0.98800001;fill:#c8c8c8;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
+ style="opacity:1;fill:#c8c8c8;fill-opacity:1;fill-rule:evenodd;stroke:black;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
<rect
- style="opacity:0.98800001;fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect3268"
width="82.832512"
height="24.243662"
Modified: ProcessDiagram/trunk/Specification/examples/compartment-cell-wrong.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/compartment-cell-wrong.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/examples/compartment-cell-wrong.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -73,7 +73,7 @@
sodipodi:nodetypes="csssssc" />
<path
sodipodi:type="arc"
- style="opacity:0.98800001;fill:#c8c8c8;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:#c8c8c8;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="path2163"
sodipodi:cx="362.64478"
sodipodi:cy="369.49905"
Modified: ProcessDiagram/trunk/Specification/examples/compartment-cell.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/compartment-cell.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/examples/compartment-cell.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -63,7 +63,7 @@
sodipodi:nodetypes="csssssc" />
<path
sodipodi:type="arc"
- style="opacity:0.98800001;fill:white;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:4.47602749;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:white;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:4.47602749;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="path3146"
sodipodi:cx="362.64478"
sodipodi:cy="369.49905"
@@ -73,7 +73,7 @@
transform="matrix(1.123183,0,0,1.111556,-44.64877,-42.33855)" />
<path
sodipodi:type="arc"
- style="opacity:0.98800001;fill:#c8c8c8;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:#c8c8c8;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="path2163"
sodipodi:cx="362.64478"
sodipodi:cy="369.49905"
Modified: ProcessDiagram/trunk/Specification/examples/compartment_overlapping_wrong.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/compartment_overlapping_wrong.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/examples/compartment_overlapping_wrong.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -53,7 +53,7 @@
inkscape:groupmode="layer"
id="layer1">
<rect
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:9.46754837;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:9.46754837;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect18724"
width="344.99072"
height="234.3768"
@@ -173,7 +173,7 @@
d="M 309.45878,717.91131 C 306.28909,728.86008 296.18333,736.87248 284.21754,736.87248 C 272.25176,736.87249 262.146,728.86008 258.97631,717.91132"
style="fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:2;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
<rect
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:0.60392157;fill-rule:nonzero;stroke:#000000;stroke-width:9;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:0.60392157;fill-rule:nonzero;stroke:#000000;stroke-width:9;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect3520"
width="206.27425"
height="158.6447"
Modified: ProcessDiagram/trunk/Specification/examples/muscle.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/muscle.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/examples/muscle.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -564,7 +564,7 @@
height="12.814734"
width="45.019276"
id="rect7372"
- style="opacity:0.98999999000000005;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#eb9664;stroke-width:1.75000000000000000;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0" />
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#eb9664;stroke-width:1.75000000000000000;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0" />
<text
xml:space="preserve"
style="font-size:4.68290234px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans"
@@ -578,7 +578,7 @@
style="font-size:8.70220947px;font-weight:normal;text-align:center;text-anchor:middle"
id="tspan3341">closed</tspan></text>
<rect
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#eb9664;stroke-width:1.75;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#eb9664;stroke-width:1.75;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
id="rect5872"
width="45.019276"
height="12.814734"
@@ -832,7 +832,7 @@
d="M 788.84763,413.95124 L 779.20541,418.28253 L 779.15148,409.6967 L 788.84763,413.95124 z"
style="fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#eb9664;stroke-width:1.74044192;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" />
<rect
- style="opacity:0.98999999000000005;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#66cc66;stroke-width:1.75000000000000000;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#66cc66;stroke-width:1.75000000000000000;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
id="rect5874"
width="45.019276"
height="12.814734"
@@ -934,7 +934,7 @@
height="12.814734"
width="45.019276"
id="rect5876"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#66cc66;stroke-width:1.75;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0" />
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#66cc66;stroke-width:1.75;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0" />
<text
id="text7030"
y="669.974"
Modified: ProcessDiagram/trunk/Specification/examples/process-reversible.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/process-reversible.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/examples/process-reversible.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -130,7 +130,7 @@
height="21.906111"
width="65.133751"
id="rect7372"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:3;stroke-linejoin:round;stroke-miterlimit:3.0999999;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0" />
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:3;stroke-linejoin:round;stroke-miterlimit:3.0999999;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0" />
<text
xml:space="preserve"
style="font-size:12px;font-style:normal;font-weight:normal;opacity:1;fill:black;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans"
Modified: ProcessDiagram/trunk/Specification/examples/stoichEx1.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/stoichEx1.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/examples/stoichEx1.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -124,7 +124,7 @@
sodipodi:nodetypes="cc" />
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
id="path3316"
sodipodi:cx="388.23349"
sodipodi:cy="148.44386"
@@ -941,7 +941,7 @@
style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-linecap:butt;stroke-linejoin:miter;marker-start:url(#TriangleInL);marker-end:none;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1" />
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
id="path3314"
sodipodi:cx="388.23349"
sodipodi:cy="148.44386"
@@ -959,7 +959,7 @@
sodipodi:nodetypes="cc" />
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
id="path3320"
sodipodi:cx="388.23349"
sodipodi:cy="148.44386"
@@ -980,7 +980,7 @@
style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-linecap:butt;stroke-linejoin:miter;marker-start:url(#TriangleInL);marker-end:none;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1" />
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
id="path3326"
sodipodi:cx="388.23349"
sodipodi:cy="148.44386"
@@ -998,7 +998,7 @@
sodipodi:nodetypes="cc" />
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
id="path3330"
sodipodi:cx="388.23349"
sodipodi:cy="148.44386"
@@ -1019,7 +1019,7 @@
style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-linecap:butt;stroke-linejoin:miter;marker-start:url(#TriangleInL);marker-end:none;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1" />
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.25;stroke-miterlimit:3.66666675;stroke-dasharray:none;stroke-opacity:1"
id="path3336"
sodipodi:cx="388.23349"
sodipodi:cy="148.44386"
Modified: ProcessDiagram/trunk/Specification/examples/wrongStateVariables.svg
===================================================================
--- ProcessDiagram/trunk/Specification/examples/wrongStateVariables.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/examples/wrongStateVariables.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -653,7 +653,7 @@
sodipodi:role="line">X</tspan></text>
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:16.11750031;stroke-miterlimit:10;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
+ style="opacity:1;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:16.11750031;stroke-miterlimit:10;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
id="path2394"
sodipodi:cx="266.68027"
sodipodi:cy="253.16034"
@@ -743,7 +743,7 @@
sodipodi:role="line">P@312</tspan></text>
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:16.11750031;stroke-miterlimit:10;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
+ style="opacity:1;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:16.11750031;stroke-miterlimit:10;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
id="path2394-9"
sodipodi:cx="266.68027"
sodipodi:cy="253.16034"
Modified: ProcessDiagram/trunk/Specification/images/GluR.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/GluR.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/images/GluR.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -97,7 +97,7 @@
sodipodi:cy="234.4164"
sodipodi:cx="187.35553"
id="path3155"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
sodipodi:type="arc" />
<path
sodipodi:nodetypes="czs"
@@ -115,7 +115,7 @@
id="g3166">
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="path3168"
sodipodi:cx="187.35553"
sodipodi:cy="234.4164"
@@ -143,7 +143,7 @@
sodipodi:cy="234.4164"
sodipodi:cx="187.35553"
id="path3176"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
sodipodi:type="arc" />
<path
sodipodi:nodetypes="czs"
@@ -161,7 +161,7 @@
id="g3182">
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="path3184"
sodipodi:cx="187.35553"
sodipodi:cy="234.4164"
@@ -189,7 +189,7 @@
sodipodi:cy="234.4164"
sodipodi:cx="187.35553"
id="path3192"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
sodipodi:type="arc" />
<path
sodipodi:nodetypes="czs"
@@ -207,7 +207,7 @@
id="g3198">
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="path3200"
sodipodi:cx="187.35553"
sodipodi:cy="234.4164"
@@ -235,7 +235,7 @@
sodipodi:cy="234.4164"
sodipodi:cx="187.35553"
id="path3208"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
sodipodi:type="arc" />
<path
sodipodi:nodetypes="czs"
@@ -253,7 +253,7 @@
id="g3214">
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="path3216"
sodipodi:cx="187.35553"
sodipodi:cy="234.4164"
@@ -281,7 +281,7 @@
sodipodi:cy="234.4164"
sodipodi:cx="187.35553"
id="path3224"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
sodipodi:type="arc" />
<path
sodipodi:nodetypes="czs"
@@ -299,7 +299,7 @@
id="g3230">
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="path3232"
sodipodi:cx="187.35553"
sodipodi:cy="234.4164"
Modified: ProcessDiagram/trunk/Specification/images/layout-branching.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/layout-branching.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/images/layout-branching.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -79,7 +79,7 @@
inkscape:groupmode="layer"
id="layer1">
<rect
- style="opacity:0.98999999000000005;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:3;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:3;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect3580"
width="1464.4697"
height="848.75537"
Modified: ProcessDiagram/trunk/Specification/images/layout-unit-information.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/layout-unit-information.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/images/layout-unit-information.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -155,7 +155,7 @@
transform="matrix(1,0,0,1.0012037,444.9075,-95.587337)"
id="g6924-7">
<rect
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:4.99699354;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:4.99699354;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
id="rect2392-9"
width="125.58038"
height="65.681862"
@@ -204,7 +204,7 @@
height="65.681862"
width="125.58038"
id="rect2392-9-9"
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:4.99699354;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0" />
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:4.99699354;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0" />
<text
transform="scale(0.96827814,1.0327611)"
id="text2837-4-7-4"
Modified: ProcessDiagram/trunk/Specification/images/refcard.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/refcard.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/images/refcard.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -670,7 +670,7 @@
id="path3567"
inkscape:connector-curvature="0" />
<rect
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
id="rect3569"
width="59.355392"
height="17.73098"
Modified: ProcessDiagram/trunk/Specification/images/stateVariable.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/stateVariable.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/Specification/images/stateVariable.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -140,7 +140,7 @@
sodipodi:role="line">value</tspan></text>
<path
sodipodi:type="arc"
- style="opacity:0.98999999;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:16.11750031;stroke-miterlimit:10;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
+ style="opacity:1;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:16.11750031;stroke-miterlimit:10;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
id="path2394"
sodipodi:cx="266.68027"
sodipodi:cy="253.16034"
Modified: ProcessDiagram/trunk/Specification/le_images/process-dimerisation.svg
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/le_images/submap-dissociated.svg
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/le_images/submap-folded.svg
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/le_images/submap-unfolded.svg
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/le_images/submap.svg
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/UserManual/images/process-dimerisation.svg
===================================================================
--- ProcessDiagram/trunk/UserManual/images/process-dimerisation.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/UserManual/images/process-dimerisation.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -98,7 +98,7 @@
style="opacity:1">
<path
sodipodi:type="arc"
- style="opacity:0.98800001000000004;fill:#ffffc8;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0;fill-opacity:1"
+ style="opacity:1;fill:#ffffc8;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0;fill-opacity:1"
id="path5309"
sodipodi:cx="776.55475"
sodipodi:cy="291.29361"
@@ -164,7 +164,7 @@
sodipodi:cy="291.29361"
sodipodi:cx="776.55475"
id="path6204"
- style="opacity:0.98800001000000004;fill:#ffffc8;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
+ style="opacity:1;fill:#ffffc8;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
sodipodi:type="arc" />
<text
id="text6200"
Modified: ProcessDiagram/trunk/UserManual/images/submap-dissociated.svg
===================================================================
--- ProcessDiagram/trunk/UserManual/images/submap-dissociated.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/UserManual/images/submap-dissociated.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -109,7 +109,7 @@
height="246.14775"
width="417.26804"
id="rect3522"
- style="opacity:0.98999999;fill:white;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:6;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:white;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:6;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
rx="43.840618" />
<path
sodipodi:type="arc"
Modified: ProcessDiagram/trunk/UserManual/images/submap-folded.svg
===================================================================
--- ProcessDiagram/trunk/UserManual/images/submap-folded.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/UserManual/images/submap-folded.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -105,7 +105,7 @@
inkscape:label="final"
style="opacity:1">
<rect
- style="opacity:0.98999999000000005;fill:#ffffc8;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:6;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:#ffffc8;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:6;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect3520"
width="206.27425"
height="158.6447"
@@ -176,7 +176,7 @@
x="583.54797"
sodipodi:role="line">Fru6P</tspan></text>
<rect
- style="opacity:0.98999999;fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:3.3145237;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:3.3145237;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect3545"
width="262.86566"
height="178.00572"
Modified: ProcessDiagram/trunk/UserManual/images/submap-unfolded.svg
===================================================================
--- ProcessDiagram/trunk/UserManual/images/submap-unfolded.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/UserManual/images/submap-unfolded.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -110,7 +110,7 @@
height="246.14775"
width="417.26804"
id="rect3522"
- style="opacity:0.98999999000000005;fill:#ffffc8;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:6;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:#ffffc8;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:6;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
rx="43.840618" />
<path
sodipodi:type="arc"
Modified: ProcessDiagram/trunk/UserManual/images/submap.svg
===================================================================
--- ProcessDiagram/trunk/UserManual/images/submap.svg 2015-02-17 21:17:12 UTC (rev 901)
+++ ProcessDiagram/trunk/UserManual/images/submap.svg 2015-04-21 09:26:59 UTC (rev 902)
@@ -145,7 +145,7 @@
id="tspan4811"
sodipodi:role="line">C</tspan></text>
<rect
- style="opacity:0.98999999000000005;fill:#96ffc8;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+ style="opacity:1;fill:#96ffc8;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect3545"
width="308.64941"
height="284.35922"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2015-02-17 21:17:25
|
Revision: 901
http://sourceforge.net/p/sbgn/code/901
Author: tczauderna
Date: 2015-02-17 21:17:12 +0000 (Tue, 17 Feb 2015)
Log Message:
-----------
fixed a typo in 2.8.6
Modified Paths:
--------------
ActivityFlow/tags/L1R1.2/sbgn_AF-level1.pdf
ActivityFlow/tags/L1R1.2/sources/equivalenceArc.tex
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/equivalenceArc.tex
Modified: ActivityFlow/tags/L1R1.2/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/tags/L1R1.2/sbgn_AF-level1.pdf 2015-02-17 19:33:27 UTC (rev 900)
+++ ActivityFlow/tags/L1R1.2/sbgn_AF-level1.pdf 2015-02-17 21:17:12 UTC (rev 901)
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From: <hua...@us...> - 2015-02-17 19:33:29
|
Revision: 900
http://sourceforge.net/p/sbgn/code/900
Author: huaiyumi
Date: 2015-02-17 19:33:27 +0000 (Tue, 17 Feb 2015)
Log Message:
-----------
SBGN-AF Level 1 Release 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: <hua...@us...> - 2015-02-17 19:33:02
|
Revision: 899
http://sourceforge.net/p/sbgn/code/899
Author: huaiyumi
Date: 2015-02-17 19:32:54 +0000 (Tue, 17 Feb 2015)
Log Message:
-----------
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: <hua...@us...> - 2015-02-17 19:29:12
|
Revision: 898
http://sourceforge.net/p/sbgn/code/898
Author: huaiyumi
Date: 2015-02-17 19:29:05 +0000 (Tue, 17 Feb 2015)
Log Message:
-----------
SBGN-AF Level 1 Release 1.2
Added Paths:
-----------
ActivityFlow/tags/L1R1.2/trunk/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hua...@us...> - 2015-02-17 19:22:13
|
Revision: 897
http://sourceforge.net/p/sbgn/code/897
Author: huaiyumi
Date: 2015-02-17 19:22:09 +0000 (Tue, 17 Feb 2015)
Log Message:
-----------
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/equivalenceArc.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2015-02-06 17:53:11 UTC (rev 896)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2015-02-17 19:22:09 UTC (rev 897)
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/Type /XObject
/Subtype /Form
@@ -3333,7 +3328,7 @@
/S /Transparency
/CS /DeviceRGB
>>
-/Resources 633 0 R
+/Resources 627 0 R
>>
stream
x\x9Cm\x90\xB1
@@ -3342,9 +3337,9 @@
endstream
endobj
-625 0 obj
+618 0 obj
<<
-/Length 634 0 R
+/Length 628 0 R
/Filter /FlateDecode
/Type /XObject
/Subtype /Form
@@ -3354,7 +3349,7 @@
/S /Transparency
/CS /DeviceRGB
>>
-/Resources 635 0 R
+/Resources 629 0 R
>>
stream
x\x9C%\x8B;
@@ -3363,9 +3358,9 @@
endstream
endobj
-636 0 obj
+630 0 obj
<<
-/Length 637 0 R
+/Length 631 0 R
/Filter /FlateDecode
/Length1 8792
>>
@@ -3420,14 +3415,14 @@
endstream
endobj
-584 0 obj
+578 0 obj
<<
/Type /XObject
/Subtype /Form
/FormType 1
/PTEX.FileName (./examples/submap-dissociated.pdf)
/PTEX.PageNumber 1
-/PTEX.InfoDict 638 0 R
+/PTEX.InfoDict 632 0 R
/BBox [0 0 841.889771 528.872009]
/Group <<
/Type /Group
@@ -3448,13 +3443,13 @@
/CA 0.988636
/ca 0.988636
>>
-/s5 639 0 R
-/s7 640 0 R
-/s9 641 0 R
+/s5 633 0 R
+/s7 634 0 R
+/s9 635 0 R
>>/XObject <<
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-/x8 643 0 R
-/x10 644 0 R
+/x6 636 0 R
+/x8 637 0 R
+/x10 638 0 R
>>>>
/Length 14858
/Filter /FlateDecode
@@ -3563,7 +3558,7 @@
endstream
endobj
-642 0 obj
+636 0 obj
<<
/Type /XObject
/Length 71
@@ -3583,7 +3578,7 @@
>>
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/Pattern <<
-/p13 648 0 R
+/p13 642 0 R
>>
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@@ -3593,7 +3588,7 @@
endstream
endobj
-643 0 obj
+637 0 obj
<<
/Type /XObject
/Length 71
@@ -3613,7 +3608,7 @@
>>
>>
/Pattern <<
-/p16 649 0 R
+/p16 643 0 R
>>
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@@ -3623,7 +3618,7 @@
endstream
endobj
-644 0 obj
+638 0 obj
<<
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/Length 71
@@ -3643,7 +3638,7 @@
>>
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/Pattern <<
-/p19 650 0 R
+/p19 644 0 R
>>
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@@ -3655,9 +3650,9 @@
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endobj
-648 0 obj
+642 0 obj
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/PatternType 1
/BBox [ 0 0 842 529]
/XStep 2742
@@ -3667,7 +3662,7 @@
/Matrix [ 1 0 0 1 0 0]
/Resources <<
/XObject <<
-/x22 655 0 R
+/x22 649 0 R
>>
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@@ -3677,9 +3672,9 @@
endstream
endobj
-649 0 obj
+643 0 obj
<<
-/Length 656 0 R
+/Length 650 0 R
/PatternType 1
/BBox [ 0 0 842 529]
/XStep 2742
@@ -3689,7 +3684,7 @@
/Matrix [ 1 0 0 1 0 0]
/Resources <<
/XObject <<
-/x26 657 0 R
+/x26 651 0 R
>>
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@@ -3699,9 +3694,9 @@
endstream
endobj
-650 0 obj
+644 0 obj
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-/Length 658 0 R
+/Length 652 0 R
/PatternType 1
/BBox [ 0 0 842 529]
/XStep 2742
@@ -3711,7 +3706,7 @@
/Matrix [ 1 0 0 1 0 0]
/Resources <<
/XObject <<
-/x30 659 0 R
+/x30 653 0 R
>>
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>>
@@ -3721,7 +3716,7 @@
endstream
endobj
-651 0 obj
+645 0 obj
<<
/Type /XObject
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@@ -3748,7 +3743,7 @@
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-652 0 obj
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@@ -3775,7 +3770,7 @@
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-653 0 obj
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endstream
endobj
-655 0 obj
+649 0 obj
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-/Length 660 0 R
+/Length 654 0 R
/Filter /FlateDecode
/Type /XObject
/Subtype /Form
@@ -3814,7 +3809,7 @@
/S /Transparency
/CS /DeviceRGB
>>
-/Resources 661 0 R
+/Resources 655 0 R
>>
stream
x\x9Cm\x90? 1 \xC5\xF7~\x8A7 Ʀ\xFF\xBB\xBA\x82ù\x8A\x83\x9C\xA0\xC8\xDDp:\xF8\xF5MO\xDBA\xA5\x94\xE4\xFDH^\xD2NJSLβ\xC3or\xBF`uҸ<\x94F9\xFBM\xD5O\xC5\xD8
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-657 0 obj
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/S /Transparency
/CS /DeviceRGB
>>
-/Resources 663 0 R
+/Resources 657 0 R
>>
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x\x9Ce\x90\xBD\x8E1 \x84{?\xC5\xD4'a\xDBɲ-
@@ -3847,9 +3842,9 @@
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-659 0 obj
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/S /Transparency
/CS /DeviceRGB
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-/Resources 665 0 R
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>>
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x\x9Cm\x901O1 \x85w\xFF\x8A7#abǾ$k$$\x86vE \xAA \xA1\xEBP\xFA\xF7\xC9\xD1&\x87T\x94!\xF1\xFB\xF9\xD9g
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[truncated message content] |
|
From: <hua...@us...> - 2015-02-06 17:53:12
|
Revision: 896
http://sourceforge.net/p/sbgn/code/896
Author: huaiyumi
Date: 2015-02-06 17:53:11 +0000 (Fri, 06 Feb 2015)
Log Message:
-----------
AF Level 1 Release 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: <hua...@us...> - 2015-02-06 17:51:46
|
Revision: 895
http://sourceforge.net/p/sbgn/code/895
Author: huaiyumi
Date: 2015-02-06 17:51:44 +0000 (Fri, 06 Feb 2015)
Log Message:
-----------
Tag no longer needed
Removed Paths:
-------------
ActivityFlow/tags/L1R1.1/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hua...@us...> - 2015-02-06 17:44:22
|
Revision: 893
http://sourceforge.net/p/sbgn/code/893
Author: huaiyumi
Date: 2015-02-06 17:44:14 +0000 (Fri, 06 Feb 2015)
Log Message:
-----------
AF Level 1 Release 1.1
Added Paths:
-----------
ActivityFlow/tags/L1R1.1/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2014-12-18 05:05:55
|
Revision: 892
http://sourceforge.net/p/sbgn/code/892
Author: tczauderna
Date: 2014-12-18 05:05:53 +0000 (Thu, 18 Dec 2014)
Log Message:
-----------
a couple of typos and minor errors have been fixed
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
ProcessDiagram/trunk/Specification/sources/concepts.tex
ProcessDiagram/trunk/Specification/sources/examples.tex
ProcessDiagram/trunk/Specification/sources/front-page.tex
ProcessDiagram/trunk/Specification/sources/glyphs.tex
ProcessDiagram/trunk/Specification/sources/introduction.tex
ProcessDiagram/trunk/Specification/sources/layout.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 2014-12-18 05:04:20 UTC (rev 891)
+++ ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2014-12-18 05:05:53 UTC (rev 892)
@@ -8,9 +8,9 @@
\section{Level 1 Release 1.0}
-The specification of was written by Nicolas \lenov{},
+The specification was written by Nicolas \lenov{},
Stuart Moodie, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir,
-Huaiyu Mi, Yukiko Matsuoka, Katja Wegner and Hiroaki Kitano. In addition,
+Huaiyu Mi, Yukiko Matsuoka, Katja Wegner, and Hiroaki Kitano. In addition,
the specification benefited much from the help of (in alphabetical order) Frank Bergmann, Sarala
Dissanayake, Ralph Gauges, Peter Ghazal, Lu Li, and Steven Watterson.
@@ -18,24 +18,24 @@
\section{Level 1 Release 1.1}
-The specification of SBGN PD Level 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, Alice Vill\'{e}ger.
+The specification of SBGN PD Level 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.
\section{Level 1 Release 1.2}
-The specification of SBGN PD Level 1.2 was modified by Stuart Moodie, with contributions from (in alphabetical order) Sarah Boyd, Nicolas \lenov{}, Huaiyu Mi.
+The specification of SBGN PD Level 1.2 was modified by Stuart Moodie, with contributions from (in alphabetical order) Sarah Boyd, Nicolas \lenov{}, and Huaiyu Mi.
\section{Level 1 Release 1.3}
-The specification of SBGN PD Level 1.3 was modified by Stuart Moodie, with contributions from (in alphabetical order), Tobias Czauderna, Nicolas \lenov{}, Anatoly Sorokin.
+The specification of SBGN PD Level 1.3 was modified by Stuart Moodie, with contributions from (in alphabetical order), Tobias Czauderna, Nicolas \lenov{}, and Anatoly Sorokin.
\section{Comprehensive list of acknowledgements}
Here is a more comprehensive list of people 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. We intend this list to be complete. We are very sorry if we forgot someone, and would be grateful if you could notify us of any omission.
-Mirit Aladjemm, Frank Bergmann, Sarah Boyd, Laurence Calzone, Melanie Courtot, Emek Demir, Ugur Dogrusoz, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Samik Ghosh, Igor Goryanin, Michael Hucka, Akiya Jouraku, Hideya Kawaji, Douglas Kell, Sohyoung Kim, Hiroaki Kitano, Kurt Kohn, Fedor Kolpakov, Nicolas \lenov{}, Lu Li, Augustin Luna, Yukiko Matsuoka, Huaiyu Mi, Stuart Moodie, Sven Sahle, Chris Sander, Herbert Sauro, Esther Schmidt, Falk Schreiber, Jacky Snoep, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Steven Watterson, Alice Vill\'{e}ger, Katja Wegner, Sarala Wimalaratne, Guanming Wu.
+Mirit Aladjemm, Frank Bergmann, Sarah Boyd, Laurence Calzone, Melanie Courtot, Tobias Czauderna, Emek Demir, Ugur Dogrusoz, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Samik Ghosh, Igor Goryanin, Michael Hucka, Akiya Jouraku, Hideya Kawaji, Douglas Kell, Sohyoung Kim, Hiroaki Kitano, Kurt Kohn, Fedor Kolpakov, Nicolas \lenov{}, Lu Li, Augustin Luna, Yukiko Matsuoka, Huaiyu Mi, Stuart Moodie, Sven Sahle, Chris Sander, Herbert Sauro, Esther Schmidt, Falk Schreiber, Jacky Snoep, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Steven Watterson, Alice Vill\'{e}ger, Katja Wegner, Sarala Wimalaratne, Guanming Wu.
The authors are also grateful to all the attendees of the SBGN meetings, as
-well as to the subscribers of the \mailto{sbg...@sb...} mailing list.
+well as to the subscribers of the \mailto{sbg...@ca...} mailing list.
\section{Financial Support}
Modified: ProcessDiagram/trunk/Specification/sources/concepts.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/concepts.tex 2014-12-18 05:04:20 UTC (rev 891)
+++ ProcessDiagram/trunk/Specification/sources/concepts.tex 2014-12-18 05:05:53 UTC (rev 892)
@@ -15,7 +15,7 @@
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.8]{images/MAPK-only}
- \caption{This example of a \PD uses two kinds of entity pool nodes: one for pools of different macromolecules (\sect{techref:macromolecule}) and another for pools of simple chemicals (\sect{techref:simpleChemical}). Most macromolecule nodes in this map are adorned with state variables (\sect{techref:stateVariable}) representing phosphorylation states. This map uses one type of process node, the process node (\sect{techref:process}), and three kind of connecting arc, consumption (\sect{techref:consumption}), production (\sect{techref:production}) and catalysis (\sect{techref:catalysis}). Finally, some entity pool nodes have dark bands along their bottoms; these are clone markers (\sect{techref:cloneMarker}) indicating that the same pool nodes appear multiple times in the map.}
+ \caption{This example of a \PD uses two kinds of entity pool nodes: one for pools of different macromolecules (\sect{techref:macromolecule}) and another for pools of simple chemicals (\sect{techref:simpleChemical}). Most macromolecule nodes in this map are adorned with state variables (\sect{techref:stateVariable}) representing phosphorylation states. This map uses one type of process node, the process (\sect{techref:process}), and three kind of connecting arc, consumption (\sect{techref:consumption}), production (\sect{techref:production}) and catalysis (\sect{techref:catalysis}). Finally, some entity pool nodes have dark bands along their bottoms; these are clone markers (\sect{techref:cloneMarker}) indicating that the same pool nodes appear multiple times in the map.}
\label{fig:eg1}
\end{figure}
Modified: ProcessDiagram/trunk/Specification/sources/examples.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/examples.tex 2014-12-18 05:04:20 UTC (rev 891)
+++ ProcessDiagram/trunk/Specification/sources/examples.tex 2014-12-18 05:05:53 UTC (rev 892)
@@ -1,8 +1,8 @@
\chapter{Complete examples of \PD Maps}
-The following maps present complete examples of SBGN Process Descriptions representing Biological processes. They by no mean exhaust the possibilities of \SBGNPDLone.
+The following maps present complete examples of SBGN Process Descriptions representing biological processes. They by no means exhaust the possibilities of \SBGNPDLone.
-\fig{glycolysis} presents an example of metabolic pathway, that examplifies the use of the \glyph{EPNs} \glyph{simple chemical}, \glyph{macromolecule}, and \glyph{clone marker}, the \glyph{PNs} \glyph{process}, and the \glyph{connecting arcs} \glyph{consumption}, \glyph{production} and \glyph{catalysis}.
+\fig{glycolysis} presents an example of metabolic pathway, that exemplifies the use of the \glyph{EPNs} \glyph{simple chemical} and \glyph{macromolecule}, \glyph{clone marker}, the \glyph{PN} \glyph{process}, and the \glyph{connecting arcs} \glyph{consumption}, \glyph{production} and \glyph{catalysis}.
\begin{figure}[htb]
\begin{center}
@@ -11,7 +11,7 @@
\end{center}
\end{figure}
-\fig{insulin} presents an example of signalling pathway, that examplifies in addition the use of the \glyph{EPNs} \glyph{phenotype}, and \glyph{state variable}, the \glyph{containers} \glyph{complex}, \glyph{compartment} and \glyph{submap}, the \glyph{PNs} \glyph{association}, and the \glyph{connecting arcs} \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.
+\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{center}
@@ -29,7 +29,7 @@
\end{center}
\end{figure}
-\fig{muscle} introduces an SBGN \PD that spans several compartments. Note that the compartment ``synaptic vesicle'' is not \textbf{contained} in the compartment ``synaptic button'' but \textbf{overlaps} it. The \glyph{simple chemical} ``ACh'' of the ''synaptic vesicle`` is not the same \glyph{EPN} than the ``ACh'' of the ``synaptic button'' and of ``synaptic cleft''. The situation is similar with the compartments ``ER'' and ``muscle cytosol''. The map exemplifies the use of the \glyph{PN} \glyph{omitted} and \glyph{dissociation}, and the \glyph{connecting arc} \glyph{necessary stimulation}.
+\fig{muscle} introduces an SBGN \PD that spans several compartments. Note that the compartment ``synaptic vesicle'' is not \textbf{contained} in the compartment ``synaptic button'' but \textbf{overlaps} it. The \glyph{simple chemical} ``ACh'' of the ''synaptic vesicle`` is not the same \glyph{EPN} than the ``ACh'' of the ``synaptic button'' and of ``synaptic cleft''. The situation is similar with the compartments ``ER'' and ``muscle cytosol''. The map exemplifies the use of the \glyph{PNs} \glyph{omitted} and \glyph{dissociation}, and the \glyph{connecting arc} \glyph{necessary stimulation}.
\begin{figure}[htb]
\begin{center}
@@ -38,7 +38,7 @@
\end{center}
\end{figure}
-\fig{IFN} introduces the use of \SBGNPDLone to encode gene regulatory networks. It also show the use of the \glyph{EPNs} \glyph{Source} and the \glyph{logical operator} \glyph{and}.
+\fig{IFN} introduces the use of \SBGNPDLone to encode gene regulatory networks. It also shows the use of the \glyph{empty set} and the \glyph{logical operator} \glyph{and}.
\begin{figure}[htb]
\begin{center}
Modified: ProcessDiagram/trunk/Specification/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/front-page.tex 2014-12-18 05:04:20 UTC (rev 891)
+++ ProcessDiagram/trunk/Specification/sources/front-page.tex 2014-12-18 05:05:53 UTC (rev 892)
@@ -38,8 +38,8 @@
\textbf{\sffamily Editors}:\\[7pt]
\begin{tabular}{l>{\hspace*{15pt}}r}
Stuart Moodie & \emph{Eight Pillars Ltd, UK}\\
-Tobias Czauderna & \emph{IPK Gatersleben, Germany}\\
-Falk Schreiber & \emph{IPK Gatersleben \& MLU Halle, Germany}\\
+Tobias Czauderna & \emph{Monash University, Australia}\\
+Falk Schreiber & \emph{Monash University, Australia \& MLU Halle, Germany}\\
Anatoly Sorokin & \emph{Institute of Cell Biophysics RAS, Russia}\\
Huaiyu Mi & \emph{University of Southern California, USA}\\
\end{tabular}
@@ -65,7 +65,7 @@
\normalsize
\begin{minipage}{5in}
\emph{To discuss any aspect of SBGN, please send your messages
- to the mailing list \mailto{sbg...@sb...}. To get
+ to the mailing list \mailto{sbg...@ca...}. To get
subscribed to the mailing list or to contact us directly,
please write to \mailto{sbg...@li...}. Bug reports and specific comments about the specification should be entered in the issue tracker \url{http://p.sf.net/sbgn/pd_tracker}.}
\end{minipage}
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2014-12-18 05:04:20 UTC (rev 891)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2014-12-18 05:05:53 UTC (rev 892)
@@ -18,7 +18,7 @@
achieve this we took our lead from other successful standards: the
Unified Modelling Language (UML) \cite{umlspec} which is a graphical
language that has been used by tens of thousands of software
-developers for over decade to describe and software system; and the
+developers for over a decade to describe and software system; and the
Systems Biology Markup Language (SBML) Level 3 Core specification
\cite{sbmll3core} which is the ``daddy'' of computational systems
biological standards and over 10 years after its inception is firmly
@@ -29,7 +29,7 @@
together (syntax) and how they are applied and their rules
(semantics). Since UML is a graphical language, the class definition
also includes, where applicable to the language element, a description
-of description of the symbols used and guidelines about how the
+of the symbols used and guidelines about how the
symbols should be drawn or laid out.
Based on these specifications we will follow the following conventions
@@ -47,7 +47,7 @@
element represented, parent classes, attributes, interactions with
other classes and any semantic rules not captured in UML.
\item Where classes correspond to a glyph, the symbol representing it
- is described and appropriate illustrations provided.
+ is described and appropriate illustrations are provided.
\end{itemize}
\section{Note on typographical convention}
@@ -72,8 +72,7 @@
Here we will describe the elements of the class definitions that are
the core of the language specification. Each definition starts with an
introduction describing the purpose of the class and what it
-represents conceptually or physically. It's context within the UML
-\PDl is then described by a detailed figure showing the class, its
+represents conceptually or physically. It's context within the \PDl is then described by a detailed figure showing the class, its
associations and its interaction with other key classes to help
understand its context and any rules that are part of the
definition. In these descriptions we will use a number of terms for
@@ -157,7 +156,7 @@
attribute definitions. These are:
\begin{description}
\item[int] An integer.
-\item[string] A string of UniCode characters.
+\item[string] A string of Unicode characters.
\item[boolean] A Boolean value that can be either True or False.
\item[object] A type that can be any value.
\item[cv] A controlled vocabulary (see \ref{sec:techref:CVs}).
@@ -193,7 +192,7 @@
described here. The glyph is described in words and graphically. In
cases where several glyphs combine in complex ways usage examples are
provided.
-\item[Layout Rules and Guidelines] In some cases the graphical layout of a glyph and is more complicated
+\item[Layout Rules and Guidelines] In some cases the graphical layout of a glyph is more complicated
and requires some additional explanation. If this is the case this
will be provided here.
\item[Changes from Previous Version] In order to help track changes between versions of the specification
@@ -1408,8 +1407,10 @@
is one and the \glyph{Complex Multimer} where the cardinality is
greater than that.
-\paragraph{\glyph{Complex Monomer}}
+\paragraph{Glyph: \glyph{Complex Monomer}}
+This glyphs represents a monomeric complex.
+
\begin{glyphDescription}
\glyphSboTerm SBO:0000253 ! non-covalent complex
\glyphContainer A \glyph{complex} possesses its own container box surrounding the juxtaposed container boxes of its components. This container box is a rectangle with cut-corners (an octagonal box with sides of two different lengths). The size of the cut-corners are adjusted so that there is no overlap between the container and the components. The container boxes of the components must not overlap.
@@ -1430,10 +1431,12 @@
\label{fig:techref:complex}
\end{figure}
+\paragraph{Glyph: \glyph{Complex Multimer}}
-\paragraph{\glyph{Complex Multimer}}
+This glyphs represents a multimeric complex.
- \begin{glyphDescription}
+\begin{glyphDescription}
+
\glyphSboTerm SBO:0000418 ! multimer of complexes
\glyphContainer A \glyph{Complex Multimer} is represented by two
identical \glyph{Complex} containers shifted horizontally and
@@ -2837,7 +2840,7 @@
\sbgnclass{CrossReference}\query{A new concept required for
consistency between tags ans submap terminals.} handles links or relationships between elements of a
-map and sub-map. At present there is only one reference glyph,
+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{clone marker} can also provide additional reference mechanisms
@@ -3854,7 +3857,7 @@
\classref{Compartment} or the \attrib{value} of the
\classref{StateVariable}. The values held by these attributes can be
taken from controlled vocabularies defined below. When displayed in
-some cases is mandatory to prefix a code indicating the type of
+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'
indicates that a value 'rna' is describing the material RNA.
@@ -4113,7 +4116,7 @@
then dissociates into the same components that formed it which
requires an appropriate clone marker to be applied. A[P] is
translocated into compartment 2 where A[P] is not cloned as it
- does not have a duplicate. The unphosphorylated from of A
+ does not have a duplicate. The unphosphorylated form of A
dimerised, but again this does not require a clone marker as these
are regarded as separate entity pools.}
\label{fig:techref:cloningrules-eg}
@@ -4152,12 +4155,13 @@
\end{description}
\fig{techref:submap-folded} represents a \glyph{submap node} that transforms
-glucose into fructose-6-phosphate. The \glyph{submap node} carries five
-terminals, four linked to EPNs and one linked to a
-\glyph{compartment}. The latter is particularly important in the case
-of EPNs present only in a \glyph{compartment} enclosed in a
-\glyph{submap node}, and that are not linked to terminals themselves. Note
-that the terminals do not define a ``direction'', such as input or
+glucose into fructose-6-phosphate.
+%The \glyph{submap node} carries five terminals, four linked to EPNs and one linked
+%to a \glyph{compartment}. The latter is particularly important in the case of EPNs
+%present only in a \glyph{compartment} enclosed in a \glyph{submap node}, and that
+%are not linked to terminals themselves.
+The \glyph{submap node} carries four terminals linked to EPNs.
+Note that the terminals do not define a ``direction'', such as input or
output. The flux of the reactions is determined by the context.
\begin{figure}[htb]
@@ -4171,7 +4175,7 @@
\glyph{submap}. Here, anything outside the \glyph{submap node} has
disappeared, and the internal \glyph{tags} are not linked to the
corresponding external \glyph{submap terminals}.\query{This example
-in the previous version fo the spec included compartment
+in the previous version of the spec included compartment
tagging. This has been removed, but the example may need refinement as
a result.}
@@ -4214,8 +4218,7 @@
\item For a valid mapping between subclasses of \sbgnclass{EntityPoolNode} in a supermap and submap to
exist, the \sbgnclass{EntityPoolNode} subclasses must be logically
identical and the \attrib{reference\_id} in their associated \sbgnclass{CrossReference} must be identical.
- identical.
-\item A \sbgnclass{SubmapNode} which do not have a corresponding
+\item A \sbgnclass{SubmapNode} which does not have a corresponding
submap is valid.
\item Submaps without a corresponding supermap are invalid\query{We
need to sort out mapping between super and sub maps to get this
Modified: ProcessDiagram/trunk/Specification/sources/introduction.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/introduction.tex 2014-12-18 05:04:20 UTC (rev 891)
+++ ProcessDiagram/trunk/Specification/sources/introduction.tex 2014-12-18 05:05:53 UTC (rev 892)
@@ -92,7 +92,7 @@
the way maps are to be generated and interpreted. In addition new
versions should be backwards compatible, \ie \PD maps that conform to
an earlier version of the \PDl within the same level should still be
-valid. This does not apply to a new levels.
+valid. This does not apply to a new level.
Capabilities and features that cannot be agreed upon and are judged
insufficiently critical to require inclusion in a given level, are
Modified: ProcessDiagram/trunk/Specification/sources/layout.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/layout.tex 2014-12-18 05:04:20 UTC (rev 891)
+++ ProcessDiagram/trunk/Specification/sources/layout.tex 2014-12-18 05:05:53 UTC (rev 892)
@@ -77,7 +77,7 @@
Edges are not allowed to overlap (\fig{layout4}). This includes touching of edges.
Furthermore, an edge is neither allowed to cross itself nor to cross
-a boundary of node more than twice or other edges more than once.
+a boundary of a node more than twice or other edges more than once.
\begin{figure}[htb]
\centering
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2014-12-18 05:04:28
|
Revision: 891
http://sourceforge.net/p/sbgn/code/891
Author: tczauderna
Date: 2014-12-18 05:04:20 +0000 (Thu, 18 Dec 2014)
Log Message:
-----------
fix front page: Falk's affiliation
Modified Paths:
--------------
ActivityFlow/trunk/sources/front-page.tex
Modified: ActivityFlow/trunk/sources/front-page.tex
===================================================================
--- ActivityFlow/trunk/sources/front-page.tex 2014-11-20 23:21:49 UTC (rev 890)
+++ ActivityFlow/trunk/sources/front-page.tex 2014-12-18 05:04:20 UTC (rev 891)
@@ -39,7 +39,7 @@
Huaiyu Mi & \emph{University of Southern California, USA}\\
Tobias Czauderna & \emph{Monash University, Australia}\\
Stuart Moodie & \emph{EMBL European Bioinformatics Institute, UK}\\
-Falk Schreiber & \emph{Monash University, Australia}\\
+Falk Schreiber & \emph{Monash University, Australia \& MLU Halle, Germany}\\
Anatoly Sorokin & \emph{Institute of Cell Biophysics, Russia }\\
\end{tabular}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hua...@us...> - 2014-11-20 23:21:52
|
Revision: 890
http://sourceforge.net/p/sbgn/code/890
Author: huaiyumi
Date: 2014-11-20 23:21:49 +0000 (Thu, 20 Nov 2014)
Log Message:
-----------
Fix PD user manual Figure 2.9
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/images/complex-examples.eps
ProcessDiagram/trunk/UserManual/images/complex-examples.png
ProcessDiagram/trunk/UserManual/images/complex-examples.svg
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
Added Paths:
-----------
ProcessDiagram/trunk/UserManual/images/complex-examples.pdf
Modified: ProcessDiagram/trunk/UserManual/images/complex-examples.eps
===================================================================
--- ProcessDiagram/trunk/UserManual/images/complex-examples.eps 2014-11-20 19:18:58 UTC (rev 889)
+++ ProcessDiagram/trunk/UserManual/images/complex-examples.eps 2014-11-20 23:21:49 UTC (rev 890)
@@ -1,8 +1,8 @@
%!PS-Adobe-3.0 EPSF-3.0
-%%Creator: cairo 1.10.2 (http://cairographics.org)
-%%CreationDate: Tue Jul 17 23:10:18 2012
+%%Creator: cairo 1.8.10 (http://cairographics.org)
+%%CreationDate: Thu Nov 20 15:18:36 2014
%%Pages: 1
-%%BoundingBox: 0 -1 679 253
+%%BoundingBox: 0 0 678 253
%%DocumentData: Clean7Bit
%%LanguageLevel: 2
%%EndComments
@@ -28,6 +28,8 @@
/S { stroke } bind def
/f { fill } bind def
/f* { eofill } bind def
+/B { fill stroke } bind def
+/B* { eofill stroke } bind def
/n { newpath } bind def
/W { clip } bind def
/W* { eoclip } bind def
@@ -63,7 +65,7 @@
%%EndProlog
11 dict begin
/FontType 42 def
-/FontName /BitstreamVeraSans-Roman def
+/FontName /f-0-0 def
/PaintType 0 def
/FontMatrix [ 1 0 0 1 0 0 ] def
/FontBBox [ 0 0 0 0 ] def
@@ -80,16 +82,16 @@
Encoding 9 /uni0050 put
Encoding 10 /uni004D put
Encoding 11 /uni0046 put
-Encoding 12 /uni0067 put
-Encoding 13 /uni006F put
-Encoding 14 /uni0062 put
-Encoding 15 /uni0061 put
-Encoding 16 /uni0049 put
-Encoding 17 /uni0032 put
-Encoding 18 /uni002B put
-Encoding 19 /uni0068 put
-Encoding 20 /uni0065 put
-Encoding 21 /uni006D put
+Encoding 12 /uni0061 put
+Encoding 13 /uni0049 put
+Encoding 14 /uni0032 put
+Encoding 15 /uni002B put
+Encoding 16 /uni0068 put
+Encoding 17 /uni0065 put
+Encoding 18 /uni006D put
+Encoding 19 /uni0067 put
+Encoding 20 /uni006F put
+Encoding 21 /uni0062 put
Encoding 22 /uni004E put
Encoding 23 /uni003A put
Encoding 24 /uni0034 put
@@ -106,208 +108,284 @@
/uni0050 9 def
/uni004D 10 def
/uni0046 11 def
-/uni0067 12 def
-/uni006F 13 def
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-/uni0061 15 def
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-/uni0032 17 def
-/uni002B 18 def
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+/uni0061 12 def
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end readonly def
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Index: ProcessDiagram/trunk/UserManual/images/complex-examples.pdf
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--- ProcessDiagram/trunk/UserManual/images/complex-examples.pdf 2014-11-20 19:18:58 UTC (rev 889)
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From: <hua...@us...> - 2014-11-20 19:19:18
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Revision: 889
http://sourceforge.net/p/sbgn/code/889
Author: huaiyumi
Date: 2014-11-20 19:18:58 +0000 (Thu, 20 Nov 2014)
Log Message:
-----------
Spec update based on discuss feedback
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/equivalenceArc.tex
ActivityFlow/trunk/sources/syntax.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-11-17 17:16:25 UTC (rev 888)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-11-20 19:18:58 UTC (rev 889)
@@ -21,24 +21,23 @@
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|
From: <hua...@us...> - 2014-11-17 17:16:33
|
Revision: 888
http://sourceforge.net/p/sbgn/code/888
Author: huaiyumi
Date: 2014-11-17 17:16:25 +0000 (Mon, 17 Nov 2014)
Log Message:
-----------
Fix AF pdf file.
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/submap.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-11-14 01:52:03 UTC (rev 887)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-11-17 17:16:25 UTC (rev 888)
@@ -25,7 +25,7 @@
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+Whqb\x88;\xB3 T\x8Aa\x8F\xF2\x9A \xBB@|\x9A\xF4\x8A\xA9\x9A\xA5\x89\xBCE2W
+\xD8p;t\xC21\x9F\xB032\x9A_\xB5\xEFJ\xA2\xAC \xABlI
@@ Diff output truncated at 100000 characters. @@
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...> - 2014-11-14 01:52:10
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Revision: 887
http://sourceforge.net/p/sbgn/code/887
Author: tczauderna
Date: 2014-11-14 01:52:03 +0000 (Fri, 14 Nov 2014)
Log Message:
-----------
a couple of typos and minor errors have been fixed
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/CVs.tex
EntityRelationship/trunk/sources/ENs.tex
EntityRelationship/trunk/sources/absoluteInhibition.tex
EntityRelationship/trunk/sources/absoluteStimulation.tex
EntityRelationship/trunk/sources/acknowledgments.tex
EntityRelationship/trunk/sources/annotation.tex
EntityRelationship/trunk/sources/assignment.tex
EntityRelationship/trunk/sources/domain.tex
EntityRelationship/trunk/sources/entity.tex
EntityRelationship/trunk/sources/er-overview.tex
EntityRelationship/trunk/sources/examples.tex
EntityRelationship/trunk/sources/grammar.tex
EntityRelationship/trunk/sources/interaction.tex
EntityRelationship/trunk/sources/layout.tex
EntityRelationship/trunk/sources/logicArc.tex
EntityRelationship/trunk/sources/modulation.tex
EntityRelationship/trunk/sources/necessaryStimulation.tex
EntityRelationship/trunk/sources/not.tex
EntityRelationship/trunk/sources/outcome.tex
EntityRelationship/trunk/sources/relationships.tex
EntityRelationship/trunk/sources/revision_history.tex
EntityRelationship/trunk/sources/semantics.tex
EntityRelationship/trunk/sources/stateVariable.tex
EntityRelationship/trunk/sources/syncEv.tex
EntityRelationship/trunk/sources/syntax.tex
EntityRelationship/trunk/sources/unitInformation.tex
EntityRelationship/trunk/sources/usermanual.tex
EntityRelationship/trunk/sources/variableValue.tex
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/trunk/sources/CVs.tex
===================================================================
--- EntityRelationship/trunk/sources/CVs.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/CVs.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -4,18 +4,18 @@
\section{Controlled vocabularies used in \SBGNERLone}\label{sec:CVs}
-Some glyphs in SBGN \ERs can contain particular kinds of textual annotations conveying information relevant to the purpose of the glyph. These annotations are carried by \glyph{units of information} (\sect{unitInformation}) or \glyph{state variable values} (\sect{stateVariable}).
+Some glyphs in SBGN \ERs can contain particular kinds of textual annotations conveying information relevant to the purpose of the glyph. These annotations are carried by \glyph{units of information} (\sect{unitInformation}) or \glyph{state variables} (\sect{stateVariable}).
-The text that appears as the unit of information decorating an entity must be prefixed with a controlled vocabulary term indicating the type of information being expressed. The prefixes are mandatory. Without the use of controlled vocabulary prefixes, it would be necessary to have different glyphs to indicate different classes of information; this would lead to an explosion in the number of symbols needed. There is no more than one \glyph{units of information} per controlled vocabulary allowed for any \glyph{Entity}. So, for example, one \glyph{units of information} of material type and one \glyph{units of information} of conceptual type.
+The text that appears as the unit of information decorating an entity must be prefixed with a controlled vocabulary term indicating the type of information being expressed. The prefixes are mandatory. Without the use of controlled vocabulary prefixes, it would be necessary to have different glyphs to indicate different classes of information; this would lead to an explosion in the number of symbols needed. There is no more than one \glyph{unit of information} per controlled vocabulary allowed for any \glyph{Entity}. So, for example, one \glyph{unit of information} of material type and one \glyph{unit of information} of conceptual type.
In the rest of this section, we describe the controlled vocabularies (CVs) used in \SBGNERLone. In each case, some CV terms are predefined by SBGN, but unless otherwise noted, \emph{they are not the only terms permitted}. Authors may use other CV values not listed here, but in such cases, they should explain the terms' meanings in a figure legend or other text accompanying the map.
\subsection{Entity material types}
\label{sec:material-types-cv}
-The material type of an \glyph{Entity} indicates its chemical structure. A list of common material types is shown in \fig{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.
+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{figure}[h]
+\begin{table}[h]
\centering
\begin{tabular}{l>{\ttfamily}ll}
\toprule
@@ -31,17 +31,17 @@
\end{tabular}
\caption{A sample of values from the \emph{material types} controlled
vocabulary (\sect{material-types-cv}).}
- \label{fig:material-types-cv}
-\end{figure}
+ \label{tab:material-types-cv}
+\end{table}
The material types are in contrast to the \emph{conceptual types} (see below). The distinction is that material types are about physical composition, while conceptual types are about functions. For example, a strand of RNA is a physical artifact, but its use as messenger RNA is a function.
\subsection{Entity conceptual types}
\label{sec:conceptual-types-cv}
-An \glyph{entity}'s \emph{conceptual type} indicates its function within the context of a given \ERm. A list of common conceptual types is shown in \fig{conceptual-types-cv}, but others are possible. The values are to be taken from the \sbo (\sbourl), specifically from the branch having identifier \sboid{SBO:0000241} (\emph{functional entity}). The labels are defined by \SBGNERLone.
+An \glyph{entity}'s \emph{conceptual type} indicates its function within the context of a given \ERm. A list of common conceptual types is shown in \tab{conceptual-types-cv}, but others are possible. The values are to be taken from the \sbo (\sbourl), specifically from the branch having identifier \sboid{SBO:0000241} (\emph{functional entity}). The labels are defined by \SBGNERLone.
-\begin{figure}[h]
+\begin{table}[h]
\centering
\begin{tabular}{l>{\ttfamily}ll}
\toprule
@@ -60,17 +60,17 @@
\end{tabular}
\caption{A sample of values from the \emph{conceptual types} vocabulary
(\sect{conceptual-types-cv}).}
- \label{fig:conceptual-types-cv}
-\end{figure}
+ \label{tab:conceptual-types-cv}
+\end{table}
\subsection{Macromolecule covalent modifications}
\label{sec:covalent-mod-cv}
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.
-\fig{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 \fig{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{figure}[h]
+\begin{table}[h]
\centering
\begin{tabular}{l>{\ttfamily}ll}
\toprule
@@ -91,13 +91,13 @@
\end{tabular}
\caption{A sample of values from the \emph{covalent modifications} vocabulary
(\sect{covalent-mod-cv}).}
- \label{fig:covalent-mod-cv}
-\end{figure}
+ \label{tab:covalent-mod-cv}
+\end{table}
\subsection{Miscellaneous terms}
\label{sec:miscellaneous-cv}
-\SBGNERLone requires several reserved characters. A special unit of information usable on interactions describe the number of identical interactors involved. Note that the value is a unitary number, and not (for example) a range. There is no provision in \SBGNPDLone for specifying a range in this context because it leads to problems of entity identifiability. Other reserved characters (see \tab{reserved-words}) are used in state variable assignments to represent truth or falsehood (T and F). Two reserved words are used in units of information carried by relationships: \emph{cis} and \emph{trans}.
+\SBGNERLone requires several reserved characters. A special unit of information usable on interactions describe the number of identical interactors involved. Note that the value is a unitary number, and not (for example) a range. There is no provision in \SBGNERLone for specifying a range in this context because it leads to problems of entity identifiability. Other reserved characters (see \tab{reserved-words}) are used in state variable assignments to represent truth or falsehood (T and F). Two reserved words are used in units of information carried by relationships: \emph{cis} and \emph{trans}.
\begin{table}[h]
\centering
Modified: EntityRelationship/trunk/sources/ENs.tex
===================================================================
--- EntityRelationship/trunk/sources/ENs.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/ENs.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -6,7 +6,7 @@
\section{Entity nodes}\label{sec:ENs}
-\glyph{Entity nodes} (ENs) represent element of truth, class of things that exist.
+\glyph{Entity nodes} (ENs) represent elements of truth, class of things that exist.
%In ontology parlance, they would be ``continuants''.
Entity nodes are the source of \glyph{influences} (\sect{influences}). \SBGNERLone{} provides three different types of \glyph{entity nodes}, the \glyph{interactors}, the \glyph{logical operators} and the \glyph{perturbing agent}.
@@ -25,7 +25,7 @@
\subsection{Logical operators}\label{sec:logic}
-A \glyph{logical operator} allows to combine elements of truth into another element of truth (if A exists and B exits, then A AND B exists) in order ot apply influences. \SBGNERLone{} provides four \glyph{logical operators}, \glyph{and}, \glyph{or}, \glyph{not} and \glyph{delay}.
+A \glyph{logical operator} allows to combine elements of truth into another element of truth (if A exists and B exits, then A AND B exists) in order to apply influences. \SBGNERLone{} provides three \glyph{logical operators}, \glyph{and}, \glyph{or}, and \glyph{not}. %\SBGNERLone{} provides four \glyph{logical operators}, \glyph{and}, \glyph{or}, \glyph{not} and \glyph{delay}.
\input{sources/and.tex}
\input{sources/or.tex}
Modified: EntityRelationship/trunk/sources/absoluteInhibition.tex
===================================================================
--- EntityRelationship/trunk/sources/absoluteInhibition.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/absoluteInhibition.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -5,7 +5,7 @@
\subsubsection{Glyph: \glyph{Absolute inhibition}}\label{sec:absoluteInhibition}
-An \glyph{absolute inhibition} precludes the existence of another relationship. A relationship modulated by an absolute inhibition can only exist when an absolute inhibition in false, whatever are the other influences this relationship is subjected to.
+An \glyph{absolute inhibition} precludes the existence of another relationship. A relationship modulated by an absolute inhibition can only exist when an absolute inhibition is false, whatever are the other influences this relationship is subjected to.
\begin{glyphDescription}
\glyphSboTerm SBO:0000407 ! absolute inhibition.
@@ -24,7 +24,7 @@
\begin{figure}[H]
\centering
\includegraphics[scale = 0.5]{images/absoluteInhibition}
- \caption{The \ER glyph for \glyph{absoluteInhibition}.}
+ \caption{The \ER glyph for \glyph{absolute inhibition}.}
\label{fig:absoluteInhibition}
\end{figure}
Modified: EntityRelationship/trunk/sources/absoluteStimulation.tex
===================================================================
--- EntityRelationship/trunk/sources/absoluteStimulation.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/absoluteStimulation.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -23,7 +23,7 @@
\begin{figure}[H]
\centering
\includegraphics[scale = 0.5]{images/absoluteStimulation}
- \caption{The \ER glyph for \glyph{absoluteStimulation}.}
+ \caption{The \ER glyph for \glyph{absolute stimulation}.}
\label{fig:absoluteStimulation}
\end{figure}
Modified: EntityRelationship/trunk/sources/acknowledgments.tex
===================================================================
--- EntityRelationship/trunk/sources/acknowledgments.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/acknowledgments.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -4,7 +4,7 @@
\section{Main contributors}
-In addition to the SBGN editors, the specification of SBGN PD benefited enormously from the contribution of many people. In particular, the specification of \SBGNERLone benefited much from deep discussions with Mirit Aladjem, Kurt Kohn, Emek Demir, Augustin Luna, Sohyoung Kim, Yukiko Matsuoka and Hiroaki Kitano.
+In addition to the SBGN editors, the specification of SBGN ER benefited enormously from the contribution of many people. In particular, the specification of \SBGNERLone benefited much from deep discussions with Mirit Aladjem, Kurt Kohn, Emek Demir, Augustin Luna, Sohyoung Kim, Yukiko Matsuoka and Hiroaki Kitano.
\section{Comprehensive list of contributors}
@@ -12,9 +12,9 @@
Mirit Aladjemm, Frank Bergmann, Michael Blinov, Sarah Boyd, Laurence Calzone, Melanie Courtot, Tobias Czauderna, Emek Demir, Ugur Dogrusoz, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Samik Ghosh, Igor Goryanin, Michael Hucka, Akiya Jouraku, Hideya Kawaji, Douglas Kell, Sohyoung Kim, Hiroaki Kitano, Kurt Kohn, Fedor Kolpakov , Nicolas Le Nov\`{e}re, Lu Li, Augustin Luna, Yukiko Matsuoka, Huaiyu Mi, Stuart Moodie, Sven Sahle, Chris Sander, Herbert Sauro, Esther Schmidt, Falk Schreiber, Jacky Snoep, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Steven Watterson, Martijn van Iersel, Alice Vill\'{e}ger, Katja Wegner, Sarala Wimalaratne, Guanming Wu.
-The authors are also grateful to all the attendees of the SBGN meetings, as well as to the subscribers of the sbg...@sb... mailing list.
+The authors are also grateful to all the attendees of the SBGN meetings, as well as to the subscribers of the sbg...@ca... mailing list.
\section{Financial support}
-The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, http://www.nedo.go.jp/). The Okinawa Institute of Science and Technology (OIST, http://www.oist.jp/), the AIST Computational Biology Research Center (AIST CBRC, http://www.cbrc.jp/index.eng.html) the British Biotechnology and Biological Sciences Research Council (BBSRC, http://www.bbsrc.ac.uk/) through a Japan Partnering Award, the European Media Laboratory (EML Research gGmbH, http://www.eml-r.org/), and the Beckman Institute at the California Institute of Technology (http://bnmc.caltech.edu) provided additional support for SBGN workshops. Some help was provided by the Japan Science and Technology Agency (JST, http://www.jst.go.jp/) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, 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, http://www.epsrc.ac.uk) during the redaction of the specification.
+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/}), 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 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/annotation.tex
===================================================================
--- EntityRelationship/trunk/sources/annotation.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/annotation.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -5,11 +5,11 @@
\section{Glyph: \glyph{Annotation}}
\label{sec:annotation}
-\SBGNERLone defines a glyph to add additional information to a map, that does not modify the semantic of the the graph. This glyph can be used to add free text, or links to external information.
+\SBGNERLone defines a glyph to add additional information to a map, that does not modify the semantic of the graph. This glyph can be used to add free text, or links to external information.
\begin{glyphDescription}
-\glyphSboTerm SBO:0000550 -- annotation.
+\glyphSboTerm SBO:0000550 ! annotation.
\glyphContainer An \glyph{annotation} is represented by a rectangular container with a folded corner, as illustrated in \fig{annotation}. This container is linked to the annotated element with a callout. The link ends up on the border of the annotated element.
Modified: EntityRelationship/trunk/sources/assignment.tex
===================================================================
--- EntityRelationship/trunk/sources/assignment.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/assignment.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -5,12 +5,12 @@
\subsubsection{Glyph: \glyph{Assignment}}\label{sec:assignment}
-\glyph{Assignment} is used to describe the setting of a state variable to a certain value. The assignment, represented by an harpoon arrow, goes from one or more \glyph{variable values} to a variable identification, represented by a \glyph{state variable} attached to the entity affected by the assignment. If an \glyph{assignment} takes several \glyph{state variable} values as input, there is an implicit XOR between them, located at the point of junction between the arcs coming from the alternative values. Since only one value can be assigned at a time, there is therefore no edge overlap in the assignment itself. The result of an assignment is represented by \glyph{outcomes}, that is by filled dots on the arrow. The result of an \glyph{assignment} can be represented by any number of \glyph{outcomes}. In the case of more than one \glyph{state variable} values, the \glyph{outcomes} must be placed on the relevant incoming branch.
+\glyph{Assignment} is used to describe the setting of a state variable to a certain value. The assignment, represented by an harpoon arrow, goes from one or more \glyph{variable values} to a variable identification, represented by a \glyph{state variable} attached to the entity affected by the assignment. If an \glyph{assignment} takes several \glyph{variable values} as input, there is an implicit XOR between them, located at the point of junction between the arcs coming from the alternative values. Since only one value can be assigned at a time, there is therefore no edge overlap in the assignment itself. The result of an assignment is represented by \glyph{outcomes}, that is by filled dots on the arrow. The result of an \glyph{assignment} can be represented by any number of \glyph{outcomes}. In the case of more than one \glyph{variable values}, the \glyph{outcomes} must be placed on the relevant incoming branch.
\begin{glyphDescription}
\glyphSboTerm SBO:0000464 ! state variable assignment
\glyphOrigin One or more variable value (section \sect{variableValue}) on their own, each containing a variable value.
- \glyphTarget A state-variable (section \sect{stateVariable}) carried by a interactor (section \sect{interactors}), containing a variable identification.
+ \glyphTarget A state-variable (section \sect{stateVariable}) carried by an entity (section \sect{entity}), containing a variable identification.
\glyphEndPoint The target extremity of an \glyph{assignment} carries an harpoon arrowhead.
\end{glyphDescription}
Modified: EntityRelationship/trunk/sources/domain.tex
===================================================================
--- EntityRelationship/trunk/sources/domain.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/domain.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -14,7 +14,7 @@
\label{fig:domain}
\end{figure}
-As any other \glyph{entity}, a nested \glyph{entity} can carry \glyph{state variables} and \glyph{units of information}. The contour of the containing \glyph{entity} must surround the totality of all contained \glyph{entities} including their \glyph{state variables} and \glyph{units of information}. This does not include the \glyph{assignments} and the \glyph{variable values}. A nested \glyph{entity} can participate to \glyph{interactions}, with ``sibling'' \glyph{entities} (part of the same containing \glyph{entity}), or others. They can also generate \glyph{influences}. For more information about the use and interpretation of entity nesting, see \sect{semanticsDomain}
+As any other \glyph{entity}, a nested \glyph{entity} can carry \glyph{state variables} and \glyph{units of information}. The contour of the containing \glyph{entity} must surround the totality of all contained \glyph{entities} including their \glyph{state variables} and \glyph{units of information}. This does not include the \glyph{assignments} and the \glyph{variable values}. A nested \glyph{entity} can participate in \glyph{interactions}, with ``sibling'' \glyph{entities} (part of the same containing \glyph{entity}), or others. They can also generate \glyph{influences}. For more information about the use and interpretation of entity nesting, see \sect{semanticsDomain}
\begin{figure}[H]
\centering
Modified: EntityRelationship/trunk/sources/entity.tex
===================================================================
--- EntityRelationship/trunk/sources/entity.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/entity.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -32,7 +32,7 @@
\begin{figure}[H]
\centering
\includegraphics[scale = 0.5]{examples/ex-entity}
- \caption{Example of an \glyph{entity} named CaMKII, that carries two \glyph{state variables} representing the phosphorylated residue threonine 286, and the residu threonine 306, a \glyph{unit of information} precising its material status (protein).}
+ \caption{Example of an \glyph{entity} named CaMKII, that carries two \glyph{state variables} representing the phosphorylated residue threonine 286 and the residue threonine 306, and a \glyph{unit of information} precising its material status (protein).}
\label{fig:ex-entity}
\end{figure}
Modified: EntityRelationship/trunk/sources/er-overview.tex
===================================================================
--- EntityRelationship/trunk/sources/er-overview.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/er-overview.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -4,22 +4,22 @@
\section{Overview of the Entity Relationship language}\label{sec:overview}
-To set the stage for what follows in this chapter, we first give a brief overview of some of the concepts in the \ER notation with the help of an example shown in \fig{eg1}.
+To set the stage for what follows in this chapter, we first give a brief overview of some of the concepts in the \ER language with the help of an example shown in \fig{eg1}.
\begin{figure}[H]
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.45]{examples/HelloWorld}
- \caption{This example of an \ERm represent an entity 1 interacting with another entity 2. The assignment of value 1 to the state variable of the entity 1 stimulates the interaction.}
+ \caption{This example of an \ERm represents an entity A interacting with another entity B. The assignment of value 1 to the state variable var of the entity A stimulates the interaction between entity A and entity B.}
\label{fig:eg1}
\end{figure}
-The essence of the \ERs is to depict the influences of entities upon the behaviour of others. The entities are classes of things that exist, either on their own, or when statements become true. For entity to be true at least one instance of it should exists otherwise entity will be false. For instance, an entity can exist (such as ``entity A'' in \fig{eg1}), instances of different entities can interact (such as ``entity A'' and ``entity B'' in \fig{eg1}), or a value can be assigned to a property of some instance of an entity (such as ``value 1'' to property ``var'' of ``entity A'' in \fig{eg1}). The influences can therefore be understood as logical consequences of existence of its instances. The stimulation of the interaction between ``entity A'' and ``entity B'' in \fig{eg1} takes place if `value 1'' is really assigned to property ``var'' of some instance of the ``entity A''. The existence of the assignment (set of instances where value is really assigned to the property) is represented by the black dot (called \glyph{outcome}). On the contrary to the \PDl, where the different processes affect each other in a way that the behaviour of the depicted system can only be understood taking into account the whole system, the relationships are essentially independent. One can imagine that each of the relationships represents a specific conclusion of a scientific experience reported in an article. Their addition on a map represents the knowledge we have of the effects of the entities represented upon each other. In \fig{eg1}, we have three statements:
+The essence of the \ERs is to depict the influences of entities upon the behaviour of others. The entities are classes of things that exist, either on their own, or when statements (interactions and assignments) become true. For entity to be true at least one instance of it should exist otherwise entity will be false. For instance, an entity can exist (such as ``entity A'' in \fig{eg1}), instances of different entities can interact (such as ``entity A'' and ``entity B'' in \fig{eg1}), or a value can be assigned to a property of some instance of an entity (such as ``value 1'' to property ``var'' of ``entity A'' in \fig{eg1}). The influences can therefore be understood as logical consequences of existence of its instances. The stimulation of the interaction between ``entity A'' and ``entity B'' in \fig{eg1} takes place if `value 1'' is really assigned to property ``var'' of some instance of the ``entity A''. The existence of the assignment (set of instances where value is really assigned to the property) is represented by the black dot (called \glyph{outcome}). On the contrary to the \PDl, where the different processes affect each other in a way that the behaviour of the depicted system can only be understood taking into account the whole system, the relationships are essentially independent. One can imagine that each of the relationships represents a specific conclusion of a scientific experiment reported in an article. Their addition on a map represents the knowledge we have of the effects of the entities represented upon each other. In \fig{eg1}, we have three statements:
\begin{itemize}
- \item ``entity 1'' can interact with ``entity 2''.
- \item property ``var'' of ``entity 1'' can take the value ``value 1''.
- \item if ``var'' is set to ``value 1'', the interaction between ``entity 1'' and ``entity 2'' is stimulated.
+ \item ``entity A'' can interact with ``entity B''.
+ \item property ``var'' of ``entity A'' can take the value ``value 1''.
+ \item if ``var'' is set to ``value 1'', the interaction between ``entity A'' and ``entity B'' is stimulated.
\end{itemize}
@@ -53,7 +53,7 @@
& An entity, the result of an interaction \\[0.5em]
Statement arc
- & Something that can be true or false, and affects or relate entities.
+ & Something that can be true or false, and affects or relates entities.
& An interaction between entities, the assignment of a value to a variable \\[0.5em]
Influence
Modified: EntityRelationship/trunk/sources/examples.tex
===================================================================
--- EntityRelationship/trunk/sources/examples.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/examples.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -1,6 +1,6 @@
\chapter{Complete examples of \SBGNERLone maps}
-The following maps present complete examples of SBGN \ERs representing biological processes. They by no mean exhaust the possibilities of \SBGNERLone.\\
+The following maps present complete examples of SBGN \ERs representing biological processes. They by no mean exhaust the possibilities of \SBGNERLone.\\
\input{sources/usermanual.tex}
Modified: EntityRelationship/trunk/sources/grammar.tex
===================================================================
--- EntityRelationship/trunk/sources/grammar.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/grammar.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -16,13 +16,13 @@
The SBGN \ERl{} is more than a collection of symbols. It is a
visual language that uses specific abstractions to describe the
-biological processes that make up e.g. a quantitative model, a signalling pathway or a metabolic network. This abstraction is the semantics of SBGN, and to describe it requires more than a definition
+biological processes that make up, e.g., a quantitative model, a signalling pathway or a metabolic network. This abstraction is the semantics of SBGN, and to describe it requires more than a definition
of the symbols and syntax of the language. We first need to define the
abstractions we are using.
-SBGN \ERs{} describe biological interactions involving biological entities. An \glyph{entity node} (\sect{ENs}), such as a molecule, influences the behaviour of other \glyph{entity nodes} via a relationships.
+SBGN \ERs{} describe biological interactions involving biological entities. An \glyph{entity node} (\sect{ENs}), such as a molecule, influences the behaviour of other \glyph{entity nodes} via a relationship.
-It may be convenient to think of a SBGN \ERs{} as listing independent rules that describe influences between \glyph{entity nodes}. Map can then be analysed with ``what if?'' queries.
+It may be convenient to think of a SBGN \ERs{} as listing independent rules that describe influences between \glyph{entity nodes}. A map can then be analysed with ``what if?'' queries.
\input{sources/syntax.tex}
\input{sources/semantics.tex}
Modified: EntityRelationship/trunk/sources/interaction.tex
===================================================================
--- EntityRelationship/trunk/sources/interaction.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/interaction.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -5,7 +5,7 @@
\subsubsection{Glyph: \glyph{Interaction}}\label{sec:interaction}
-\glyph{Interaction} represents an interaction between two or more \glyph{entities} or \glyph{outcomes}, whether a non-covalent physical interaction, or a functional interaction, e.g. genetic interaction. The interaction is represented by a circle which connect to arrows pointing to the interactors involved in the interaction. In the case of a binary interaction, the circle may be ommitted. The realisation of the interaction is represented by \glyph{outcomes} (see section \ref{sec:outcome}), that is by filled dots. These \glyph{outcomes} are located on the circle representing the interaction. In the case of a binary interaction represented without circle, the \glyph{outcomes} can be placed anywhere between the arrowheads. The realisations of an interaction can be represented by any number of \glyph{outcomes}. The \glyph{influences} (\ref{sec:influences}) targeting an interaction end up on the external side of the circle, between the \glyph{outcomes}.
+\glyph{Interaction} represents an interaction between two or more \glyph{entities} or \glyph{outcomes}, whether a non-covalent physical interaction, or a functional interaction, e.g. genetic interaction. The interaction is represented by a circle which connects to arrows pointing to the interactors involved in the interaction. In the case of a binary interaction, the circle may be ommitted. The realisation of the interaction is represented by \glyph{outcomes} (see section \ref{sec:outcome}), that is by filled dots. These \glyph{outcomes} are located on the circle representing the interaction. In the case of a binary interaction represented without circle, the \glyph{outcomes} can be placed anywhere between the arrowheads. The realisations of an interaction can be represented by any number of \glyph{outcomes}. The \glyph{influences} (\ref{sec:influences}) targeting an interaction end up on the external side of the circle, between the \glyph{outcomes}.
\begin{glyphDescription}
\glyphSboTerm SBO:0000342 molecular or genetic interaction
@@ -18,7 +18,7 @@
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/interaction}
- \caption{The \ER glyph for \glyph{interaction}. Top left, binary interaction between two entities. The circle can be ommitted, and the \glyph{outcomes} located anywhere on the \glyph{interaction}. Bottom left, because the cardinality of the entity A is 2, the interaction is not a binary one, but a n-ary one. The circle cannot be ommitted. Bottom right, n-ary interaction with three different entities. Top right, intra-molecular interaction; }
+ \caption{The \ER glyph for \glyph{interaction}. Top left, binary interaction between two entities. The circle can be ommitted, and the \glyph{outcomes} located anywhere on the \glyph{interaction}. Bottom left, because the cardinality of the entity A is 2, the interaction is not a binary one, but a n-ary one. The circle cannot be ommitted. Bottom right, n-ary interaction with three different entities. Top right, intra-molecular interaction.}
\label{fig:interaction}
\end{figure}
Modified: EntityRelationship/trunk/sources/layout.tex
===================================================================
--- EntityRelationship/trunk/sources/layout.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/layout.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -15,7 +15,7 @@
Those layout guidelines are independent of the method used to produce the map, and apply to both manually drawn maps as well as maps produced by an automatic layout algorithm. The guidelines do not deal with interactive aspects (e.\,g.~the effect of zooming). Further information about automatic network layout (graph drawing) can be found, for example, in the books of Di Battista and co-authors~\cite{DiBattista:1998} and Kaufmann and Wagner~\cite{Kaufmann:2001}.
-Please note that the color of objects do not carry any meaning in SBGN. Although one can use colors to emphasize part of a map or encode additional information, the meaning of the map should not depend on the colors. Furthermore, objects can have different sizes and size is also meaningless in SBGN. For example, a transition node may be larger than a protein node. Also the meaning of a graph should be conserved upon scaling as far as possible.
+Please note that the color of objects has no meaning in SBGN. Although one can use colors to emphasize parts of a map or encode additional information, the meaning of the map should not depend on the colors. Furthermore, objects can have different sizes and size is also meaningless in SBGN. For example, a transition node may be larger than a protein node. Also the meaning of a graph should be conserved upon scaling as far as possible.
\newpage
@@ -29,7 +29,7 @@
Nodes are only allowed to overlap in the case that the overlapping nodes define a glyph. Examples are stacking auxiliary items such as an \glyph{unit of information} on top of an \glyph{entity}, or an \glyph{interaction} and nesting \glyph{entities} to represent domains (\sect{domain}). In other cases, nodes are not allowed to overlap (\fig{layout1}). This includes the touching of nodes.
-\begin{figure}[h!]
+\begin{figure}[!htb]
\centering
\includegraphics[scale=0.3]{images/layout-node-node}
\caption{Nodes must not overlap.}\label{fig:layout1}
@@ -41,7 +41,7 @@
In case of node-edge crossing the edge must be drawn on the top of the node (\fig{layout2}). See also recommendation \ref{crosEdNo} (crossing between edges and nodes should be avoided).
-\begin{figure}[h!]
+\begin{figure}[!htb]
\centering
\includegraphics[scale=0.3]{images/layout-node-edge}
\caption{If an edge crosses a node, the edge must be drawn on top of the node.}\label{fig:layout2}
@@ -51,7 +51,7 @@
Edges are not allowed to overlap the border lines of nodes (\fig{layout3}).
-\begin{figure}[h!]
+\begin{figure}[!htb]
\centering
\includegraphics[scale=0.3]{images/layout-node-border-edge}
\caption{Edges must not overlap node borders.}\label{fig:layout3}
@@ -61,7 +61,7 @@
Edges are not allowed to overlap (\fig{layout4}). This includes touching of edges. Furthermore, an edge is neither allowed to cross itself nor to cross a boundary of node more than twice or other edges more than once.
-\begin{figure}[h!]
+\begin{figure}[!htb]
\centering
\includegraphics[scale=0.3]{images/layout-edge-edge}
\caption{Edges must not overlap.}\label{fig:layout4}
@@ -71,7 +71,7 @@
Nodes have to be drawn horizontally or vertically, any other rotation of elements is not allowed (\fig{layout5}).
-\begin{figure}[h!]
+\begin{figure}[!htb]
\centering
\includegraphics[scale=0.3]{images/layout-orientation}
\caption{The node orientation must be horizontally or vertically.}\label{fig:layout5}
@@ -81,7 +81,7 @@
The \glyph{interaction arcs} linking more than two \glyph{interactor nodes} are attached to a circle. Several outcomes of an interaction are not allowed to overlap (\fig{layout6}).
-\begin{figure}[h!]
+\begin{figure}[!htb]
\centering
\includegraphics[scale=0.3]{images/layout-connecting-arcs}
\caption{Arcs linking more than two \glyph{interactor nodes} are attached to a circle and outcomes of an interaction are not allowed to overlap.}\label{fig:layout6}
@@ -101,17 +101,17 @@
%
\subsection{Recommendations}
-Recommendations are rules which should be followed if possible to produce layouts may be easier to understand.
+Recommendations are rules which should be followed if possible to produce layouts which are easier to understand.
\subsubsection{Multiple \glyph{entities} to represent the same concept}\label{multEnt}
-Because rules (the influence of one entity node on a relationship) are independent of each other, a given ``entity'' (the concept) can be represented by many \glyph{entities} (the symbols). If a map is particularly large and an entity highly influenced or influential, it may be a good idea to represent the entity several time, limiting the influences to or from each instance. However, if systematised, such a procedure would lead to disconnected maps difficult to read and interpret. It is recommended to adopt a parsimonious approach, and multiply the symbols representing an entity only when the map become unreadable without doing so.
+Because rules (the influence of one entity node on a relationship) are independent of each other, a given ``entity'' (the concept) can be represented by many \glyph{entities} (the symbols). If a map is particularly large and an entity highly influenced or influential, it may be a good idea to represent the entity several times, limiting the influences to or from each instance. However, if systematised, such a procedure would lead to disconnected maps difficult to read and interpret. It is recommended to adopt a parsimonious approach, and multiply the symbols representing an entity only when the map become unreadable without doing so.
\subsubsection{Node-edge crossing}\label{crosEdNo}
Crossings between edges and nodes should be avoided. See also requirement \ref{crosEdNoRe} (in case of node-edge crossings the edge must be drawn on the top of the node).
-\begin{figure}[h!]
+\begin{figure}[!htb]
\centering
\includegraphics[scale=0.3]{images/layout-node-edge-2}
\caption{Edges should not cross node.}\label{fig:layout7}
@@ -140,7 +140,8 @@
\item Edge length: Long edges should be avoided.
\item Number of edge bends: Edges should be drawn with as few bends as possible.
\item Similar and symmetric parts: Similar parts of a map should be drawn in a similar way, and symmetric parts should be drawn symmetrically.
- \item Proximity information: Related elements (e.\,g.~nodes connected by an arc or all elements within a submap) should be drawn close together.
+% \item Proximity information: Related elements (e.\,g.~nodes connected by an arc or all elements within a submap) should be drawn close together.
+ \item Proximity information: Related elements (e.\,g.~nodes connected by an arc) should be drawn close together.
\end{itemize}
%\normalcolor
\ No newline at end of file
Modified: EntityRelationship/trunk/sources/logicArc.tex
===================================================================
--- EntityRelationship/trunk/sources/logicArc.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/logicArc.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -8,7 +8,7 @@
the outcome of a logic operator.
\begin{glyphDescription}
- \glyphSboTerm SBO:0000398 - logical relationship.
+ \glyphSboTerm SBO:0000398 ! logical relationship.
\glyphOrigin Any \glyph{interactor} (\sect{interactors}) or \glyph{logical operator} (\sect{logic}).
\glyphTarget Any \glyph{logical operator} (\sect{logic}).
\glyphEndPoint No particular symbol is used to represent a logic arc.
Modified: EntityRelationship/trunk/sources/modulation.tex
===================================================================
--- EntityRelationship/trunk/sources/modulation.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/modulation.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -4,7 +4,7 @@
%\color{blue}
\subsubsection{Glyph: \glyph{Modulation}}\label{sec:modulation}
-A \glyph{modulation} affects the propensity, or the chances to happen, of the target relationship. Such a modulation can affect the relationship \textbf{positively or negatively}, or even both ways depending on the conditions. A \glyph{modulation} can also be used when one does not know the precise direction of the effect, for instance if there are conflicting evidence.
+A \glyph{modulation} affects the propensity, or the chances to happen, of the target relationship. Such a modulation can affect the relationship \textbf{positively or negatively}, or even both ways depending on the conditions. A \glyph{modulation} can also be used when one does not know the precise direction of the effect, for instance if there are conflicting evidences.
\begin{glyphDescription}
\glyphSboTerm SBO:0000168 ! control.
Modified: EntityRelationship/trunk/sources/necessaryStimulation.tex
===================================================================
--- EntityRelationship/trunk/sources/necessaryStimulation.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/necessaryStimulation.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -24,7 +24,7 @@
\begin{figure}[H]
\centering
\includegraphics[scale = 0.5]{images/necessaryStimulation}
- \caption{The \ER glyph for \glyph{necessaryStimulation}.}
+ \caption{The \ER glyph for \glyph{necessary stimulation}.}
\label{fig:necessaryStimulation}
\end{figure}
Modified: EntityRelationship/trunk/sources/not.tex
===================================================================
--- EntityRelationship/trunk/sources/not.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/not.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -4,7 +4,7 @@
%\color{blue}
\subsubsection{Glyph: \glyph{Not}}\label{sec:not}
-The glyph \glyph{not} is used to denote that the output influence only happen in the absence of the input \glyph{entity node}.
+The glyph \glyph{not} is used to denote that the output influence only happens in the absence of the input \glyph{entity node}.
\begin{glyphDescription}
Modified: EntityRelationship/trunk/sources/outcome.tex
===================================================================
--- EntityRelationship/trunk/sources/outcome.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/outcome.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -5,7 +5,7 @@
%\color{blue}
\subsubsection{Glyph: \glyph{Outcome}}\label{sec:outcome}
-In \ERs, an \glyph{outcome} represents the actualisation of a \glyph{statement} (\sect{statements}). It is not entity on its own, but subset of all possible entity instances where \glyph{statement} is true. For instance, if an \glyph{interaction} represents a non-covalent binding, the \glyph{outcome} represents all possible complexes that has two interactors bound to each other. If an \glyph{interaction} represents a genetic interaction, for instance derived from genetic screenings, the \glyph{outcome} represents the result of the presence of the two polymorphisms. If an \glyph{assignment} represents the phosphorylation of a protein, the \glyph{outcome} represents all possible complexes and free molecules where this protein is phosphorylated.
+In \ERs, an \glyph{outcome} represents the actualisation of a \glyph{statement} (\sect{statements}). It is not an entity on its own, but a subset of all possible entity instances where \glyph{statement} is true. For instance, if an \glyph{interaction} represents a non-covalent binding, the \glyph{outcome} represents all possible complexes that has two interactors bound to each other. If an \glyph{interaction} represents a genetic interaction, for instance derived from genetic screenings, the \glyph{outcome} represents the result of the presence of the two polymorphisms. If an \glyph{assignment} represents the phosphorylation of a protein, the \glyph{outcome} represents all possible complexes and free molecules where this protein is phosphorylated.
An \glyph{outcome} represent a particular instance of a realisation, and therefore, from one outcome must depart only one influence. An outcome being an \glyph{entity node}, it cannot receive influences. It exists. It cannot more or less exist.
Modified: EntityRelationship/trunk/sources/relationships.tex
===================================================================
--- EntityRelationship/trunk/sources/relationships.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/relationships.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -18,7 +18,7 @@
\subsection{Statements}\label{sec:statements}
-\glyph{Statements} can be true or false. \glyph{Statements} are targets of \glyph{Influences}. They are not true themselves, but can carry \glyph{Outcomes}( see \sect{outcome}). \SBGNERLone{} provides three types of statements, \glyph{Assignment}, \glyph{Interaction} and \glyph{Phenotype}.
+\glyph{Statements} can be true or false. \glyph{Statements} are targets of \glyph{Influences}. They are not true themselves, but can carry \glyph{Outcomes} (see \sect{outcome}). \SBGNERLone{} provides three types of statements, \glyph{Assignment}, \glyph{Interaction} and \glyph{Phenotype}.
\input{sources/assignment.tex}
\input{sources/interaction.tex}
Modified: EntityRelationship/trunk/sources/revision_history.tex
===================================================================
--- EntityRelationship/trunk/sources/revision_history.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/revision_history.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -50,7 +50,7 @@
Added caption 'Auxiliary items' for \glyph{necessary stimulation} and \glyph{absolute inhibition} & track: 3115480\\\hline
A section has been added to describe the \glyph{variable value} as a proper glyph & \\\hline
Mentions of \glyph{non-interaction} have been removed from 6 places & track: 3115477\\\hline
-A section has been added to describe the \glyph{variable value} as a proper glyph & \\\hline
+%A section has been added to describe the \glyph{variable value} as a proper glyph & \\\hline
\end{supertabular}
\end{center}
Modified: EntityRelationship/trunk/sources/semantics.tex
===================================================================
--- EntityRelationship/trunk/sources/semantics.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/semantics.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -5,15 +5,15 @@
\subsection{Entities and states}
-An \glyph{entity} (\sect{entity}) represents set of individual instances of some kind (molecules, agents etc). The difference from \SBGNPDLone \glyph{entity pool node} is that \glyph{entity} instances are independent, while \glyph{entity pool node} form one nonseparable object acting as a whole. Set of \glyph{state variables} (\sect{stateVariable}) and their \glyph{values} (\sect{variableValue}) describe a part of the \glyph{entity} instances state space. The \glyph{entity}, or interaction \glyph{outcome} (\sect{outcome}) acquire the true state if the set of entity instances compatible with the \glyph{entity} state, or actualisation of interaction is non-empty.
+An \glyph{entity} (\sect{entity}) represents a set of individual instances of some kind (molecules, agents etc). The difference from \SBGNPDLone \glyph{entity pool node} is that \glyph{entity} instances are independent, while \glyph{entity pool node} form one nonseparable object acting as a whole. A set of \glyph{state variables} (\sect{stateVariable}) and their \glyph{values} (\sect{variableValue}) describe a part of the \glyph{entity} instances state space. The \glyph{entity}, or interaction \glyph{outcome} (\sect{outcome}) acquire the true state if the set of entity instances compatible with the \glyph{entity} state, or actualisation of interaction is non-empty.
\subsection{Statements}
-An \glyph{interaction} (\sect{interaction}) linking the \glyph{interactors} $A$ and $B$ means: ``any instance of $A$ can interacts with instances of $B$''. An \glyph{outcome} on an \glyph{interaction} represents the cases when the statement is true, that is subset of all instances of $A$ and $B$ between which the interaction effectively exists. If the interaction is a physical interaction between molecules, the \glyph{outcome} represents the all possible complexes where interactors are really bound to each other, and in that case interaction is always considered as reversible. It is used as follow: ``when (or if) $A$ interacts with $B$ then \ldots''.\\[\baselineskip]
+An \glyph{interaction} (\sect{interaction}) linking the \glyph{interactors} $A$ and $B$ means: ``any instance of $A$ can interact with instances of $B$''. An \glyph{outcome} on an \glyph{interaction} represents the cases when the statement is true, that is subset of all instances of $A$ and $B$ between which the interaction effectively exists. If the interaction is a physical interaction between molecules, the \glyph{outcome} represents all possible complexes where interactors are really bound to each other, and in that case interaction is always considered as reversible. It is used as follow: ``when (or if) $A$ interacts with $B$ then \ldots''.\\[\baselineskip]
\noindent
-An \glyph{assignment} (\sect{assignment}) linking a state variable value $v$ to a \glyph{state-variable} $V$ of an \glyph{entity} $E$ means: ``$v$ is assigned to $V$ of $E$'' or ``$V$ of $E$ takes the value $v$''. An \glyph{outcome} on an \glyph{assignment} represents the cases when the statement is true, that is all instances of $E$ (free or as a complex subunint) on which the variable effectively displays the value. It is used as follows: ``when (or if) $V$ of $E$ takes the value $v$ then \ldots'' or more succintly ``when (or if) $E\{V => v\}$ then \ldots''.\\[\baselineskip]
+An \glyph{assignment} (\sect{assignment}) linking a \glyph{variable value} $v$ to a \glyph{state variable} $V$ of an \glyph{entity} $E$ means: ``$v$ is assigned to $V$ of $E$'' or ``$V$ of $E$ takes the value $v$''. An \glyph{outcome} on an \glyph{assignment} represents the cases when the statement is true, that is all instances of $E$ (free or as a complex subunint) on which the variable effectively displays the value. It is used as follows: ``when (or if) $V$ of $E$ takes the value $v$ then \ldots'' or more succintly ``when (or if) $E\{V => v\}$ then \ldots''.\\[\baselineskip]
\noindent
A \glyph{phenotype} (\sect{phenotype}) $P$ means: ``$P$ exists''.\\[\baselineskip]
@@ -58,8 +58,8 @@
\noindent
A \glyph{not} (\sect{not}) linking a \glyph{logic arc} originating from an \glyph{entity node} $E$ and an influence $F$ means: `` $F$ takes place only if $E$ does not exist''.\\[\baselineskip]
-\noindent
-A \glyph{delay} (\sect{delay}) linking a \glyph{logic arc} originating from an \glyph{entity node} $E$ and an influence $F$ means: ``If $E$ exists then $F$ takes place, but not immediately''.\\[\baselineskip]
+%\noindent
+%A \glyph{delay} (\sect{delay}) linking a \glyph{logic arc} originating from an \glyph{entity node} $E$ and an influence $F$ means: ``If $E$ exists then $F$ takes place, but not immediately''.\\[\baselineskip]
\subsection{Cis and trans relationships}\label{sec:cis-trans-semantics}
@@ -112,7 +112,7 @@
\subsection{(In)Validation of ER maps}
-Based on the definitions above, it should be possible to use the toolkit of formal logic to analyse \ERs{}. In particular, one can envision to build truth tables describing the consequences of the existences of the various entities. Those table should point to inconsistencies leading to contradictory predicates.
+Based on the definitions above, it should be possible to use the toolkit of formal logic to analyse \ERs{}. In particular, one can envision to build truth tables describing the consequences of the existences of the various entities. Those tables should point to inconsistencies leading to contradictory predicates.
% Give an example of a wrong ER map.
Modified: EntityRelationship/trunk/sources/stateVariable.tex
===================================================================
--- EntityRelationship/trunk/sources/stateVariable.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/stateVariable.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -17,7 +17,7 @@
\glyphSboTerm Not applicable.
-\glyphContainer A \glyph{state variable} is represented by a ''stadium'' container, that is two semicircles of same radius joined by parallel segments, as shown in \fig{state-var}. The parallel segment axis should be tangent to the border of the glyph of the \glyph{EN} being modified by the \glyph{state variable}. The center of the bounding box of a \glyph{state variable} should be located on the mid-line of the border of the \glyph{EN}.
+\glyphContainer A \glyph{state variable} is represented by a ''stadium'' container, that is two semicircles of same radius joined by parallel segments, as shown in \fig{state-var}. The parallel segment axis should be tangent to the border of the glyph of the \glyph{entity} being modified by the \glyph{state variable}. The center of the bounding box of a \glyph{state variable} should be located on the mid-line of the border of the \glyph{entity}.
\glyphLabel A \glyph{state variable} is identified by a label placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
@@ -28,7 +28,7 @@
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/stateVariable}
- \caption{The \ER glyph for \glyph{state variable}. From left to right, horizontal state variable, vertical state variable, \glyph{location}, \glyph{existence}.}
+ \caption{The \ER glyph for \glyph{state variable}. From left to right, horizontal \glyph{state variable}, vertical \glyph{state variable}, \glyph{location}, \glyph{existence}.}
\label{fig:state-var}
\end{figure}
Modified: EntityRelationship/trunk/sources/syncEv.tex
===================================================================
--- EntityRelationship/trunk/sources/syncEv.tex 2014-11-11 23:57:04 UTC (rev 886)
+++ EntityRelationship/trunk/sources/syncEv.tex 2014-11-14 01:52:03 UTC (rev 887)
@@ -1,6 +1,6 @@
\section{Synchronous events}\label{sec:syncev}
-\SBGNERLone Version 2 allows the description of multiple consequences of the event that happens simultaneously. There are cases in which one interaction should influence several other in synchrony, for example the chemical reaction:
+\SBGNERLone Version 2 allows the description of multiple consequences of the event that happens simultaneously. There are cases in which one interaction should influence several others in synchrony, for example the chemical reaction:
\begin{figure}[H]
\centering
@@ -9,7 +9,7 @@
\label{fig:synchronousPD}
\end{figure}
-Use two outcomes or two stimulation links \fig{asynchronous} is not appropriate in this case as all statement in \ER are independent. According to that diagram on \fig{asynchronous} it is possible that \glyph{entity} $B$ is created, but \glyph{entity} $A$ is not deleted, because outcomes are independent and not guarantied to be in true state.
+Use two outcomes or two stimulation links \fig{asynchronous} is not appropriate in this case as all statement in \ER are independent. According to the diagram in \fig{asynchronous} it is possible that \glyph{entity} $B$ is created, but \glyph{entity} $A$ is not deleted, because outcomes are independent and not guarantied to be in true state.
\begin{figure}[H]
\centering
@@ -18,7 +18,7 @@
\label{fig:asynchronous}
\end{figure}
-To represent multiple consequences of the statement the influence arc is splitted to represent multiple consequences of the event as shown on \fig{s...
[truncated message content] |
|
From: <hua...@us...> - 2014-11-11 23:57:17
|
Revision: 886
http://sourceforge.net/p/sbgn/code/886
Author: huaiyumi
Date: 2014-11-11 23:57:04 +0000 (Tue, 11 Nov 2014)
Log Message:
-----------
Update the AF revision history
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/revision_history.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-11-07 18:24:59 UTC (rev 885)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-11-11 23:57:04 UTC (rev 886)
@@ -1,30 +1,47 @@
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[truncated message content] |
|
From: <hua...@us...> - 2014-11-07 18:25:07
|
Revision: 885
http://sourceforge.net/p/sbgn/code/885
Author: huaiyumi
Date: 2014-11-07 18:24:59 +0000 (Fri, 07 Nov 2014)
Log Message:
-----------
Update AF Compartment overlap section
Modified Paths:
--------------
ActivityFlow/trunk/examples/compartment_overlapping.eps
ActivityFlow/trunk/examples/compartment_overlapping.pdf
ActivityFlow/trunk/examples/compartment_overlapping.png
ActivityFlow/trunk/examples/compartment_overlapping.svg
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/compartment.tex
ActivityFlow/trunk/sources/layout.tex
Modified: ActivityFlow/trunk/examples/compartment_overlapping.eps
===================================================================
--- ActivityFlow/trunk/examples/compartment_overlapping.eps 2014-11-04 23:52:17 UTC (rev 884)
+++ ActivityFlow/trunk/examples/compartment_overlapping.eps 2014-11-07 18:24:59 UTC (rev 885)
@@ -1,1371 +1,7348 @@
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[truncated message content] |
|
From: <hua...@us...> - 2014-11-04 23:52:22
|
Revision: 884
http://sourceforge.net/p/sbgn/code/884
Author: huaiyumi
Date: 2014-11-04 23:52:17 +0000 (Tue, 04 Nov 2014)
Log Message:
-----------
Modified Paths:
--------------
ActivityFlow/trunk/images/logicArc.eps
ActivityFlow/trunk/images/refcard.eps
ActivityFlow/trunk/images/refcard.pdf
ActivityFlow/trunk/images/refcard.png
ActivityFlow/trunk/images/refcard.svg
ActivityFlow/trunk/sbgn_AF-level1.pdf
Modified: ActivityFlow/trunk/images/logicArc.eps
===================================================================
--- ActivityFlow/trunk/images/logicArc.eps 2014-11-04 23:19:47 UTC (rev 883)
+++ ActivityFlow/trunk/images/logicArc.eps 2014-11-04 23:52:17 UTC (rev 884)
@@ -1,594 +1,286 @@
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Modified: ActivityFlow/trunk/images/refcard.eps
===================================================================
--- ActivityFlow/trunk/images/refcard.eps 2014-11-04 23:19:47 UTC (rev 883)
+++ ActivityFlow/trunk/images/refcard.eps 2014-11-04 23:52:17 UTC (rev 884)
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