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From: <hua...@us...> - 2014-11-04 23:19:53
|
Revision: 883
http://sourceforge.net/p/sbgn/code/883
Author: huaiyumi
Date: 2014-11-04 23:19:47 +0000 (Tue, 04 Nov 2014)
Log Message:
-----------
Modified Paths:
--------------
ActivityFlow/trunk/images/logicArc.pdf
ActivityFlow/trunk/images/logicArc.png
ActivityFlow/trunk/images/logicArc.svg
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/CVs.tex
ActivityFlow/trunk/sources/af-overview.tex
ActivityFlow/trunk/sources/and.tex
ActivityFlow/trunk/sources/annotation.tex
ActivityFlow/trunk/sources/delay.tex
ActivityFlow/trunk/sources/glyphs.tex
ActivityFlow/trunk/sources/logicArc.tex
ActivityFlow/trunk/sources/not.tex
ActivityFlow/trunk/sources/or.tex
ActivityFlow/trunk/sources/syntax.tex
Modified: ActivityFlow/trunk/images/logicArc.pdf
===================================================================
(Binary files differ)
Modified: ActivityFlow/trunk/images/logicArc.png
===================================================================
(Binary files differ)
Modified: ActivityFlow/trunk/images/logicArc.svg
===================================================================
--- ActivityFlow/trunk/images/logicArc.svg 2014-10-31 23:42:34 UTC (rev 882)
+++ ActivityFlow/trunk/images/logicArc.svg 2014-11-04 23:19:47 UTC (rev 883)
@@ -1,5 +1,6 @@
<?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://creativecommons.org/ns#"
@@ -12,9 +13,8 @@
height="376.09"
id="svg2"
sodipodi:version="0.32"
- inkscape:version="0.46"
+ inkscape:version="0.48+devel r9813"
version="1.0"
- sodipodi:docbase="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/images"
sodipodi:docname="logicArc.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape"
inkscape:export-filename="/Users/mi/Documents/SBGN/subversion/sbgn-af/images/logicArc.png"
@@ -79,7 +79,8 @@
inkscape:window-y="0"
showguides="true"
inkscape:guide-bbox="true"
- showgrid="false">
+ showgrid="false"
+ inkscape:window-maximized="0">
<sodipodi:guide
orientation="vertical"
position="301.42857"
@@ -116,7 +117,7 @@
ry="0" />
<text
xml:space="preserve"
- 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-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;font-family:Bitstream Vera Sans"
x="198.28571"
y="178.80878"
id="text2841"><tspan
@@ -129,7 +130,7 @@
x="198.28571"
y="208.80878"
style="font-size:24px;font-weight:normal;text-align:center;text-anchor:middle"
- id="tspan2857">AN</tspan></text>
+ id="tspan2857">BA</tspan></text>
<path
transform="translate(323.85714,-103.71428)"
sodipodi:type="arc"
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-10-31 23:42:34 UTC (rev 882)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-11-04 23:19:47 UTC (rev 883)
@@ -1,398 +1,50 @@
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|
From: <hua...@us...> - 2014-10-31 23:42:44
|
Revision: 882
http://sourceforge.net/p/sbgn/code/882
Author: huaiyumi
Date: 2014-10-31 23:42:34 +0000 (Fri, 31 Oct 2014)
Log Message:
-----------
Add SBO term to "annotation"
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sources/glyphs.tex
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2014-10-27 04:35:43 UTC (rev 881)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2014-10-31 23:42:34 UTC (rev 882)
@@ -2791,7 +2791,7 @@
\begin{glyphDescription}
-\glyphSboTerm SBO:NEW
+\glyphSboTerm SBO:0000550 ! annotation
\glyphContainer An \glyph{annotation} is represented by a rectangular
container with a folded corner, as illustrated in
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <tcz...@us...> - 2014-10-27 04:35:49
|
Revision: 881
http://sourceforge.net/p/sbgn/code/881
Author: tczauderna
Date: 2014-10-27 04:35:43 +0000 (Mon, 27 Oct 2014)
Log Message:
-----------
a couple of typos and minor errors have been fixed
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/CVs.tex
ActivityFlow/trunk/sources/acknowledgments.tex
ActivityFlow/trunk/sources/af-overview.tex
ActivityFlow/trunk/sources/annotation.tex
ActivityFlow/trunk/sources/biologicalActivity.tex
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ActivityFlow/trunk/sources/grammar.tex
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ActivityFlow/trunk/sources/necessaryStimulation.tex
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ActivityFlow/trunk/sources/revision_history.tex
ActivityFlow/trunk/sources/syntax.tex
ActivityFlow/trunk/sources/unitInformation.tex
ActivityFlow/trunk/sources/unknown_infl.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-10-22 21:02:34 UTC (rev 880)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-10-27 04:35:43 UTC (rev 881)
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From: <hua...@us...> - 2014-10-22 21:02:38
|
Revision: 880
http://sourceforge.net/p/sbgn/code/880
Author: huaiyumi
Date: 2014-10-22 21:02:34 +0000 (Wed, 22 Oct 2014)
Log Message:
-----------
Draft of AF Version 1.2
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.bib
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/acknowledgments.tex
ActivityFlow/trunk/sources/front-page.tex
ActivityFlow/trunk/sources/introduction.tex
ActivityFlow/trunk/sources/latex-style.tex
ActivityFlow/trunk/sources/refcard.tex
ActivityFlow/trunk/sources/revision_history.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.bib
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.bib 2014-08-27 19:57:56 UTC (rev 879)
+++ ActivityFlow/trunk/sbgn_AF-level1.bib 2014-10-22 21:02:34 UTC (rev 880)
@@ -81,3 +81,30 @@
pages = {117--129}
}
+@article{LeNovere:NatBiotechnol:2009,
+ author = {Le Nov\`{e}re, Nicolas and Hucka, Michael and Mi, Huaiyu and Moodie, Stuart and Schreiber, Falk and Sorokin, Anatoly and Demir, Emek and Wegner, Katja and Aladjem, Mirit I. and Wimalaratne, Sarala M. and Bergman, Frank T. and Gauges, Ralph and Ghazal, Peter and Kawaji, Hideya and Li, Lu and Matsuoka, Yukiko and Vill\'{e}ger, Alice and Boyd, Sarah E. and Calzone, Laurence and Courtot, Melanie and Dogrusoz, Ugur and Freeman, Tom C. and Funahashi, Akira and Ghosh, Samik and Jouraku, Akiya and Kim, Sohyoung and Kolpakov, Fedor and Luna, Augustin and Sahle, Sven and Schmidt, Esther and Watterson, Steven and Wu, Guanming and Goryanin, Igor and Kell, Douglas B. and Sander, Chris and Sauro, Herbert and Snoep, Jacky L. and Kohn, Kurt and Kitano, Hiroaki},
+ title = {The Systems Biology Graphical Notation.},
+ journal = {Nat Biotechnol},
+ uuid = {2AE4D97A-8150-45B6-89E2-31A93EB12768},
+ volume = {27},
+ number = {8},
+ pages = {735-41},
+ organization = {EMBL European Bioinformatics Institute, Hinxton, UK. lenov\@ebi.ac.uk},
+ address = {United States},
+ month = {8},
+ year = {2009},
+ doi = {10.1038/nbt.1558},
+ ISSN = {1546-1696},
+ US_NLM_ID = {9604648},
+ PII = {nbt.1558},
+ pubmedid = {19668183},
+ sentelink = {file:///Users/mi/Desktop/Mi_Library.sente6lib/Contents/Attachments/Le%20Nove%CC%80re%2C%20N/2009/The%20Systems%20Biology%20Graphical.pdf,Sente,},
+ url = {},
+ keywords = {research support, n.i.h., extramural;Systems Biology;historical article;Software;Internet;History, 20th Century;research support, non-u.s. gov't;research support, n.i.h., intramural;Computer Graphics},
+ EndNote_reference_number = {516},
+ Web_data_source = {PubMed},
+ Citation_identifier = {LeNov\`{e}re 2009},
+ publicationStatus = {Published},
+ abstract = {Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.}
+}
+
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-08-27 19:57:56 UTC (rev 879)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2014-10-22 21:02:34 UTC (rev 880)
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[truncated message content] |
|
From: <hua...@us...> - 2014-08-27 19:58:10
|
Revision: 879
http://sourceforge.net/p/sbgn/code/879
Author: huaiyumi
Date: 2014-08-27 19:57:56 +0000 (Wed, 27 Aug 2014)
Log Message:
-----------
Update refcard
Modified Paths:
--------------
ActivityFlow/trunk/examples/Action_potential.eps
ActivityFlow/trunk/examples/Action_potential.pdf
ActivityFlow/trunk/examples/Action_potential.png
ActivityFlow/trunk/examples/Action_potential.svg
ActivityFlow/trunk/images/refcard.eps
ActivityFlow/trunk/images/refcard.pdf
ActivityFlow/trunk/images/refcard.png
ActivityFlow/trunk/images/refcard.svg
Modified: ActivityFlow/trunk/examples/Action_potential.eps
===================================================================
--- ActivityFlow/trunk/examples/Action_potential.eps 2014-08-26 07:15:13 UTC (rev 878)
+++ ActivityFlow/trunk/examples/Action_potential.eps 2014-08-27 19:57:56 UTC (rev 879)
@@ -1,6177 +1,1788 @@
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[truncated message content] |
|
From: <lp...@us...> - 2014-08-26 07:15:20
|
Revision: 878
http://sourceforge.net/p/sbgn/code/878
Author: lptolik
Date: 2014-08-26 07:15:13 +0000 (Tue, 26 Aug 2014)
Log Message:
-----------
SBO for annotation glyph fixed
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/annotation.tex
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/trunk/sources/annotation.tex
===================================================================
--- EntityRelationship/trunk/sources/annotation.tex 2014-08-18 11:48:47 UTC (rev 877)
+++ EntityRelationship/trunk/sources/annotation.tex 2014-08-26 07:15:13 UTC (rev 878)
@@ -9,7 +9,7 @@
\begin{glyphDescription}
-\glyphSboTerm SBO:NEW
+\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.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2014-08-18 11:49:00
|
Revision: 877
http://sourceforge.net/p/sbgn/code/877
Author: lptolik
Date: 2014-08-18 11:48:47 +0000 (Mon, 18 Aug 2014)
Log Message:
-----------
First draft for public review
Added Paths:
-----------
EntityRelationship/tags/L1V2DraftReview1/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2014-08-18 11:36:31
|
Revision: 876
http://sourceforge.net/p/sbgn/code/876
Author: lptolik
Date: 2014-08-18 11:36:25 +0000 (Mon, 18 Aug 2014)
Log Message:
-----------
L1V2 spec proposal draft for sbgn-discuss
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/ENs.tex
EntityRelationship/trunk/sources/glyphs.tex
EntityRelationship/trunk/sources/relationships.tex
Added Paths:
-----------
EntityRelationship/trunk/examples/gef.eps
EntityRelationship/trunk/examples/gef.pdf
EntityRelationship/trunk/examples/gef.png
EntityRelationship/trunk/examples/gef.svg
EntityRelationship/trunk/images/entity-identity.eps
EntityRelationship/trunk/images/entity-identity.pdf
EntityRelationship/trunk/images/entity-identity.png
EntityRelationship/trunk/images/entity-identity.svg
EntityRelationship/trunk/images/simultaneous.eps
EntityRelationship/trunk/images/simultaneous.pdf
EntityRelationship/trunk/images/simultaneous.svg
EntityRelationship/trunk/images/synchronous-PD.eps
EntityRelationship/trunk/images/synchronous-PD.pdf
EntityRelationship/trunk/images/synchronous-PD.png
EntityRelationship/trunk/images/synchronous-PD.svg
EntityRelationship/trunk/images/synchronous.eps
EntityRelationship/trunk/images/synchronous.pdf
EntityRelationship/trunk/images/synchronous.svg
EntityRelationship/trunk/sources/syncEv.tex
Added: EntityRelationship/trunk/examples/gef.eps
===================================================================
--- EntityRelationship/trunk/examples/gef.eps (rev 0)
+++ EntityRelationship/trunk/examples/gef.eps 2014-08-18 11:36:25 UTC (rev 876)
@@ -0,0 +1,463 @@
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[truncated message content] |
|
From: <lp...@us...> - 2014-08-14 08:07:39
|
Revision: 875
http://sourceforge.net/p/sbgn/code/875
Author: lptolik
Date: 2014-08-14 08:07:36 +0000 (Thu, 14 Aug 2014)
Log Message:
-----------
fixed authorship
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/front-page.tex
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/trunk/sources/front-page.tex
===================================================================
--- EntityRelationship/trunk/sources/front-page.tex 2014-08-14 07:21:23 UTC (rev 874)
+++ EntityRelationship/trunk/sources/front-page.tex 2014-08-14 08:07:36 UTC (rev 875)
@@ -31,10 +31,14 @@
\begin{tabular}{l>{\hspace*{15pt}}r}
Anatoly Sorokin & \emph{Institute of Cell Biophysics RAS, RU}\\
Nicolas \lenov & \emph{Babraham Institute, UK}\\
-Emek Demir & \emph{Memorial Sloan-Kettering Institute, USA}\\
-Huaiyu Mi & \emph{University of Southern California, USA}\\
-Stuart Moodie & \emph{EMBL-EBI, UK}\\
-Alice Vill\'{e}ger & \emph{Freelance IT Consultant, UK}
+Stuart Moodie & \emph{Eight Pillars Ltd, UK}\\
+Tobias Czauderna & \emph{Monash University, Australia}\\
+Falk Schreiber & \emph{Monash University, Australia \& MLU Halle, Germany}\\
+Huaiyu Mi & \emph{University of Southern California, USA}\\
+%Emek Demir & \emph{Memorial Sloan-Kettering Institute, USA}\\
+%Huaiyu Mi & \emph{University of Southern California, USA}\\
+%Stuart Moodie & \emph{EMBL-EBI, UK}\\
+%Alice Vill\'{e}ger & \emph{Freelance IT Consultant, UK}
\end{tabular}
\vfill
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2014-08-14 07:21:30
|
Revision: 874
http://sourceforge.net/p/sbgn/code/874
Author: lptolik
Date: 2014-08-14 07:21:23 +0000 (Thu, 14 Aug 2014)
Log Message:
-----------
L1V2 spec proposal
Modified Paths:
--------------
EntityRelationship/trunk/examples/ex-interaction-influences.svg
EntityRelationship/trunk/examples/ex-stimulation.eps
EntityRelationship/trunk/examples/ex-stimulation.pdf
EntityRelationship/trunk/examples/ex-stimulation.png
EntityRelationship/trunk/examples/ex-stimulation.svg
EntityRelationship/trunk/images/interaction.eps
EntityRelationship/trunk/images/interaction.pdf
EntityRelationship/trunk/images/interaction.png
EntityRelationship/trunk/images/interaction.svg
EntityRelationship/trunk/images/refcard.svg
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/CVs.tex
EntityRelationship/trunk/sources/ENs.tex
EntityRelationship/trunk/sources/absoluteStimulation.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/front-page.tex
EntityRelationship/trunk/sources/interaction.tex
EntityRelationship/trunk/sources/logicArc.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/syntax.tex
EntityRelationship/trunk/sources/variableValue.tex
EntityRelationship/trunk/sources/working.tex
Added Paths:
-----------
EntityRelationship/trunk/examples/ex-interaction-influences.eps
EntityRelationship/trunk/examples/ex-interaction-influences.pdf
EntityRelationship/trunk/examples/rtk-binding.pdf
EntityRelationship/trunk/examples/rtk-binding.png
EntityRelationship/trunk/examples/rtk-binding.svg
EntityRelationship/trunk/examples/rtk-complex.pdf
EntityRelationship/trunk/examples/rtk-complex.png
EntityRelationship/trunk/examples/rtk-dimer-control.pdf
EntityRelationship/trunk/examples/rtk-dimer-control.png
EntityRelationship/trunk/examples/rtk-dimer-control.svg
EntityRelationship/trunk/examples/rtk-dimerisation.pdf
EntityRelationship/trunk/examples/rtk-dimerisation.png
EntityRelationship/trunk/examples/rtk-dimerisation.svg
EntityRelationship/trunk/examples/rtk-entities.pdf
EntityRelationship/trunk/examples/rtk-entities.png
EntityRelationship/trunk/examples/rtk-entities.svg
EntityRelationship/trunk/examples/rtk-kinase-activation.pdf
EntityRelationship/trunk/examples/rtk-kinase-activation.png
EntityRelationship/trunk/examples/rtk-kinase-activation.svg
EntityRelationship/trunk/examples/rtk-states.pdf
EntityRelationship/trunk/examples/rtk-states.png
EntityRelationship/trunk/examples/rtk-states.svg
EntityRelationship/trunk/examples/rtk.pdf
EntityRelationship/trunk/examples/rtk.png
EntityRelationship/trunk/examples/rtk.sbgn
EntityRelationship/trunk/examples/rtk.svg
EntityRelationship/trunk/images/entity-granularity.eps
EntityRelationship/trunk/images/entity-granularity.pdf
EntityRelationship/trunk/images/entity-granularity.png
EntityRelationship/trunk/images/entity-granularity.svg
EntityRelationship/trunk/sources/usermanual.tex
Added: EntityRelationship/trunk/examples/ex-interaction-influences.eps
===================================================================
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+++ EntityRelationship/trunk/examples/ex-interaction-influences.eps 2014-08-14 07:21:23 UTC (rev 874)
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[truncated message content] |
|
From: <stu...@us...> - 2014-08-12 22:03:13
|
Revision: 873
http://sourceforge.net/p/sbgn/code/873
Author: stumoodie
Date: 2014-08-12 22:02:58 +0000 (Tue, 12 Aug 2014)
Log Message:
-----------
This is a draft version for review.
Modified Paths:
--------------
ProcessDiagram/tags/L1V2DraftForReview1/UserManual/sbgn_PD-level1-user.pdf
Added Paths:
-----------
ProcessDiagram/tags/L1V2DraftForReview1/
ProcessDiagram/tags/L1V2DraftForReview1/Specification/
ProcessDiagram/tags/L1V2DraftForReview1/Specification/images/Fig12.png
ProcessDiagram/tags/L1V2DraftForReview1/Specification/images/Fig12.sbgn
ProcessDiagram/tags/L1V2DraftForReview1/Specification/images/Fig13.png
ProcessDiagram/tags/L1V2DraftForReview1/Specification/images/Fig13.sbgn
ProcessDiagram/tags/L1V2DraftForReview1/Specification/images/Fig14.png
ProcessDiagram/tags/L1V2DraftForReview1/Specification/images/Fig14.sbgn
ProcessDiagram/tags/L1V2DraftForReview1/Specification/images/Fig15.png
ProcessDiagram/tags/L1V2DraftForReview1/Specification/images/Fig15.sbgn
ProcessDiagram/tags/L1V2DraftForReview1/Specification/images/simpleChemical.svg
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sbgn_PD-level1.pdf
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sbgn_PD-level1.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/concepts.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/front-page.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/glyphs.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/introduction.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/latex-macros.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/validation.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/worked_examples.tex
ProcessDiagram/tags/L1V2DraftForReview1/UserManual/sbgn_PD-level1-user.bbl
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ProcessDiagram/tags/L1V2DraftForReview1/Specification/
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ProcessDiagram/tags/L1V2DraftForReview1/Specification/sbgn_PD-level1.pdf
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sbgn_PD-level1.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/concepts.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/front-page.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/glyphs.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/introduction.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/latex-macros.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/validation.tex
ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/worked_examples.tex
ProcessDiagram/tags/L1V2DraftForReview1/UserManual/sbgn_PD-level1-user.bbl
ProcessDiagram/tags/L1V2DraftForReview1/sources/
Index: ProcessDiagram/tags/L1V2DraftForReview1
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Copied: ProcessDiagram/tags/L1V2DraftForReview1/Specification/sbgn_PD-level1.pdf (from rev 872, ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf)
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Deleted: ProcessDiagram/tags/L1V2DraftForReview1/Specification/sbgn_PD-level1.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2014-02-05 21:58:18 UTC (rev 871)
+++ ProcessDiagram/tags/L1V2DraftForReview1/Specification/sbgn_PD-level1.tex 2014-08-12 22:02:58 UTC (rev 873)
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-% =============================================================================
-% $Id$
-% Top-level latex file for the SBGN Process Description specification document.
-%
-% $HeadURL$
-% =============================================================================
-
-\documentclass[a4paper,11pt,oneside]{memoir}
-\usepackage[utf8]{inputenc} % unicode support
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-\usepackage{array}
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-\usepackage{fourier}
-%\usepackage{layouts}
-
-\usepackage[pdftex]{graphicx}
-\DeclareGraphicsExtensions{.pdf,.png}
-
-
- \usepackage[pdftex]{hyperref}
-
-\usepackage{rotating}
-
-% Booktabs for sharp-looking \toprule, \midrule, \bottomrule in tables.
-
-\usepackage{booktabs}
-
-\pagestyle{ruled}
-\chapterstyle{madsen}
-\setsecheadstyle{\Large\bfseries\raggedright\sffamily}
-\setsubsecheadstyle{\large\bfseries\raggedright\sffamily}
-\setsubsubsecheadstyle{\bfseries\raggedright\sffamily}
-\setparaheadstyle{\bfseries\raggedright}
-\setsubparaheadstyle{\bfseries\itshape\raggedright}
-\setsubparaindent{0cm}
-
-
-%% ----------------------------------------------------------------------------
-%% Layout customizations and macro definitions.
-%% ----------------------------------------------------------------------------
-
-%\input{sources/latex-style}
-\input{sources/latex-macros}
-
-
-%% ----------------------------------------------------------------------------
-\begin{document}
-%% ----------------------------------------------------------------------------
-
-\frontmatter
-
-\input{sources/front-page}
-%\input{sources/toc}
-
-\tableofcontents
-
-\mainmatter
-\linenumbers
-
-\part{SBGN Primer}
-
-\include{sources/introduction}
-\include{sources/concepts}
-\include{sources/language_overview}
-%\include{sources/primer}
-
-\include{sources/worked_examples}
-
-\part{Technical Reference}
-\label{part:techref}
-
-\include{sources/glyphs}
-\include{sources/layout}
-
-
-\include{sources/acknowledgments}
-
-\appendix
-
-\include{sources/examples}
-\include{sources/refcard}
-\include{sources/validation}
-\include{sources/working}
-\include{sources/revision_history}
-
-\backmatter
-
-\clearpage
-\bibliographystyle{unsrt}
-\bibliography{sbgn_PD-level1}
-
-
-%% ----------------------------------------------------------------------------
-\end{document}
-%% ----------------------------------------------------------------------------
-
-
-% The following is for [X]Emacs users. Please leave in place.
-% Local Variables:
-% TeX-master: t
-% End:
Copied: ProcessDiagram/tags/L1V2DraftForReview1/Specification/sbgn_PD-level1.tex (from rev 872, ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex)
===================================================================
--- ProcessDiagram/tags/L1V2DraftForReview1/Specification/sbgn_PD-level1.tex (rev 0)
+++ ProcessDiagram/tags/L1V2DraftForReview1/Specification/sbgn_PD-level1.tex 2014-08-12 22:02:58 UTC (rev 873)
@@ -0,0 +1,122 @@
+% =============================================================================
+% $Id$
+% Top-level latex file for the SBGN Process Description specification document.
+%
+% $HeadURL$
+% =============================================================================
+
+\documentclass[a4paper,12pt,oneside]{memoir}
+\usepackage[utf8]{inputenc} % unicode support
+\RequirePackage[T1]{fontenc}
+\RequirePackage{pifont}
+\RequirePackage{times}
+\usepackage[pdftex,rgb,usenames,svgnames,table]{xcolor}
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+\usepackage{supertabular}
+\usepackage{multirow}
+\usepackage{multicol}
+\usepackage{enumitem}
+\usepackage{lscape}
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+\usepackage{array}
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+\usepackage{xspace}
+\usepackage{float}
+\usepackage{framed}
+\usepackage[left=2cm,right=2cm,top=2.5cm,bottom=2cm]{geometry}
+\usepackage{eso-pic}
+\usepackage{ifthen}
+%\usepackage[american]{varioref}
+\usepackage[normalem]{ulem}
+\usepackage[right,pagewise,modulo]{lineno}
+\usepackage[olditem,oldenum]{paralist}
+\usepackage{fourier}
+%\usepackage{layouts}
+
+\usepackage[pdftex]{graphicx}
+\DeclareGraphicsExtensions{.pdf,.png}
+
+
+ \usepackage[pdftex]{hyperref}
+
+\usepackage{rotating}
+
+% Booktabs for sharp-looking \toprule, \midrule, \bottomrule in tables.
+
+\usepackage{booktabs}
+
+\pagestyle{ruled}
+\chapterstyle{madsen}
+\setsecheadstyle{\Large\bfseries\raggedright\sffamily}
+\setsubsecheadstyle{\large\bfseries\raggedright\sffamily}
+\setsubsubsecheadstyle{\bfseries\raggedright\sffamily}
+\setparaheadstyle{\bfseries\raggedright}
+\setsubparaheadstyle{\bfseries\itshape\raggedright}
+\setsubparaindent{0cm}
+
+\setsecnumdepth{subsection}
+
+%% ----------------------------------------------------------------------------
+%% Layout customizations and macro definitions.
+%% ----------------------------------------------------------------------------
+
+%\input{sources/latex-style}
+\input{sources/latex-macros}
+
+
+%% ----------------------------------------------------------------------------
+\begin{document}
+%% ----------------------------------------------------------------------------
+
+\frontmatter
+
+\input{sources/front-page}
+%\input{sources/toc}
+
+\tableofcontents
+
+\mainmatter
+\linenumbers
+
+%\part{SBGN Primer}
+
+\include{sources/introduction}
+\include{sources/concepts}
+%\include{sources/language_overview}
+%\include{sources/primer}
+
+%\include{sources/worked_examples}
+
+%\part{Technical Reference}
+%\label{part:techref}
+
+\include{sources/glyphs}
+\include{sources/layout}
+
+
+\include{sources/acknowledgments}
+
+\appendix
+
+\include{sources/examples}
+\include{sources/refcard}
+\include{sources/validation}
+\include{sources/working}
+\include{sources/revision_history}
+
+\backmatter
+
+\clearpage
+\bibliographystyle{unsrt}
+\bibliography{sbgn_PD-level1}
+
+
+%% ----------------------------------------------------------------------------
+\end{document}
+%% ----------------------------------------------------------------------------
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: t
+% End:
Deleted: ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/concepts.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/concepts.tex 2014-02-05 21:58:18 UTC (rev 871)
+++ ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/concepts.tex 2014-08-12 22:02:58 UTC (rev 873)
@@ -1,107 +0,0 @@
-\chapter{Concepts}
-\label{chp:concepts}
-
-\section{Overview of SBGN \PDs}
-\label{sec:PD-overview}
-
-To briefly describe what SBGN \PDl is about, let's give a brief overview of some of the relevant concepts with the help of an example shown in \fig{eg1}. It is a simple map for part of a mitogen-activated protein kinase (MAPK) cascade. The larger nodes in the figure (some of which are in the shape of rounded rectangles and others in the shape of circles) represent biological materials---things like macromolecules and simple chemicals (NB: the nodes representing physical entities (or proxies to physical entities) will always be colored in yellow in this document. Color is not part of the SBGN specification though).
-% [!] yellow is not just for EPNs, it is also occasionally used for glyphs such as stoichiometry labels, modulation arrowheads, compartments, logical operators and units of information (when introducing these glyphs). Is the explanation on colors clear enough? (e.g. also the fact they are not part of the specs, but still allowed?). Should this explanation be expanded a bit in a short paragraph of its own? Or at least a different sentence? I did find the parenthesis a bit distracting the first time I read this paragraph.
-The biological materials are altered via processes (colored in green in this document), which are indicated in \PDl by lines with arrows and other decorations. In this particular map, all of the processes happen to be the same: processes catalyzed by biochemical entities.
-The directions of the arrows indicate the direction of the processes; for example, unphosphorylated RAF kinase proceeds to phosphorylated RAF kinase via a process catalyzed by RAS. Although ATP and ADP are shown as incidental to the phosphorylations on this particular graph, they are involved in the same process as the proteins getting
-phosphorylated. The small circles on the nodes for RAF and other entity pools represent state variables (in this case, phosphorylation sites).
-
-% Redo the figure with colors
-\begin{figure}[htb]
- \centering
- \vspace*{-0.75em}
- \includegraphics[scale=0.8]{images/MAPK-only}
- \caption{This example of a \PD uses two kinds of entity pool nodes: one for pools of different macromolecules (\sect{macromolecule}) and another for pools of simple chemicals (\sect{simpleChemical}). Most macromolecule nodes in this map are adorned with state variables (\sect{stateVariable}) representing phosphorylation states. This map uses one type of process node, the process node (\sect{process}), and three kind of connecting arc, consumption (\sect{consumption}), production (\sect{production}) and catalysis (\sect{catalysis}). Finally, some entity pool nodes have dark bands along their bottoms; these are clone markers (\sect{cloneMarker}) indicating that the same pool nodes appear multiple times in the map.}
- \label{fig:eg1}
-\end{figure}
-
-The essence of the \PDs is \emph{change}: it shows how different entities in the system process from one form to another. The entities themselves can be many different things. In the example of \fig{eg1}, they are either pools of macromolecules or pools of simple chemicals, but as will become clear later in this chapter, they can be other conceptual and material constructs as well. Note also that we speak of \emph{entity pools} rather than individuals; this is because in biochemical network models, one does not focus on single molecules, but rather collections of molecules of the same kind. The molecules in a given pool are considered indistinguishable from each other. The way in which one type of entity is transformed into another is conveyed by a \emph{process node} and arcs between entity pool nodes and process nodes indicate an influence by the entities on the processes. In the case of \fig{eg1}, those arcs describe consumption (\sect{consumption}), production (\sect{production}) and catalysis
-(\sect{catalysis}), but others are possible. Finally, nodes in \PDs are usually not repeated; if they do need to be repeated, they are marked with \emph{clone markers}---specific modifications to the appearance of the node (\sect{cloneMarker}). The details of this and other aspects of \PD notation are explained in the rest of this chapter.
-
-A reference card depicting all the symbols of \SBGNPDLone is present at the end of this document.
-
-Lets look at a few additional examples which show typical biological processes and their SBGN \PD representation. In \fig{eg2} a reversible reaction with two substrates and one product is shown. The enzyme E catalyzes an irreversible (metabolic) process which consumes two substrates (S1 and S2) and produces one product (P1). The enzyme is a protein, therefore represented as a \emph{macromolecule}. Substrates and product of the biochemical reaction are represented by \emph{simple chemicals}. The consumption of S1 and S2 is represented by the \emph{consumption arcs}. The \emph{production arc} represents the synthesis of P1.
-
-In \fig{eg3} the formation of a complex is shown. Two \emph{macromolecule} entities X and Y form the \emph{complex} X\underline{ }Y. Complex formation is represented using the \emph{association} process node with ingoing \emph{consumption} and outgoing \emph{production} arcs. The \emph{complex} glyph surrounds subunits X and Y.
-
-\begin{figure}[htb]
- \centering
- \vspace*{-0.75em}
- \includegraphics[scale=0.5]{images/Fig12}
- \caption{This example of a \PD shows an irreversible catalysis with 2 substrates and 1 products.}
- \label{fig:eg2}
-\end{figure}
-
-\begin{figure}[htb]
- \centering
- \vspace*{-0.75em}
- \includegraphics[scale=0.5]{images/Fig13}
- \caption{This example of a \PD shows an irreversible catalysis with 2 substrates and 1 products.}
- \label{fig:eg3}
-\end{figure}
-
-In \fig{eg4} the regulation of a target gene by a transcription factor without knowledge about the promoter binding is shown. A transcription factor (TF) protein together with a target gene promoter X triggers the\emph{process} of transcription. Direct binding of the TF to the target gene promoter has not been experimentally verified, therefore the \emph{logical operator} AND is used to describe the yet unspecified interaction between TF and target gene. The TF protein is a \emph{macromolecule} of the \emph{material type} 'protein' (mt:prot) whereas the gene promoter is given as a \emph{nucleic acid feature} with the \emph{conceptual type} 'gene' (ct:gene). The connecting arc \emph{necessary stimulation} is applied to indicate that the stimulation by both regulator and target is necessary for the transcription process to take place. The target gene messenger as a product of the transcription process is represented by a \emph{nucleic acid feature} with the \emph{conceptual type} 'mRNA' (ct:mRNA). The \emph{unspecified source} symbol is used to represent the large number of substrates of a transcription process (i.e. trinucleotides).
-
-A last example is show in \fig{eg5}, which shows passive transport or diffusion of a molecule. The \emph{macromolecule} X in the cytosol serves as the substrate of a process leading to the production of the \emph{macromolecule} X in the nucleus. This process describes the passive transport of X from one \emph{compartment} to the other. The two macromolecules X do not carry the clone marker because the containing compartment is part of their identity.
-
-More examples can be found in a list of so called SBGN bricks~\cite{Junker:2012}, which are building blocks representing basic biological patterns. These bricks can be used for assembly into different kinds of biological networks such as metabolic and regulatory networks.
-
-\begin{figure}[htb]
- \centering
- \vspace*{-0.75em}
- \includegraphics[scale=0.5]{images/Fig14}
- \caption{This example of a \PD shows a regulation of a target gene by a transcription factor without knowledge about the promoter binding.}
- \label{fig:eg4}
-\end{figure}
-
-
-\begin{figure}[htb]
- \centering
- \vspace*{-0.75em}
- \includegraphics[scale=0.5]{images/Fig15}
- \caption{This example of a \PD shows a passive transport of a molecule.}
- \label{fig:eg5}
-\end{figure}
-
-\section{Some more concept text}
-
-\SBGNPDLone is a visual language. Like any language like English it has a vocabulary, which in the case of SBGN is represented by the symbols that we call glyphs. Again like English our language has grammar, which are the underlying rules and concepts of the language that define its meaning. This specification aims to provide a detailed description of both the vocabulary and grammar rules of the language as a reference. However, to understand this it is essential to grasp what an \PDm describes.
-
-The first thing to understand is the SBGN-PD does not describe biochemical reactions or gene expression --- at least not directly. Instead this language describes collections --- pools --- of entities that are manipulated by processes which can convert them from one type of entity to another. An entity pool that is the input to a process is said to consumed and that which is an output is produced. There is a third class of entity pool associated with a process: namely those that affect --- modulate --- the rate at which a process converts entity from one set of pools to another. The amount of entity in a modulating pools is not changed by the process. These very briefly are the key concepts of PD and are illustrated in figure \ref{fig:keyconcepts}.
-
-\begin{figure}[htb]
-\begin{center}
-\scalebox{0.5}{\includegraphics{images/keyconcepts}}
-\caption{A process consuming the entity pools A and B and producing the entity pools C and D. The entity pool E modulates the process. The process is represented as a square. Each (unspecified) entity pool is represented as an ellipsis identified by a label. The relationships between the process and each entity pool involved are represented by connecting lines called arcs. Depending on the type of relationship (consumption, production, modulation), these arcs are decorated with different symbols (respectively nothing, arrowhead, and diamond).}\label{fig:keyconcepts}
-\end{center}
-\end{figure}
-
-So how do this enable us to describe biological processes? Very simply. Figure \ref{fig:biochem} illustrates a biochemical reaction and shows how the essential components of that reaction, substrate, product and enzyme catalyst are all conveniently described by the representation. Likewise in figure \ref{fig:genereg} we can see again the concept of entity pools and process flow can be applied to gene regulation. This approach gives us a lot of flexibility and enables one to summarise biological processes that may incorporate many biochemical reactions (figure \ref{fig:summarisingproc}).
-
-
-%%% Diff EPN & Process types here.
-
-In the above examples of biological processes a number of different glyphs where used to illustrate different biological entities: the macromolecule, the simple chemical and the gene.
-
-
-%%% Compartments.
-
-
-%%% Clone markers and identity
-
-%%% Logic gates
-
-%%% Maps & Submaps
-
-
-%%%Overview of the UML/Class specification.
-
-\subsection{Graph, diagram or map?}
-
-A graph is a very technical term that belongs to mathematics and is uncommon in biology. Diagram is a concept that encompasses more than just graph. Examples are Venn diagrams for instance. Therefore, we recommend using the term map for SBGN representations. Those representations effectively permit users to travel and orient themselves in a biological system. Map is also the term most frequently used by the different communities, whether in metabolism, signaling or genomics.
-
-
Copied: ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/concepts.tex (from rev 872, ProcessDiagram/trunk/Specification/sources/concepts.tex)
===================================================================
--- ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/concepts.tex (rev 0)
+++ ProcessDiagram/tags/L1V2DraftForReview1/Specification/sources/concepts.tex 2014-08-12 22:02:58 UTC (rev 873)
@@ -0,0 +1,107 @@
+\chapter{Language Overview}
+\label{chp:concepts}
+
+% \section{Overview of SBGN \PDs}
+\label{sec:PD-overview}
+
+ To briefly describe what SBGN \PDl is about, let's give a brief overview of some of the relevant concepts with the help of an example shown in \fig{eg1}. It is a simple map for part of a mitogen-activated protein kinase (MAPK) cascade. The larger nodes in the figure (some of which are in the shape of rounded rectangles and others in the shape of circles) represent biological materials---things like macromolecules and simple chemicals (NB: the nodes representing physical entities (or proxies to physical entities) will always be colored in yellow in this document. Color is not part of the SBGN specification though).
+% % [!] yellow is not just for EPNs, it is also occasionally used for glyphs such as stoichiometry labels, modulation arrowheads, compartments, logical operators and units of information (when introducing these glyphs). Is the explanation on colors clear enough? (e.g. also the fact they are not part of the specs, but still allowed?). Should this explanation be expanded a bit in a short paragraph of its own? Or at least a different sentence? I did find the parenthesis a bit distracting the first time I read this paragraph.
+ The biological materials are altered via processes (colored in green in this document), which are indicated in \PDl by lines with arrows and other decorations. In this particular map, all of the processes happen to be the same: processes catalyzed by biochemical entities.
+ The directions of the arrows indicate the direction of the processes; for example, unphosphorylated RAF kinase proceeds to phosphorylated RAF kinase via a process catalyzed by RAS. Although ATP and ADP are shown as incidental to the phosphorylations on this particular graph, they are involved in the same process as the proteins getting
+ phosphorylated. The small circles on the nodes for RAF and other entity pools represent state variables (in this case, phosphorylation sites).
+
+% Redo the figure with colors
+\begin{figure}[htb]
+ \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.}
+ \label{fig:eg1}
+\end{figure}
+
+The essence of the \PDs is \emph{change}: it shows how different entities in the system process from one form to another. The entities themselves can be many different things. In the example of \fig{eg1}, they are either pools of macromolecules or pools of simple chemicals, but as will become clear later in this chapter, they can be other conceptual and material constructs as well. Note also that we speak of \emph{entity pools} rather than individuals; this is because in biochemical network models, one does not focus on single molecules, but rather collections of molecules of the same kind. The molecules in a given pool are considered indistinguishable from each other. The way in which one type of entity is transformed into another is conveyed by a \emph{process node} and arcs between entity pool nodes and process nodes indicate an influence by the entities on the processes. In the case of \fig{eg1}, those arcs describe consumption (\sect{techref:consumption}), production (\sect{techref:production}) and catalysis
+(\sect{techref:catalysis}), but others are possible. Finally, nodes in \PDs are usually not repeated; if they do need to be repeated, they are marked with \emph{clone markers}---specific modifications to the appearance of the node (\sect{techref:cloneMarker}). The details of this and other aspects of \PD notation are explained in the rest of this chapter.
+
+A reference card depicting all the symbols of \SBGNPDLone is present at the end of this document.
+
+Lets look at a few additional examples which show typical biological processes and their SBGN \PD representation. In \fig{eg2} a reversible reaction with two substrates and one product is shown. The enzyme E catalyzes an irreversible (metabolic) process which consumes two substrates (S1 and S2) and produces one product (P1). The enzyme is a protein, therefore represented as a \emph{macromolecule}. Substrates and product of the biochemical reaction are represen...
[truncated message content] |
|
From: <stu...@us...> - 2014-08-12 21:59:18
|
Revision: 872
http://sourceforge.net/p/sbgn/code/872
Author: stumoodie
Date: 2014-08-12 21:59:05 +0000 (Tue, 12 Aug 2014)
Log Message:
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Revised and improved text based on Tobias comments. Removed the worked examples for the moment and much of the user manual. This will be separated from the rest of the spec for the moment.
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ProcessDiagram/trunk/Specification/sources/concepts.tex
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Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2014-02-05 21:58:18 UTC (rev 871)
+++ ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2014-08-12 21:59:05 UTC (rev 872)
@@ -5,7 +5,7 @@
% $HeadURL$
% =============================================================================
-\documentclass[a4paper,11pt,oneside]{memoir}
+\documentclass[a4paper,12pt,oneside]{memoir}
\usepackage[utf8]{inputenc} % unicode support
\RequirePackage[T1]{fontenc}
\RequirePackage{pifont}
@@ -23,6 +23,7 @@
\usepackage{xspace}
\usepackage{float}
\usepackage{framed}
+\usepackage[left=2cm,right=2cm,top=2.5cm,bottom=2cm]{geometry}
\usepackage{eso-pic}
\usepackage{ifthen}
%\usepackage[american]{varioref}
@@ -53,6 +54,7 @@
\setsubparaheadstyle{\bfseries\itshape\raggedright}
\setsubparaindent{0cm}
+\setsecnumdepth{subsection}
%% ----------------------------------------------------------------------------
%% Layout customizations and macro definitions.
@@ -76,17 +78,17 @@
\mainmatter
\linenumbers
-\part{SBGN Primer}
+%\part{SBGN Primer}
\include{sources/introduction}
\include{sources/concepts}
-\include{sources/language_overview}
+%\include{sources/language_overview}
%\include{sources/primer}
-\include{sources/worked_examples}
+%\include{sources/worked_examples}
-\part{Technical Reference}
-\label{part:techref}
+%\part{Technical Reference}
+%\label{part:techref}
\include{sources/glyphs}
\include{sources/layout}
Modified: ProcessDiagram/trunk/Specification/sources/concepts.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/concepts.tex 2014-02-05 21:58:18 UTC (rev 871)
+++ ProcessDiagram/trunk/Specification/sources/concepts.tex 2014-08-12 21:59:05 UTC (rev 872)
@@ -1,26 +1,26 @@
-\chapter{Concepts}
+\chapter{Language Overview}
\label{chp:concepts}
-\section{Overview of SBGN \PDs}
+% \section{Overview of SBGN \PDs}
\label{sec:PD-overview}
-To briefly describe what SBGN \PDl is about, let's give a brief overview of some of the relevant concepts with the help of an example shown in \fig{eg1}. It is a simple map for part of a mitogen-activated protein kinase (MAPK) cascade. The larger nodes in the figure (some of which are in the shape of rounded rectangles and others in the shape of circles) represent biological materials---things like macromolecules and simple chemicals (NB: the nodes representing physical entities (or proxies to physical entities) will always be colored in yellow in this document. Color is not part of the SBGN specification though).
-% [!] yellow is not just for EPNs, it is also occasionally used for glyphs such as stoichiometry labels, modulation arrowheads, compartments, logical operators and units of information (when introducing these glyphs). Is the explanation on colors clear enough? (e.g. also the fact they are not part of the specs, but still allowed?). Should this explanation be expanded a bit in a short paragraph of its own? Or at least a different sentence? I did find the parenthesis a bit distracting the first time I read this paragraph.
-The biological materials are altered via processes (colored in green in this document), which are indicated in \PDl by lines with arrows and other decorations. In this particular map, all of the processes happen to be the same: processes catalyzed by biochemical entities.
-The directions of the arrows indicate the direction of the processes; for example, unphosphorylated RAF kinase proceeds to phosphorylated RAF kinase via a process catalyzed by RAS. Although ATP and ADP are shown as incidental to the phosphorylations on this particular graph, they are involved in the same process as the proteins getting
-phosphorylated. The small circles on the nodes for RAF and other entity pools represent state variables (in this case, phosphorylation sites).
+ To briefly describe what SBGN \PDl is about, let's give a brief overview of some of the relevant concepts with the help of an example shown in \fig{eg1}. It is a simple map for part of a mitogen-activated protein kinase (MAPK) cascade. The larger nodes in the figure (some of which are in the shape of rounded rectangles and others in the shape of circles) represent biological materials---things like macromolecules and simple chemicals (NB: the nodes representing physical entities (or proxies to physical entities) will always be colored in yellow in this document. Color is not part of the SBGN specification though).
+% % [!] yellow is not just for EPNs, it is also occasionally used for glyphs such as stoichiometry labels, modulation arrowheads, compartments, logical operators and units of information (when introducing these glyphs). Is the explanation on colors clear enough? (e.g. also the fact they are not part of the specs, but still allowed?). Should this explanation be expanded a bit in a short paragraph of its own? Or at least a different sentence? I did find the parenthesis a bit distracting the first time I read this paragraph.
+ The biological materials are altered via processes (colored in green in this document), which are indicated in \PDl by lines with arrows and other decorations. In this particular map, all of the processes happen to be the same: processes catalyzed by biochemical entities.
+ The directions of the arrows indicate the direction of the processes; for example, unphosphorylated RAF kinase proceeds to phosphorylated RAF kinase via a process catalyzed by RAS. Although ATP and ADP are shown as incidental to the phosphorylations on this particular graph, they are involved in the same process as the proteins getting
+ phosphorylated. The small circles on the nodes for RAF and other entity pools represent state variables (in this case, phosphorylation sites).
% Redo the figure with colors
\begin{figure}[htb]
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.8]{images/MAPK-only}
- \caption{This example of a \PD uses two kinds of entity pool nodes: one for pools of different macromolecules (\sect{macromolecule}) and another for pools of simple chemicals (\sect{simpleChemical}). Most macromolecule nodes in this map are adorned with state variables (\sect{stateVariable}) representing phosphorylation states. This map uses one type of process node, the process node (\sect{process}), and three kind of connecting arc, consumption (\sect{consumption}), production (\sect{production}) and catalysis (\sect{catalysis}). Finally, some entity pool nodes have dark bands along their bottoms; these are clone markers (\sect{cloneMarker}) indicating that the same pool nodes appear multiple times in the map.}
+ \caption{This example of a \PD uses two kinds of entity pool nodes: one for pools of different macromolecules (\sect{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.}
\label{fig:eg1}
\end{figure}
-The essence of the \PDs is \emph{change}: it shows how different entities in the system process from one form to another. The entities themselves can be many different things. In the example of \fig{eg1}, they are either pools of macromolecules or pools of simple chemicals, but as will become clear later in this chapter, they can be other conceptual and material constructs as well. Note also that we speak of \emph{entity pools} rather than individuals; this is because in biochemical network models, one does not focus on single molecules, but rather collections of molecules of the same kind. The molecules in a given pool are considered indistinguishable from each other. The way in which one type of entity is transformed into another is conveyed by a \emph{process node} and arcs between entity pool nodes and process nodes indicate an influence by the entities on the processes. In the case of \fig{eg1}, those arcs describe consumption (\sect{consumption}), production (\sect{production}) and catalysis
-(\sect{catalysis}), but others are possible. Finally, nodes in \PDs are usually not repeated; if they do need to be repeated, they are marked with \emph{clone markers}---specific modifications to the appearance of the node (\sect{cloneMarker}). The details of this and other aspects of \PD notation are explained in the rest of this chapter.
+The essence of the \PDs is \emph{change}: it shows how different entities in the system process from one form to another. The entities themselves can be many different things. In the example of \fig{eg1}, they are either pools of macromolecules or pools of simple chemicals, but as will become clear later in this chapter, they can be other conceptual and material constructs as well. Note also that we speak of \emph{entity pools} rather than individuals; this is because in biochemical network models, one does not focus on single molecules, but rather collections of molecules of the same kind. The molecules in a given pool are considered indistinguishable from each other. The way in which one type of entity is transformed into another is conveyed by a \emph{process node} and arcs between entity pool nodes and process nodes indicate an influence by the entities on the processes. In the case of \fig{eg1}, those arcs describe consumption (\sect{techref:consumption}), production (\sect{techref:production}) and catalysis
+(\sect{techref:catalysis}), but others are possible. Finally, nodes in \PDs are usually not repeated; if they do need to be repeated, they are marked with \emph{clone markers}---specific modifications to the appearance of the node (\sect{techref:cloneMarker}). The details of this and other aspects of \PD notation are explained in the rest of this chapter.
A reference card depicting all the symbols of \SBGNPDLone is present at the end of this document.
@@ -67,20 +67,20 @@
\label{fig:eg5}
\end{figure}
-\section{Some more concept text}
+%\section{Some more concept text}
-\SBGNPDLone is a visual language. Like any language like English it has a vocabulary, which in the case of SBGN is represented by the symbols that we call glyphs. Again like English our language has grammar, which are the underlying rules and concepts of the language that define its meaning. This specification aims to provide a detailed description of both the vocabulary and grammar rules of the language as a reference. However, to understand this it is essential to grasp what an \PDm describes.
+% \SBGNPDLone is a visual language. Like any language like English it has a vocabulary, which in the case of SBGN is represented by the symbols that we call glyphs. Again like English our language has grammar, which are the underlying rules and concepts of the language that define its meaning. This specification aims to provide a detailed description of both the vocabulary and grammar rules of the language as a reference. However, to understand this it is essential to grasp what an \PDm describes.
-The first thing to understand is the SBGN-PD does not describe biochemical reactions or gene expression --- at least not directly. Instead this language describes collections --- pools --- of entities that are manipulated by processes which can convert them from one type of entity to another. An entity pool that is the input to a process is said to consumed and that which is an output is produced. There is a third class of entity pool associated with a process: namely those that affect --- modulate --- the rate at which a process converts entity from one set of pools to another. The amount of entity in a modulating pools is not changed by the process. These very briefly are the key concepts of PD and are illustrated in figure \ref{fig:keyconcepts}.
+% The first thing to understand is the SBGN-PD does not describe biochemical reactions or gene expression --- at least not directly. Instead this language describes collections --- pools --- of entities that are manipulated by processes which can convert them from one type of entity to another. An entity pool that is the input to a process is said to consumed and that which is an output is produced. There is a third class of entity pool associated with a process: namely those that affect --- modulate --- the rate at which a process converts entity from one set of pools to another. The amount of entity in a modulating pools is not changed by the process. These very briefly are the key concepts of PD and are illustrated in figure \ref{fig:keyconcepts}.
-\begin{figure}[htb]
-\begin{center}
-\scalebox{0.5}{\includegraphics{images/keyconcepts}}
-\caption{A process consuming the entity pools A and B and producing the entity pools C and D. The entity pool E modulates the process. The process is represented as a square. Each (unspecified) entity pool is represented as an ellipsis identified by a label. The relationships between the process and each entity pool involved are represented by connecting lines called arcs. Depending on the type of relationship (consumption, production, modulation), these arcs are decorated with different symbols (respectively nothing, arrowhead, and diamond).}\label{fig:keyconcepts}
-\end{center}
-\end{figure}
+% \begin{figure}[htb]
+% \begin{center}
+% \scalebox{0.5}{\includegraphics{images/keyconcepts}}
+% \caption{A process consuming the entity pools A and B and producing the entity pools C and D. The entity pool E modulates the process. The process is represented as a square. Each (unspecified) entity pool is represented as an ellipsis identified by a label. The relationships between the process and each entity pool involved are represented by connecting lines called arcs. Depending on the type of relationship (consumption, production, modulation), these arcs are decorated with different symbols (respectively nothing, arrowhead, and diamond).}\label{fig:keyconcepts}
+% \end{center}
+% \end{figure}
-So how do this enable us to describe biological processes? Very simply. Figure \ref{fig:biochem} illustrates a biochemical reaction and shows how the essential components of that reaction, substrate, product and enzyme catalyst are all conveniently described by the representation. Likewise in figure \ref{fig:genereg} we can see again the concept of entity pools and process flow can be applied to gene regulation. This approach gives us a lot of flexibility and enables one to summarise biological processes that may incorporate many biochemical reactions (figure \ref{fig:summarisingproc}).
+% So how do this enable us to describe biological processes? Very simply. Figure \ref{fig:biochem} illustrates a biochemical reaction and shows how the essential components of that reaction, substrate, product and enzyme catalyst are all conveniently described by the representation. Likewise in figure \ref{fig:genereg} we can see again the concept of entity pools and process flow can be applied to gene regulation. This approach gives us a lot of flexibility and enables one to summarise biological processes that may incorporate many biochemical reactions (figure \ref{fig:summarisingproc}).
%%% Diff EPN & Process types here.
@@ -100,8 +100,8 @@
%%%Overview of the UML/Class specification.
-\subsection{Graph, diagram or map?}
+% \subsection{Graph, diagram or map?}
-A graph is a very technical term that belongs to mathematics and is uncommon in biology. Diagram is a concept that encompasses more than just graph. Examples are Venn diagrams for instance. Therefore, we recommend using the term map for SBGN representations. Those representations effectively permit users to travel and orient themselves in a biological system. Map is also the term most frequently used by the different communities, whether in metabolism, signaling or genomics.
+% A graph is a very technical term that belongs to mathematics and is uncommon in biology. Diagram is a concept that encompasses more than just graph. Examples are Venn diagrams for instance. Therefore, we recommend using the term map for SBGN representations. Those representations effectively permit users to travel and orient themselves in a biological system. Map is also the term most frequently used by the different communities, whether in metabolism, signaling or genomics.
Modified: ProcessDiagram/trunk/Specification/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/front-page.tex 2014-02-05 21:58:18 UTC (rev 871)
+++ ProcessDiagram/trunk/Specification/sources/front-page.tex 2014-08-12 21:59:05 UTC (rev 872)
@@ -37,11 +37,11 @@
\textbf{\sffamily Editors}:\\[7pt]
\begin{tabular}{l>{\hspace*{15pt}}r}
-Stuart Moodie & \emph{EMBL European Bioinformatics Institute, UK}\\
-Nicolas \lenov & \emph{EMBL European Bioinformatics Institute, UK}\\
-Emek Demir & \emph{Sloan-Kettering Institute, USA}\\
-Huaiyu Mi & \emph{University of Southern California, USA}\\
-Alice Vill\'{e}ger & \emph{Freelance IT Consultant, London, UK}\\
+Stuart Moodie & \emph{Eight Pillars Ltd, UK}\\
+Tobias Czauderna & \emph{IPK Gatersleben, Germany}\\
+Falk Schreiber & \emph{IPK Gatersleben \& MLU Halle, Germany}\\
+Anatoly Sorokin & \emph{Institute of Cell Biophysics RAS, Russia}\\
+Huaiyu Mi & \emph{University of Southern California, USA}\\
\end{tabular}
% \vspace*{1em}
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2014-02-05 21:58:18 UTC (rev 871)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2014-08-12 21:59:05 UTC (rev 872)
@@ -3,7 +3,7 @@
% $HeadURL$
-\chapter{Language Elements}
+\chapter{Language Specification}
\label{chp:glyphs}
@@ -20,31 +20,34 @@
language that has been used by tens of thousands of software
developers for over decade to describe and software system; and the
Systems Biology Markup Language (SBML) Level 3 Core specification
-\cite{sbmll3core} which is the ``original'' computational systems
-biological standard and after 10 years 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 description of
-the symbols used and guidelines about how the symbols should be drawn
-or laid out.
+\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 description 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
in this chapter:
\begin{itemize}
-\item The language will be described by a UML class model, a language
- element of language concept being represented as a class.
-\item Each class will be defined in detail. The definition will
- describe parent classes, attributes, interactions with other classes and any rules
- the apply to that class.
-\item Where classes correspond to glyphs, or where appropriate, a
-detailed description of the glyph will be given.
-\item Any rules or concepts that apply to the language as a whole are
- defined after the individual class definitions.
+\item The language will be described by a UML class model:
+ \begin{itemize}
+ \item each language element or concept being represented as a
+ class.
+ \item the syntax being represented 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
+ is described and appropriate illustrations provided.
\end{itemize}
\section{Note on typographical convention}
@@ -66,17 +69,15 @@
\section{How to read the Language Specification}
-Here will describe the elements of the class definitions that are the
-core of the language specification. Each definition starts with an
+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
associations and its interaction with other key classes to help
understand its context and any rules that are part of the
-definition.
-
-A number of terms are used within the specification that
-for clarity we define here:
+definition. In these descriptions we will use a number of terms for
+which it makes sense to provide a brief glossary here:
\begin{description}
\item[class] A class describes a set of objects that share the same
specifications of features, constraints, and semantics (from the UML
@@ -111,8 +112,8 @@
attribute. For example an attribute of type \sbgnclass{int} must have a
value that is a integer.
\end{description}
-
-
+%
+%
\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.9\textwidth]{images/exampleuml}
@@ -121,10 +122,9 @@
\label{fig:techref:umlexample}
\end{center}
\end{figure}
-
-The UML class diagrams used will look something like the examples in
-figure \ref{fig:techref:umlexample}. The UML elements in this diagram are the
-only ones used in this specification and again as an aid to
+%
+The UML class diagrams look like the examples in
+figure \ref{fig:techref:umlexample}. Again as an aid to
understanding their meanings are described below:
\begin{description}
\item[class] See above for definition. The class symbol displays each
@@ -152,7 +152,7 @@
other class adjacent to the arrow head (F) to satisfy its
specification or implementation.
\end{description}
-
+%
The specification uses a number of primitive types that are used in
attribute definitions. These are:
\begin{description}
@@ -166,56 +166,43 @@
\end{description}
-\subsection{An example definition}
+\subsection{Definition format}
-Here we will provide an example specification. In this section is an
-overview of the class and its concepts.
+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.
-\subsubsection{Generalisation}
-
-This section defines the inheritance relationship(s) between this
+\begin{description}
+\item[Generalisation] This section defines the inheritance relationship(s) between this
class and any other classes.
-
-\subsubsection{Attributes}
-
-Here any attributes specific to this class are defined and their
+\item[Attributes] Here any attributes specific to this class are defined and their
meaning or purpose described. Attributes from superclasses are part of
this classes definition but are not defined here explicitly.
-
-\subsubsection{Associations}
-
-Any associations are defined and described. Again associations from
-superclasses are not included here, but are part of this classes definition.
-
-\subsubsection{Notation}
-
-If the class corresponds to one or more glyphs then each glyph is
+\item[Associations] Any associations are defined and described. Again associations from
+superclasses are not included here, but are part of this classes
+definition.
+\item[Unique Key] The attributes that together uniquely identify the
+ \PD element or concept. If this is ommited then there is no unique
+ key. See section~\ref{sec:techref:uniquenessdefinition} for more
+ information about identity and uniqueness.
+\item[Ru...
[truncated message content] |
|
From: <stu...@us...> - 2014-02-05 21:58:24
|
Revision: 871
http://sourceforge.net/p/sbgn/code/871
Author: stumoodie
Date: 2014-02-05 21:58:18 +0000 (Wed, 05 Feb 2014)
Log Message:
-----------
fixed some issues, reorganised stuff and started worked examples.
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg
ProcessDiagram/trunk/Specification/images/sbgn_model_revised/45.session
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/worked_examples.tex
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bbl
Added Paths:
-----------
ProcessDiagram/trunk/Specification/worked_example_ideas/
ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contrib2.png
ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contribution.png
ProcessDiagram/trunk/Specification/worked_example_ideas/Wnt_signaling_pathway.pdf
ProcessDiagram/trunk/Specification/worked_example_ideas/example1_1.pdf
ProcessDiagram/trunk/Specification/worked_example_ideas/p53_pathway.pdf
ProcessDiagram/trunk/Specification/worked_example_ideas/smadModelSBGN.png
Removed Paths:
-------------
ProcessDiagram/trunk/sources/
Modified: ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg 2013-12-18 14:04:31 UTC (rev 870)
+++ ProcessDiagram/trunk/Specification/images/cloningrules-eg.svg 2014-02-05 21:58:18 UTC (rev 871)
@@ -13,7 +13,7 @@
height="748.77167"
id="svg2"
version="1.1"
- inkscape:version="0.48.2 r9819"
+ inkscape:version="0.48.4 r9939"
sodipodi:docname="cloningrules-eg.svg">
<defs
id="defs4">
@@ -79,16 +79,16 @@
borderopacity="1.0"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
- inkscape:zoom="0.91503662"
- inkscape:cx="310.42966"
+ inkscape:zoom="1.0780152"
+ inkscape:cx="1015.429"
inkscape:cy="594.67682"
inkscape:document-units="px"
inkscape:current-layer="g3801"
showgrid="false"
- inkscape:window-width="1744"
- inkscape:window-height="1152"
- inkscape:window-x="1768"
- inkscape:window-y="7"
+ inkscape:window-width="1280"
+ inkscape:window-height="707"
+ inkscape:window-x="0"
+ inkscape:window-y="0"
inkscape:window-maximized="0"
showguides="true"
inkscape:guide-bbox="true"
@@ -630,7 +630,7 @@
sodipodi:cy="445.86218"
sodipodi:rx="20.5"
sodipodi:ry="20.5"
- d="m 156.7299,442.54536 a 20.5,20.5 0 1 1 -0.002,-0.009"
+ d="m 156.7299,442.54536 c 1.83183,11.17266 -5.74041,21.71488 -16.91307,23.54672 -11.17267,1.83183 -21.71489,-5.74041 -23.54673,-16.91307 -1.83183,-11.17266 5.74041,-21.71489 16.91307,-23.54672 11.16909,-1.83125 21.70892,5.73565 23.54522,16.90391"
sodipodi:start="6.1206745"
sodipodi:end="12.403407"
sodipodi:open="true"
@@ -649,7 +649,7 @@
sodipodi:open="true"
sodipodi:end="12.403407"
sodipodi:start="6.1206745"
- d="m 616.33622,-25.643531 a 19.79899,19.79899 0 1 1 -0.001,-0.0088"
+ d="m 616.33622,-25.643531 c 1.76919,10.790607 -5.54411,20.972336 -16.33472,22.7415283 -10.7906,1.7691924 -20.97233,-5.544109 -22.74153,-16.3347153 -1.76919,-10.790607 5.54411,-20.972336 16.33472,-22.741528 10.78715,-1.768626 20.96656,5.539519 22.74007,16.325869"
sodipodi:ry="19.79899"
sodipodi:rx="19.79899"
sodipodi:cy="-22.440125"
@@ -662,7 +662,7 @@
sodipodi:open="true"
sodipodi:end="12.403407"
sodipodi:start="6.1206745"
- d="m 422.66353,-82.711029 a 14.142136,14.142136 0 1 1 -0.001,-0.0063"
+ d="m 422.66353,-82.711029 c 1.26371,7.707576 -3.96007,14.980239 -11.66765,16.243948 -7.70758,1.263709 -14.98024,-3.960078 -16.24395,-11.667654 -1.26371,-7.707576 3.96008,-14.980239 11.66766,-16.243948 7.7051,-1.263304 14.97611,3.956799 16.24291,11.661335"
sodipodi:ry="14.142136"
sodipodi:rx="14.142136"
sodipodi:cy="-80.422882"
@@ -672,7 +672,7 @@
sodipodi:type="arc" />
</g>
<g
- transform="matrix(0.89908128,0.43778175,-0.43778175,0.89908128,754.66443,-93.499644)"
+ transform="matrix(0.91728031,-0.39824218,0.39824218,0.91728031,496.11722,12.926638)"
id="g5385">
<rect
style="fill:none;stroke:#000000;stroke-width:1;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:30"
@@ -958,7 +958,7 @@
sodipodi:open="true"
sodipodi:end="12.403407"
sodipodi:start="6.1206745"
- d="m 156.7299,442.54536 a 20.5,20.5 0 1 1 -0.002,-0.009"
+ d="m 156.7299,442.54536 c 1.83183,11.17266 -5.74041,21.71488 -16.91307,23.54672 -11.17267,1.83183 -21.71489,-5.74041 -23.54673,-16.91307 -1.83183,-11.17266 5.74041,-21.71489 16.91307,-23.54672 11.16909,-1.83125 21.70892,5.73565 23.54522,16.90391"
sodipodi:ry="20.5"
sodipodi:rx="20.5"
sodipodi:cy="445.86218"
Modified: ProcessDiagram/trunk/Specification/images/sbgn_model_revised/45.session
===================================================================
--- ProcessDiagram/trunk/Specification/images/sbgn_model_revised/45.session 2013-12-18 14:04:31 UTC (rev 870)
+++ ProcessDiagram/trunk/Specification/images/sbgn_model_revised/45.session 2014-02-05 21:58:18 UTC (rev 871)
@@ -42,7 +42,7 @@
1279 1115 100 18 0 0
classdiagram_ref 161453 // SBGNArcsView
1833 1028 100 18 0 0
- active classdiagram_ref 208429 // EntityDefinitionView
+ classdiagram_ref 208429 // EntityDefinitionView
1279 1115 100 18 0 0
classdiagram_ref 214957 // SBGNNodeView
1026 908 100 18 0 0
@@ -50,11 +50,11 @@
1026 908 100 18 0 0
classdiagram_ref 188205 // StateVariableView
1026 908 100 18 0 0
- classdiagram_ref 134957 // EntityPoolNodeView
- 1026 908 100 14 0 0
+ active classdiagram_ref 134957 // EntityPoolNodeView
+ 1279 1115 100 14 0 0
end
show_stereotypes
-selected classdiagram_ref 208429 // EntityDefinitionView
+selected classdiagram_ref 134957 // EntityPoolNodeView
open
classdiagram_ref 134701 // MapView
class_ref 158637 // Phenotype
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sources/worked_examples.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/worked_examples.tex 2013-12-18 14:04:31 UTC (rev 870)
+++ ProcessDiagram/trunk/Specification/sources/worked_examples.tex 2014-02-05 21:58:18 UTC (rev 871)
@@ -1,3 +1,56 @@
\chapter{Worked Examples}
\label{chp:worked-egs}
+\begin{comment}
+
+\end{comment}
+
+
+\section{Introduction}
+
+\section{Example 1: Basic Metabolism}
+
+We will start off simply and show how \PD can be used to represent
+metabolism. The example (shown in figure \ref{fig:weg1}) shows a cycle
+in which acetyl-CoA is converted to 3-hydroxy-3-methylglutaryl-CoA and
+back again. The notation is pretty intuitive, but let's explain it in
+terms of SBGN. Acetyl-CoA (1) is represented using the small molecule
+(stadium) glyph as are all the other small molecules in the
+diagram. The name inside the glyph can be anything, but you should use
+a nomenclature that is widely understood by your readership --- the
+aim of SBGN is communication after all. The reaction (2) converting
+acetyl-CoA to acetoacetyl-CoA is indicated by the arrow bisected by
+the box. In reality this is three glyphs. The square is the process
+node glyph indicating that some process is occurring, the line on the
+left-hand-side is the consumption arc and the arrow out of the process
+node is the production arc. Together they state that there is a
+process which converts Acetyl A into Acetyl-CoA. Of course a reaction
+can be described by using just these elements, but in this example the
+reaction is catalysed by the enzyme ACAT1 (3). The enzyme is shown
+using the macromolecule symbol (rounded rectangle) and the catalysis
+by the catalysis arc (the circular arrowhead). We can see that the
+other reactions are catalysed also.
+
+\begin{figure}[htb]
+\includegraphics[width=\linewidth,clip,trim=5cm 12cm 5cm 12.5cm]{worked_example_ideas/example1_1}
+\caption{An excerpt of Acetyl CoA metabolism drawn in SBGN. The
+ correct interpretation is described in the text.}
+\label{fig:weg1}
+\end{figure}
+
+ Generally in SBGN, the exact nature of a process is not shown by the
+process node glyph, but is described by its interaction with other
+glyphs. Thus we can see that process (4) in the example takes
+acetyl-CoA and acetoacetyl-CoA as substrates and produces
+3-hydroxy-3-methylglutaryl-CoA in a reaction catalysed by HMGCS2.
+
+
+\section{Example 2: Cell Signalling}
+
+
+
+\section{Example 3: Transport}
+
+
+\section{Example 4: Events and Phenotypes}
+
Added: ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contrib2.png
===================================================================
(Binary files differ)
Index: ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contrib2.png
===================================================================
--- ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contrib2.png 2013-12-18 14:04:31 UTC (rev 870)
+++ ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contrib2.png 2014-02-05 21:58:18 UTC (rev 871)
Property changes on: ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contrib2.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+image/png
\ No newline at end of property
Added: ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contribution.png
===================================================================
(Binary files differ)
Index: ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contribution.png
===================================================================
--- ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contribution.png 2013-12-18 14:04:31 UTC (rev 870)
+++ ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contribution.png 2014-02-05 21:58:18 UTC (rev 871)
Property changes on: ProcessDiagram/trunk/Specification/worked_example_ideas/AM_contribution.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+image/png
\ No newline at end of property
Added: ProcessDiagram/trunk/Specification/worked_example_ideas/Wnt_signaling_pathway.pdf
===================================================================
(Binary files differ)
Index: ProcessDiagram/trunk/Specification/worked_example_ideas/Wnt_signaling_pathway.pdf
===================================================================
--- ProcessDiagram/trunk/Specification/worked_example_ideas/Wnt_signaling_pathway.pdf 2013-12-18 14:04:31 UTC (rev 870)
+++ ProcessDiagram/trunk/Specification/worked_example_ideas/Wnt_signaling_pathway.pdf 2014-02-05 21:58:18 UTC (rev 871)
Property changes on: ProcessDiagram/trunk/Specification/worked_example_ideas/Wnt_signaling_pathway.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/pdf
\ No newline at end of property
Added: ProcessDiagram/trunk/Specification/worked_example_ideas/example1_1.pdf
===================================================================
(Binary files differ)
Index: ProcessDiagram/trunk/Specification/worked_example_ideas/example1_1.pdf
===================================================================
--- ProcessDiagram/trunk/Specification/worked_example_ideas/example1_1.pdf 2013-12-18 14:04:31 UTC (rev 870)
+++ ProcessDiagram/trunk/Specification/worked_example_ideas/example1_1.pdf 2014-02-05 21:58:18 UTC (rev 871)
Property changes on: ProcessDiagram/trunk/Specification/worked_example_ideas/example1_1.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/pdf
\ No newline at end of property
Added: ProcessDiagram/trunk/Specification/worked_example_ideas/p53_pathway.pdf
===================================================================
(Binary files differ)
Index: ProcessDiagram/trunk/Specification/worked_example_ideas/p53_pathway.pdf
===================================================================
--- ProcessDiagram/trunk/Specification/worked_example_ideas/p53_pathway.pdf 2013-12-18 14:04:31 UTC (rev 870)
+++ ProcessDiagram/trunk/Specification/worked_example_ideas/p53_pathway.pdf 2014-02-05 21:58:18 UTC (rev 871)
Property changes on: ProcessDiagram/trunk/Specification/worked_example_ideas/p53_pathway.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/pdf
\ No newline at end of property
Added: ProcessDiagram/trunk/Specification/worked_example_ideas/smadModelSBGN.png
===================================================================
(Binary files differ)
Index: ProcessDiagram/trunk/Specification/worked_example_ideas/smadModelSBGN.png
===================================================================
--- ProcessDiagram/trunk/Specification/worked_example_ideas/smadModelSBGN.png 2013-12-18 14:04:31 UTC (rev 870)
+++ ProcessDiagram/trunk/Specification/worked_example_ideas/smadModelSBGN.png 2014-02-05 21:58:18 UTC (rev 871)
Property changes on: ProcessDiagram/trunk/Specification/worked_example_ideas/smadModelSBGN.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+image/png
\ No newline at end of property
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bbl
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bbl 2013-12-18 14:04:31 UTC (rev 870)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bbl 2014-02-05 21:58:18 UTC (rev 871)
@@ -1,50 +1,50 @@
-\begin{thebibliography}{1}
-
-\bibitem{LeNovere:2009p1}
-N~Le~Nov\`{e}re, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber,
- Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit~I Aladjem, M~Sarala
- Wimalaratne, Frank~T Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji,
- Lu~Li, Yukiko Matsuoka, Alice Villeger, Sarah~E Boyd, Laurence Calzone,
- M\'{e}lanie 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, and
- Hiroaki Kitano.
-\newblock The systems biology graphical notation.
-\newblock {\em Nat Biotechnol}, 27(8):735--741, 2009.
-\newblock 10.1038/nbt.1558.
-
-\bibitem{Moodie:2011}
-Stuart Moodie, Nicolas Le~Nov\`{e}re, Emek Demir, Huaiyu Mi, and Alice
- Vill\'{e}ger.
-\newblock Systems biology graphical notation: Process description language
- level 1.
-\newblock {\em Nature Precedings}, 2011.
-
-\bibitem{Junker:2012}
-Astrid Junker, Anatoly Sorokin, Tobias Czauderna, Falk Schreiber, and Alexander
- Mazein.
-\newblock Wiring diagrams in biology: towards the standardized representation
- of biological information.
-\newblock {\em Trends in Biotechnology}, 30(11):555--557, 2012.
-
-\bibitem{Courtot:2011}
-M.~Courtot, N.~Juty, C.~Kn{\"u}pfer, D.~Waltemath, A.~Zhukova, A.~Dr{\"a}ger,
- M.~Dumontier, A.~Finney, M.~Golebiewski, J.~Hastings, et~al.
-\newblock Controlled vocabularies and semantics in systems biology.
-\newblock {\em Molecular systems biology}, 7(1), 2011.
-
-\bibitem{Hucka:2003}
-M.~Hucka, A.~Finney, H.~M. Sauro, H.~Bolouri, J.~C. Doyle, H.~Kitano, A.~P.
- Arkin, B.~J. Bornstein, D.~Bray, A.~Cornish-Bowden, A.~A. Cuellar, S.~Dronov,
- E.~D. Gilles, M.~Ginkel, V.~Gor, I.~I. Goryanin, W.~J. Hedley, T.~C. Hodgman,
- J.-H. Hofmeyr, P.~J. Hunter, N.~S. Juty, J.~L. Kasberger, A.~Kremling,
- U.~Kummer, N.~Le~Nov\`{e}re, L.~M. Loew, D.~Lucio, P.~Mendes, E.~Minch, E.~D.
- Mjolsness, Y.~Nakayama, M.~R. Nelson, P.~F. Nielsen, T.~Sakurada, J.~C.
- Schaff, B.~E. Shapiro, T.~S. Shimizu, H.~D. Spence, J.~Stelling,
- K.~Takahashi, M.~Tomita, J.~Wagner, and J.~Wang.
-\newblock The {S}ystems {B}iology {M}arkup {L}anguage ({SBML}): A medium for
- representation and exchange of biochemical network models.
-\newblock {\em Bioinformatics}, 19(4):524--531, 2003.
-
-\end{thebibliography}
+\begin{thebibliography}{1}
+
+\bibitem{LeNovere:2009p1}
+N~Le~Nov\`{e}re, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber,
+ Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit~I Aladjem, M~Sarala
+ Wimalaratne, Frank~T Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji,
+ Lu~Li, Yukiko Matsuoka, Alice Villeger, Sarah~E Boyd, Laurence Calzone,
+ M\'{e}lanie 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, and
+ Hiroaki Kitano.
+\newblock The systems biology graphical notation.
+\newblock {\em Nat Biotechnol}, 27(8):735--741, 2009.
+\newblock 10.1038/nbt.1558.
+
+\bibitem{Moodie:2011}
+Stuart Moodie, Nicolas Le~Nov\`{e}re, Emek Demir, Huaiyu Mi, and Alice
+ Vill\'{e}ger.
+\newblock Systems biology graphical notation: Process description language
+ level 1.
+\newblock {\em Nature Precedings}, 2011.
+
+\bibitem{Junker:2012}
+Astrid Junker, Anatoly Sorokin, Tobias Czauderna, Falk Schreiber, and Alexander
+ Mazein.
+\newblock Wiring diagrams in biology: towards the standardized representation
+ of biological information.
+\newblock {\em Trends in Biotechnology}, 30(11):555--557, 2012.
+
+\bibitem{Courtot:2011}
+M.~Courtot, N.~Juty, C.~Kn{\"u}pfer, D.~Waltemath, A.~Zhukova, A.~Dr{\"a}ger,
+ M.~Dumontier, A.~Finney, M.~Golebiewski, J.~Hastings, et~al.
+\newblock Controlled vocabularies and semantics in systems biology.
+\newblock {\em Molecular systems biology}, 7(1), 2011.
+
+\bibitem{Hucka:2003}
+M.~Hucka, A.~Finney, H.~M. Sauro, H.~Bolouri, J.~C. Doyle, H.~Kitano, A.~P.
+ Arkin, B.~J. Bornstein, D.~Bray, A.~Cornish-Bowden, A.~A. Cuellar, S.~Dronov,
+ E.~D. Gilles, M.~Ginkel, V.~Gor, I.~I. Goryanin, W.~J. Hedley, T.~C. Hodgman,
+ J.-H. Hofmeyr, P.~J. Hunter, N.~S. Juty, J.~L. Kasberger, A.~Kremling,
+ U.~Kummer, N.~Le~Nov\`{e}re, L.~M. Loew, D.~Lucio, P.~Mendes, E.~Minch, E.~D.
+ Mjolsness, Y.~Nakayama, M.~R. Nelson, P.~F. Nielsen, T.~Sakurada, J.~C.
+ Schaff, B.~E. Shapiro, T.~S. Shimizu, H.~D. Spence, J.~Stelling,
+ K.~Takahashi, M.~Tomita, J.~Wagner, and J.~Wang.
+\newblock The {S}ystems {B}iology {M}arkup {L}anguage ({SBML}): A medium for
+ representation and exchange of biochemical network models.
+\newblock {\em Bioinformatics}, 19(4):524--531, 2003.
+
+\end{thebibliography}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2013-12-18 14:04:33
|
Revision: 870
http://sourceforge.net/p/sbgn/code/870
Author: lptolik
Date: 2013-12-18 14:04:31 +0000 (Wed, 18 Dec 2013)
Log Message:
-----------
fix #27 Error in SBGN-ER Specifications
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/inhibition.tex
Property Changed:
----------------
EntityRelationship/trunk/
Index: EntityRelationship/trunk
===================================================================
--- EntityRelationship/trunk 2013-12-18 13:52:23 UTC (rev 869)
+++ EntityRelationship/trunk 2013-12-18 14:04:31 UTC (rev 870)
Property changes on: EntityRelationship/trunk
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,47 ##
+.git
+.gitignore
+
+# TeX files #
+######################
+*.aux
+*.glo
+*.idx
+*.log
+*.toc
+*.ist
+*.acn
+*.acr
+*.alg
+*.bbl
+*.blg
+*.dvi
+*.glg
+*.gls
+*.ilg
+*.ind
+*.lof
+*.lot
+*.maf
+*.mtc
+*.mtc1
+*.out
+*.synctex.gz
+
+# FixMe files #
+######################
+*.lox
+
+# FixMe files #
+######################
+*.xdy
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+Icon?
+ehthumbs.db
+Thumbs.db
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/trunk/sources/inhibition.tex
===================================================================
--- EntityRelationship/trunk/sources/inhibition.tex 2013-12-18 13:52:23 UTC (rev 869)
+++ EntityRelationship/trunk/sources/inhibition.tex 2013-12-18 14:04:31 UTC (rev 870)
@@ -8,7 +8,7 @@
An \glyph{inhibition} affects \textbf{negatively} the strength, or the probability, of the target relationship. This inhibition can be for instance a steric hindrance or a negative allosteric regulation.
\begin{glyphDescription}
- \glyphSboTerm SBO:0000170 ! inhibition.
+ \glyphSboTerm SBO:0000169 ! inhibition.
\glyphOrigin Any \glyph{entity node} (\sect{ENs}).
\glyphTarget Any \glyph{relationship} (\sect{relationships}).
\glyphEndPoint The target extremity of a \glyph{inhibition} carries a bar perpendicular to the arc.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2013-12-18 13:52:27
|
Revision: 869
http://sourceforge.net/p/sbgn/code/869
Author: lptolik
Date: 2013-12-18 13:52:23 +0000 (Wed, 18 Dec 2013)
Log Message:
-----------
sync proposal is added; text corrections
Modified Paths:
--------------
EntityRelationship/trunk/examples/PCR.eps
EntityRelationship/trunk/examples/PCR.pdf
EntityRelationship/trunk/examples/PCR.png
EntityRelationship/trunk/examples/PCR.svg
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sbgn_ER-level1.tex
EntityRelationship/trunk/sources/assignment.tex
EntityRelationship/trunk/sources/domain.tex
EntityRelationship/trunk/sources/entity.tex
EntityRelationship/trunk/sources/inhibition.tex
EntityRelationship/trunk/sources/layout.tex
EntityRelationship/trunk/sources/modulation.tex
EntityRelationship/trunk/sources/relationships.tex
EntityRelationship/trunk/sources/revision_history.tex
EntityRelationship/trunk/sources/syntax.tex
Added Paths:
-----------
EntityRelationship/trunk/proposals/
EntityRelationship/trunk/proposals/simultaneous/
EntityRelationship/trunk/proposals/simultaneous/asynchronous.svg
EntityRelationship/trunk/proposals/simultaneous/figureA.png
EntityRelationship/trunk/proposals/simultaneous/figureB.png
EntityRelationship/trunk/proposals/simultaneous/figureC.png
EntityRelationship/trunk/proposals/simultaneous/figureD.png
EntityRelationship/trunk/proposals/simultaneous/simultaneous.svg
EntityRelationship/trunk/proposals/simultaneous/synchronous.svg
EntityRelationship/trunk/proposals/simultaneous/synchronous.txt
Modified: EntityRelationship/trunk/examples/PCR.eps
===================================================================
--- EntityRelationship/trunk/examples/PCR.eps 2013-12-16 12:01:02 UTC (rev 868)
+++ EntityRelationship/trunk/examples/PCR.eps 2013-12-18 13:52:23 UTC (rev 869)
@@ -1,2852 +1,1325 @@
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+/pdfmark where { pop globaldict /?pdfmark /exec load put }
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From: <lp...@us...> - 2013-12-16 12:01:05
|
Revision: 868
http://sourceforge.net/p/sbgn/code/868
Author: lptolik
Date: 2013-12-16 12:01:02 +0000 (Mon, 16 Dec 2013)
Log Message:
-----------
process is removed and annotation is added
Added Paths:
-----------
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ActivityFlow/trunk/images/annotation.pdf
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Added: ActivityFlow/trunk/images/annotation.eps
===================================================================
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Added: ActivityFlow/trunk/sources/annotation.tex
===================================================================
--- ActivityFlow/trunk/sources/annotation.tex (rev 0)
+++ ActivityFlow/trunk/sources/annotation.tex 2013-12-16 12:01:02 UTC (rev 868)
@@ -0,0 +1,35 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Annotation
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{Glyph: \glyph{Annotation}}
+\label{sec:annotation}
+
+\SBGNAFLone 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.
+
+\begin{glyphDescription}
+
+\glyphSboTerm SBO:NEW
+
+\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.
+
+\glyphLabel An \glyph{annotation} contains information placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
+
+\glyphAux An \glyph{annotation} does not carry any auxiliary unit.
+\end{glyphDescription}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.3]{images/annotation}
+ \caption{The \ER glyph for \glyph{annotation}.}
+ \label{fig:annotation}
+\end{figure}
+
+%\begin{figure}[H]
+% \centering
+% \includegraphics[scale = 0.5]{examples/ex-annotation}
+% \caption{Example of \glyph{annotations} adding information to the description of the trans-phosphorylation of CaMKII.}
+% \label{fig:ex-annotation}
+%\end{figure}
+
+%\normalcolor
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2013-12-16 12:00:16
|
Revision: 867
http://sourceforge.net/p/sbgn/code/867
Author: lptolik
Date: 2013-12-16 12:00:13 +0000 (Mon, 16 Dec 2013)
Log Message:
-----------
process is removed and annotation is added
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/glyphs.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2013-12-16 11:46:21 UTC (rev 866)
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|
From: <lp...@us...> - 2013-12-16 11:46:24
|
Revision: 866
http://sourceforge.net/p/sbgn/code/866
Author: lptolik
Date: 2013-12-16 11:46:21 +0000 (Mon, 16 Dec 2013)
Log Message:
-----------
before majour rearrangement
Added Paths:
-----------
ActivityFlow/tags/L1R1.1RC2/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2013-12-16 10:46:10
|
Revision: 865
http://sourceforge.net/p/sbgn/code/865
Author: lptolik
Date: 2013-12-16 10:46:04 +0000 (Mon, 16 Dec 2013)
Log Message:
-----------
fix the references on the frontpage
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/front-page.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2013-12-16 09:35:32 UTC (rev 864)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2013-12-16 10:46:04 UTC (rev 865)
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[truncated message content] |
|
From: <lp...@us...> - 2013-12-16 09:35:38
|
Revision: 864
http://sourceforge.net/p/sbgn/code/864
Author: lptolik
Date: 2013-12-16 09:35:32 +0000 (Mon, 16 Dec 2013)
Log Message:
-----------
fix the compilation problem
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/latex-style.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2013-10-27 15:46:15 UTC (rev 863)
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+R\xF4Jr\xE15h\xDA'W\x8D\xEA\xB5\xA0h\xD6
+N\xECrEC\xCB\xC2 \xF0+\xB0\x9BϏd\xF0\xFC\x81\xC7 \xA8\xF4P\xE0WRAVv'E\xF5V
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From: <tcz...@us...> - 2013-10-27 15:46:20
|
Revision: 863
http://sourceforge.net/p/sbgn/code/863
Author: tczauderna
Date: 2013-10-27 15:46:15 +0000 (Sun, 27 Oct 2013)
Log Message:
-----------
fixed a lot of warnings
fixed a lot of references
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
ProcessDiagram/trunk/Specification/sources/concepts.tex
ProcessDiagram/trunk/Specification/sources/glyphs.tex
ProcessDiagram/trunk/Specification/sources/introduction.tex
ProcessDiagram/trunk/Specification/sources/language_overview.tex
ProcessDiagram/trunk/Specification/sources/worked_examples.tex
ProcessDiagram/trunk/Specification/sources/working.tex
ProcessDiagram/trunk/Specification/validation-rules/000002.tex
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib 2013-04-25 17:10:19 UTC (rev 862)
+++ ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib 2013-10-27 15:46:15 UTC (rev 863)
@@ -9,6 +9,16 @@
pages = {research0012.1-research0012.10.}
}
+@article{Courtot:2011,
+ title={Controlled vocabularies and semantics in systems biology},
+ author={Courtot, M. and Juty, N. and Kn{\"u}pfer, C. and Waltemath, D. and Zhukova, A. and Dr{\"a}ger, A. and Dumontier, M. and Finney, A. and Golebiewski, M. and Hastings, J. and others},
+ journal={Molecular systems biology},
+ volume={7},
+ number={1},
+ year={2011},
+ publisher={Nature Publishing Group}
+}
+
@Article{Demir:2002,
author = {Demir, E. and Babur, O. and Dogrusoz., U and Gursoy, A. and Nisanci, G. and Cetin-Atalay, R. and Ozturk, M.},
title = {PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways},
@@ -109,6 +119,16 @@
pages = {1-13}
}
+@Article{Junker:2012,
+ author = {Astrid Junker and Anatoly Sorokin and Tobias Czauderna and Falk Schreiber and Alexander Mazein},
+ title = {Wiring diagrams in biology: towards the standardized representation of biological information},
+ journal = {Trends in Biotechnology},
+ year = {2012},
+ volume = {30},
+ number = {11},
+ pages = {555-557},
+}
+
@InProceedings{Maimon:2001,
author = {Ron Maimon and Sam Browning},
title = {Diagrammatic notation and computational structure of gene networks},
@@ -138,6 +158,14 @@
pages = {36}
}
+@Article{Moodie:2011,
+ author = {Moodie, Stuart and Le Nov\`{e}re, Nicolas and Demir, Emek and Mi, Huaiyu and Vill\'{e}ger, Alice},
+ title = {Systems Biology Graphical Notation: Process Description language Level 1},
+ journal = {Nature Precedings},
+ year = {2011},
+ url = {http://dx.doi.org/10.1038/npre.2011.3721.4}
+}
+
@Article{Pirson:2000,
author = {I. Pirson and N. Fortemaison and C. Jacobs and S. Dremier and J. E. Dumont and C. Maenhaut},
title = {The visual display of regulatory information and networks},
@@ -162,9 +190,9 @@
%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/
-@article{Novere:2009p1,
-author = {Nicolas Novere and Michael Hucka and Huaiyu Mi and Stuart Moodie and Falk Schreiber and Anatoly Sorokin and Emek Demir and Katja Wegner and Mirit Aladjem and Sarala Wimalaratne and Frank Bergman and Ralph Gauges and Peter Ghazal and Hideya Kawaji and Lu Li and Yukiko Matsuoka and Alice Villeger and Sarah Boyd and Laurence Calzone and Melanie Courtot and Ugur Dogrusoz and Tom Freeman and Akira Funahashi and Samik Ghosh and Akiya Jouraku and Sohyoung Kim and Fedor Kolpakov and Augustin Luna and Sven Sahle and Esther Schmidt and Steven Watterson and Guanming Wu and Igor Goryanin and Douglas Kell and Chris Sander and Herbert Sauro and Jacky Snoep and Kurt Kohn and Hiroaki Kitano},
-journal = {Nat Biotech},
+@article{LeNovere:2009p1,
+author = {Nicolas Le Nov\`{e}re and Michael Hucka and Huaiyu Mi and Stuart Moodie and Falk Schreiber and Anatoly Sorokin and Emek Demir and Katja Wegner and Mirit Aladjem and Sarala Wimalaratne and Frank Bergman and Ralph Gauges and Peter Ghazal and Hideya Kawaji and Lu Li and Yukiko Matsuoka and Alice Vill\'{e}ger and Sarah Boyd and Laurence Calzone and Melanie Courtot and Ugur Dogrus{\"o}z and Tom Freeman and Akira Funahashi and Samik Ghosh and Akiya Jouraku and Sohyoung Kim and Fedor Kolpakov and Augustin Luna and Sven Sahle and Esther Schmidt and Steven Watterson and Guanming Wu and Igor Goryanin and Douglas Kell and Chris Sander and Herbert Sauro and Jacky Snoep and Kurt Kohn and Hiroaki Kitano},
+journal = {Nature Biotechnology},
title = {The Systems Biology Graphical Notation},
note = {10.1038/nbt.1558},
number = {8},
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2013-04-25 17:10:19 UTC (rev 862)
+++ ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2013-10-27 15:46:15 UTC (rev 863)
@@ -86,6 +86,7 @@
\include{sources/worked_examples}
\part{Technical Reference}
+\label{part:techref}
\include{sources/glyphs}
\include{sources/layout}
Modified: ProcessDiagram/trunk/Specification/sources/concepts.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/concepts.tex 2013-04-25 17:10:19 UTC (rev 862)
+++ ProcessDiagram/trunk/Specification/sources/concepts.tex 2013-10-27 15:46:15 UTC (rev 863)
@@ -11,7 +11,7 @@
phosphorylated. The small circles on the nodes for RAF and other entity pools represent state variables (in this case, phosphorylation sites).
% Redo the figure with colors
-\begin{figure}[h]
+\begin{figure}[htb]
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.8]{images/MAPK-only}
@@ -28,7 +28,7 @@
In \fig{eg3} the formation of a complex is shown. Two \emph{macromolecule} entities X and Y form the \emph{complex} X\underline{ }Y. Complex formation is represented using the \emph{association} process node with ingoing \emph{consumption} and outgoing \emph{production} arcs. The \emph{complex} glyph surrounds subunits X and Y.
-\begin{figure}[h]
+\begin{figure}[htb]
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.5]{images/Fig12}
@@ -36,7 +36,7 @@
\label{fig:eg2}
\end{figure}
-\begin{figure}[h]
+\begin{figure}[htb]
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.5]{images/Fig13}
@@ -50,7 +50,7 @@
More examples can be found in a list of so called SBGN bricks~\cite{Junker:2012}, which are building blocks representing basic biological patterns. These bricks can be used for assembly into different kinds of biological networks such as metabolic and regulatory networks.
-\begin{figure}[h]
+\begin{figure}[htb]
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.5]{images/Fig14}
@@ -59,7 +59,7 @@
\end{figure}
-\begin{figure}[h]
+\begin{figure}[htb]
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.5]{images/Fig15}
@@ -76,7 +76,7 @@
\begin{figure}[htb]
\begin{center}
\scalebox{0.5}{\includegraphics{images/keyconcepts}}
-\caption{A process consuming the entity pools A and B and producing the entity pools C and D. The entity pool E modulates the process. The process is represented as a square. Each (unspecified) entity pool is represented as an ellipsis identified by a label. The relationships between the process and each entity pool involved are represented by connecting lines called arcs. Depending on the type of relationship (consumption, production, modulation), these arcs are decorated with different symbols (respectively nothing, arrowhead, and diamond).}\label{fig:key concepts}
+\caption{A process consuming the entity pools A and B and producing the entity pools C and D. The entity pool E modulates the process. The process is represented as a square. Each (unspecified) entity pool is represented as an ellipsis identified by a label. The relationships between the process and each entity pool involved are represented by connecting lines called arcs. Depending on the type of relationship (consumption, production, modulation), these arcs are decorated with different symbols (respectively nothing, arrowhead, and diamond).}\label{fig:keyconcepts}
\end{center}
\end{figure}
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2013-04-25 17:10:19 UTC (rev 862)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2013-10-27 15:46:15 UTC (rev 863)
@@ -83,9 +83,9 @@
specification \cite{umlspec}).
\item[subclass] A class that inherits attributes, behaviour and
associations from another class. For example in figure
- \ref{fig:umlexample} ``class C is a subclass of class A''.
+ \ref{fig:techref:umlexample} ``class C is a subclass of class A''.
\item[superclass] A class that is an ancestor of another class. For
- example in figure \ref{fig:umlexample} ``class A is a superclass of class B'''.
+ example in figure \ref{fig:techref:umlexample} ``class A is a superclass of class B'''.
\item[generalisation] A relationship in UML that defines a
subclass/superclass relationship.
\item[association] A semantic relationship between two
@@ -118,12 +118,12 @@
\includegraphics[width=0.9\textwidth]{images/exampleuml}
\caption{An example of the UML elements used in this
specification. The diagram is explained more fully in the text.}
-\label{fig:umlexample}
+\label{fig:techref:umlexample}
\end{center}
\end{figure}
The UML class diagrams used will look something like the examples in
-figure \ref{fig:umlexample}. The UML elements in this diagram are the
+figure \ref{fig:techref:umlexample}. The UML elements in this diagram are the
only ones used in this specification and again as an aid to
understanding their meanings are described below:
\begin{description}
@@ -160,7 +160,7 @@
\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:CVs}).
+\item[cv] A controlled vocabulary (see \ref{sec:techref:CVs}).
\item[enum] A value that must be chosen from on of an enumerated set
of predefined values.
\end{description}
@@ -227,7 +227,7 @@
associations between classes are shown to simplify the
diagram. These details are provided in the UML class diagrams
associated with most class definitions.}
-\label{fig:sbgnoverviewuml}
+\label{fig:techref:sbgnoverviewuml}
% \end{center}
% \end{figure}
\end{sidewaysfigure}
@@ -235,7 +235,7 @@
\section{Overview}
The UML model describing the \PDl is summarised in figure
-\ref{fig:sbgnoverviewuml}. The model has a root class
+\ref{fig:techref:sbgnoverviewuml}. The model has a root class
\sbgnclass{SBGNElement} for all language elements and care has been
taken keep the model as simple as possible. This includes minimising
the use of multiple inheritance and reflecting the directed graph
@@ -246,10 +246,10 @@
(\sbgnclass{AuxiliaryUnit}). There are a number of language rules that
the model and the individual class specification cannot capture and
these are dealt with later in the chapter after the class definitions
-in section \ref{sec:definitions}.
+in section \ref{sec:techref:definitions}.
\section{Definitions}
-\label{sec:definitions}
+\label{sec:techref:definitions}
\subsection{SBGNElement}
\label{defn:SBGNElement}
@@ -257,7 +257,7 @@
All the glyphs in \SBGNPDLone inherit from
\sbgnclass{SBGNElement}\query{A new concept}. This is an abstract or conceptual class that
helps organise \PD conceptually. \sbgnclass{SBGNElement} (figure
-\ref{fig:mapuml}) has a single attribute \attrib{id} that is an
+\ref{fig:techref:mapuml}) has a single attribute \attrib{id} that is an
identifying attribute. This means that all SBGN elements defined here,
which ultimately extend \sbgnclass{SBGNBase}, can all be uniquely
identified from each other. This makes sense if you think that a glyph
@@ -284,24 +284,24 @@
Not defined in the previous version.
\subsection{Map}
-\label{defn:Map}\label{sec:map}
+\label{defn:Map}\label{sec:techref:map}
-\begin{figure}[h!]
+\begin{figure}[htb]
\centering
\includegraphics[width=0.55\textwidth]{images/mapuml}
\caption{UML definition of Map and \sbgnclass{SBGNElement}.}
- \label{fig:mapuml}
+ \label{fig:techref:mapuml}
\end{figure}
The \sbgnclass{Map}\query{Defining this explicitly is new, but the
concept of the map as a container of glyphs has always existed in
- the \PDl} (figure \ref{fig:mapuml}) is a container that
+ the \PDl} (figure \ref{fig:techref:mapuml}) is a container that
holds all the glyphs (\classref{SBGNGlyph}) drawn in a \PDm. A map may
represent a submap or a supermap and should comply with the rules set
-out in section \ref{sec:mapsubmaps}. The \attrib{elements} held should be
+out in section \ref{sec:techref:mapsubmaps}. The \attrib{elements} held should be
logically unique and conform to the identity rules in section
-\ref{sec:uniquenessdefinition}.
+\ref{sec:techref:uniquenessdefinition}.
\subsubsection{Generalisation}
@@ -325,7 +325,7 @@
\begin{itemize}
\item A map is valid if it is empty (although not very useful).
\item All instances of \classref{SBGNGlyph} must be unique (see
- section \ref{sec:uniquenessdefinition}).
+ section \ref{sec:techref:uniquenessdefinition}).
\end{itemize}
\subsubsection{Notation}
@@ -346,7 +346,7 @@
\centering
\includegraphics[width=0.9\textwidth]{images/glyphauxuml}
\caption{UML definition of the \sbgnclass{SBGNGlyph} and its subclasses.}
- \label{fig:glyphauxuml}
+ \label{fig:techref:glyphauxuml}
\end{figure}
The \sbgnclass{SBGNGlyph} is the fundamental building blocks of the
@@ -385,10 +385,10 @@
\centering
\includegraphics[width=0.75\textwidth]{images/auxiliaryunituml}
\caption{UML definition of the Auxiliary Unit and its subclasses.}
- \label{fig:auxiliaryunituml}
+ \label{fig:techref:auxiliaryunituml}
\end{figure}
- The \sbgnclass{AuxiliaryUnit} (figure \ref{fig:auxiliaryunituml}) represents symbols that may be used to
+ The \sbgnclass{AuxiliaryUnit} (figure \ref{fig:techref:auxiliaryunituml}) represents symbols that may be used to
adorn glyphs. In doing so they change the meaning of the glyph and/or provide
additional information about it.
@@ -423,10 +423,10 @@
\includegraphics[width=0.55\textwidth]{images/sbgnnodearcuml}
\caption{UML definition of the \sbgnclass{SBGNNode} and
\sbgnclass{SBGNArc} classes.}
- \label{fig:sbgnnodearcuml}
+ \label{fig:techref:sbgnnodearcuml}
\end{figure}
-The \sbgnclass{SBGNNode} (figure \ref{fig:sbgnnodearcuml}) represents
+The \sbgnclass{SBGNNode} (figure \ref{fig:techref:sbgnnodearcuml}) represents
the nodes in the graph structure that is the core representation
within the \PDl. The nodes are connected to glyphs descended from
\sbgnclass{SBGNArc} for form a direct graph.
@@ -464,7 +464,7 @@
\subsection{SBGNArc}
\label{defn:SBGNArc}
-The \sbgnclass{SBGNArc} (figure \ref{fig:sbgnnodearcuml}) represents
+The \sbgnclass{SBGNArc} (figure \ref{fig:techref:sbgnnodearcuml}) represents
the directed arcs (also know as directed edges) in the directed graph
structure that is the core representation within \PDl. The arc is
connected to two nodes descended from \sbgnclass{SBGNNode}, one at
@@ -509,7 +509,7 @@
definition. The diagram shows how these classes interact with the
entity pool, state variable and so influence
\sbgnclass{EntityPoolNode} logical identity.}
- \label{fig:entitytypeuml}
+ \label{fig:techref:entitytypeuml}
\end{figure}
The \sbgnclass{EntityType}\query{The concept of an entity pool's type
@@ -519,7 +519,7 @@
EPNs.} is one of the core concepts in the \PDl. It
defines the type of entity that is instantiated by one or more
entity pools in a \PDm. The \sbgnclass{EntityType} has associated
-state variable definitions (see figure \ref{fig:entitytypeuml}) and
+state variable definitions (see figure \ref{fig:techref:entitytypeuml}) and
this enforces one of the core rules in the \PDl that once a state is
associated with an entity type it must be used by all entity pools of
that type.
@@ -540,7 +540,7 @@
\attitem{natures}{cv}{*} The nature of the entity pool node as defined
by a controlled vocabulary. Zero, one or more values may be set, but
each one must belong to a different controlled vocabulary (see
- section \ref{sec:CVs})\query{This has been discussed on the mailing
+ section \ref{sec:techref:CVs})\query{This has been discussed on the mailing
list where this seems to be the consensus solution}.
\end{attributes}
@@ -585,7 +585,7 @@
preserve the same state variables whenever it is used.} defines the state variables
used by an \sbgnclass{EntityType} and therefore those state variables
that must exists in an \sbgnclass{EntityPoolNode} (see figure
-\ref{fig:entitytypeuml}).
+\ref{fig:techref:entitytypeuml}).
\subsubsection{Generalisation}
@@ -620,7 +620,7 @@
concept did exist in the language.
\subsection{EntityPoolNode}
-\label{sec:EPNs}\label{defn:EntityPoolNode}\label{sec:EPN}
+\label{sec:techref:EPNs}\label{defn:EntityPoolNode}\label{sec:techref:EPN}
An entity pool is a population of entities that cannot be
distinguished from each other, when it comes to the \SBGNPDLone
@@ -638,10 +638,10 @@
\centering
\includegraphics[width=0.85\textwidth]{images/epnuml}
\caption{UML definition of the entity pool node and its descendant glyphs.}
- \label{fig:epnuml}
+ \label{fig:techref:epnuml}
\end{figure}
-The \sbgnclass{EntityPoolNode} (figure \ref{fig:epnuml}) is the
+The \sbgnclass{EntityPoolNode} (figure \ref{fig:techref:epnuml}) is the
definition of the entity pool and it shares an \sbgnclass{EntityType}
with other identical entities\query{Although this concept is discussed
it is not explicitly defined previously.}. An instance of an entity pools is
@@ -649,8 +649,8 @@
its \attrib{cardinality}, its \attrib{owning\_compartment} and the
\attrib{value}s of its \sbgnclass{StateVariable}s (where
appropriate). It must belong to a compartment or be associated with
-the map (c.f.\, section \ref{sec:compartment}) and can contain a clone
-marker if it is cloned (see section \ref{sec:epnuniqueness})--- note
+the map (c.f.\, section \ref{sec:techref:compartment}) and can contain a clone
+marker if it is cloned (see section \ref{sec:techref:epnuniqueness})--- note
that not all EPNs can be cloned.
\subsubsection{Generalisation}
@@ -673,7 +673,7 @@
that this EPN belongs too.
\associtem{entity\_type}{EntityType}{1} The type of this entity pool.
\associtem{clone\_marker}{CloneMarker}{0..1} The clone marker
- decorator. See section \ref{sec:cloneMarker} for its use.
+ decorator. See section \ref{sec:techref:cloneMarker} for its use.
\associtem{displayed\_attributes}{AttributeValue}{*} One or
more decorators used to display attribute values\query{This is an
alternate way of using the Unit of Information to display
@@ -699,8 +699,8 @@
\attrib{owning\_compartment} is not set. We interpret this as
belonging to an invisible default compartment.
\item \attrib{natures} can only use the material type (section
- \ref{sec:material-types-cv}), conceptual type (section \ref{sec:conceptual-types-cv}) or physical
- characteristics (section \ref{sec:physical-characteristics-cv}) controlled vocabularies.
+ \ref{sec:techref:material-types-cv}), conceptual type (section \ref{sec:techref:conceptual-types-cv}) or physical
+ characteristics (section \ref{sec:techref:physical-characteristics-cv}) controlled vocabularies.
\item The appropriate subclass of \sbgnclass{CloneMarker} must be used
to distinguish logically identical instances of this class.
\item the \sbgnclass{EntityPoolNode} must be associated with at least
@@ -739,7 +739,7 @@
is part of the logical key of the \sbgnclass{EntityPoolNode}.
\subsection{Empty Set}
-\label{sec:sourceSink}
+\label{sec:techref:sourceSink}
It is useful to have the ability to represent the creation of an entity or
a state from an unspecified source, that is, from something that one does
@@ -776,11 +776,11 @@
\includegraphics[width=0.75\textwidth]{images/emptysetuml}
\caption{The UML definition of the \glyph{EmptySet} and its context
in relation to other elements of the \PDl.}
- \label{fig:emptysetuml}
+ \label{fig:techref:emptysetuml}
\end{figure}
The definition of the \glyph{Empty Set} is shown in figure
-\ref{fig:emptysetuml}. The empty set is not a subclass of \sbgnclass{EntityPoolNode} as it does not
+\ref{fig:techref:emptysetuml}. The empty set is not a subclass of \sbgnclass{EntityPoolNode} as it does not
represent a single pool of entities and does not share any of the
other attributes of an \sbgnclass{EntityPoolNode}, nor does it belong to a particular
compartment\query{This is a significant change to the semantics from
@@ -819,16 +819,16 @@
\glyphContainer Represented by the mathematical symbol for ``empty
set'', that is, a circle crossed by a bar linking the upper-right and
lower-left corners of an invisible square drawn around the circle ($\emptyset$).
-\fig{sourceSink} illustrates this. The symbol should be linked to one
+\fig{techref:sourceSink} illustrates this. The symbol should be linked to one
and only one edge in a map.
\glyphLabel None
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[width = 0.1\textwidth]{images/sourceSink}
\caption{The \glyph{empty set} glyph.}
- \label{fig:sourceSink}
+ \label{fig:techref:sourceSink}
\end{figure}
\subsubsection{Changes from Previous Version}
@@ -842,7 +842,7 @@
\subsection{StatelessEPN}
\label{defn:StatelessEPN}
-The \sbgnclass{StatelessEPN} (figure \ref{fig:statelessepnuml})
+The \sbgnclass{StatelessEPN} (figure \ref{fig:techref:statelessepnuml})
represents a pool where the entities do not change `state'. In
other-words the entities do not undergo any physical change that is
useful to record in a \PDm. Therefore they cannot be assigned
@@ -853,7 +853,7 @@
\includegraphics[width=0.75\textwidth]{images/statelessepnuml}
\caption{UML definition of the stateless entity pool node and its
descendant glyphs.}
- \label{fig:statelessepnuml}
+ \label{fig:techref:statelessepnuml}
\end{figure}
\subsubsection{Generalisation}
@@ -881,7 +881,7 @@
Not defined in the previous version.
\subsection{Simple chemical}
-\label{sec:simpleChemical}
+\label{sec:techref:simpleChemical}
A \sbgnclass{SimpleChemical} is the `opposite' of a macromolecule
(\sect{macromolecule}): it is a chemical compound that is \emph{not}
@@ -920,10 +920,10 @@
\glyphSboTerm SBO:0000247 ! simple chemical \glyphContainer A
\glyph{simple chemical} is represented by a `stadium' symbol: a
circle split in two with a rectangle inserted between them (see
- figure \ref{fig:simpleChemical}). If desired the rectangle can have
+ figure \ref{fig:techref:simpleChemical}). If desired the rectangle can have
zero length and the symbol is then identical to a circle
- (\fig{simpleChemical}). To avoid confusion with the Unspecified
- Entity (\ref{sec:unspecifiedEntity}), this form of the glyph must remain a
+ (\fig{techref:simpleChemical}). To avoid confusion with the Unspecified
+ Entity (\ref{sec:techref:unspecifiedEntity}), this form of the glyph must remain a
circle and cannot be deformed into an eclipse.
\glyphLabel The identification of the \glyph{simple chemical} is
@@ -934,28 +934,28 @@
permitted to spill outside the container.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{images/simpleChemical}
\caption{The \PD glyph for \glyph{simple chemical monomer}. The stadium
form and circular forms are shown, as are the cloned forms of the glyph.}
- \label{fig:simpleChemical}
+ \label{fig:techref:simpleChemical}
\end{figure}
\paragraph{Glyph: \glyph{Simple chemical multimer}}
\begin{glyphDescription}
\glyphSboTerm SBO:0000421 ! multimer of simple chemicals
-\glyphContainer A \glyph{simple chemical multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other. \fig{simpleChemicalMultimer} illustrates the glyph.
+\glyphContainer A \glyph{simple chemical multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other. \fig{techref:simpleChemicalMultimer} illustrates the glyph.
\glyphLabel The multimer carries an identifying label. The label is placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the top monomer's container. The label may spill outside of the container.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{images/simpleChemicalMultimer}
\caption{The \PD glyph for \glyph{simple chemical multimer}. The
figures show the stadium and circular forms, and their cloned variants.}
- \label{fig:simpleChemicalMultimer}
+ \label{fig:techref:simpleChemicalMultimer}
\end{figure}
\subsubsection{Changes from Previous Version}
@@ -966,7 +966,7 @@
without straight horizontal elements so that it becomes a circle.
\subsection{UnspecifiedEntity}
-\label{sec:unspecifiedEntity}
+\label{sec:techref:unspecifiedEntity}
The simplest type of \sbgnclass{EntityPoolNode} is the
\sbgnclass{UnspecifiedEntity} --- one whose type is unknown or simply
@@ -1009,9 +1009,9 @@
\begin{glyphDescription}
\glyphSboTerm SBO:0000285 ! material entity of unspecified nature
\glyphContainer An \glyph{unspecified entity} is represented by an
-elliptic container, as shown in \ref{fig:unspecified}. Note that this
+elliptic container, as shown in \ref{fig:techref:unspecified}. Note that this
must remain an ellipse to avoid confusion with the Simple Chemical
-glyph, which is a circle (c.f.\, \ref{sec:simpleChemical}).
+glyph, which is a circle (c.f.\, \ref{sec:techref:simpleChemical}).
\glyphLabel An \glyph{unspecified entity} 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,
@@ -1020,11 +1020,11 @@
container.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[width=2.5in]{images/unspecified}
\caption{The \PD glyph for \glyph{unspecified entity}.}
- \label{fig:unspecified}
+ \label{fig:techref:unspecified}
\end{figure}
\subsubsection{Changes from Previous Version}
@@ -1032,7 +1032,7 @@
No changes from the previous version.
\subsection{Perturbing Agent}
-\label{sec:perturbing agent}
+\label{sec:techref:perturbing agent}
Biochemical networks can be affected by external influences. Those
influences can be the effect of well-defined physical perturbing
@@ -1071,7 +1071,7 @@
\begin{glyphDescription}
\glyphSboTerm SBO:0000405 ! perturbing agent
\glyphContainer A \glyph{perturbing agent} is represented by a modified hexagon
-having two opposite concave faces, as illustrated in \fig{perturbing agent}.
+having two opposite concave faces, as illustrated in \fig{techref:perturbing agent}.
\glyphLabel A \glyph{perturbing agent} is identified by a label placed in an
unbordered box containing a string of characters. The characters can be
distributed on several lines to improve readability, although this is not
@@ -1079,11 +1079,11 @@
\glyph{perturbing agent} container. The label may spill outside of the container.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{images/perturbing_agent}
\caption{The \PD glyph for \glyph{perturbing agent}.}
- \label{fig:perturbing agent}
+ \label{fig:techref:perturbing agent}
\end{figure}
\subsubsection{Changes from Previous Version}
@@ -1097,7 +1097,7 @@
chemical modifcation or conformational change, which we wish to record
in a \PDm. This information is captured via the
\sbgnclass{StateVariable} (as can be seen in figure
-\ref{fig:statefulepnuml}). The \sbgnclass{LabellecCloneMarker} must be
+\ref{fig:techref:statefulepnuml}). The \sbgnclass{LabellecCloneMarker} must be
used to indicated that the \sbgnclass{StatefulEPN} is cloned.
\begin{figure}[htb]
@@ -1105,7 +1105,7 @@
\includegraphics[width=0.75\textwidth]{images/statefulepnuml}
\caption{UML definition of the stateful entity pool node: showing its
descendants and its association with state variables.}
- \label{fig:statefulepnuml}
+ \label{fig:techref:statefulepnuml}
\end{figure}
\subsubsection{Generalisation}
@@ -1140,7 +1140,7 @@
Not defined explicitly in the previous version.
\subsection{Macromolecule}
-\label{sec:macromolecule}
+\label{sec:techref:macromolecule}
Many biological processes involve \emph{macromolecules}: biochemical
substances that are built up from the covalent linking of
@@ -1184,57 +1184,57 @@
\begin{glyphDescription}
\glyphSboTerm SBO:0000245 ! macromolecule
\glyphContainer A macromolecule is represented by a rectangular container with rounded
-corners, as illustrated in \fig{macromolecule}.
+corners, as illustrated in \fig{techref:macromolecule}.
\glyphLabel A \glyph{macromolecule} is identified by a label placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[width = 3.5in]{images/macromolecule}
\caption{The \PD glyph for \glyph{macromolecule}, shown plain and
unadorned on the left, and with an additional state variable and a
unit of information in the middle and the cloned form on the right.}
- \label{fig:macromolecule}
+ \label{fig:techref:macromolecule}
\end{figure}
\paragraph{Glyph: \glyph{Macromolecule multimer}}
\begin{glyphDescription}
\glyphSboTerm SBO:0000420 ! multimer of macromolecules
-\glyphContainer A \glyph{multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other. \fig{macromolMultimer} illustrates the glyph.
+\glyphContainer A \glyph{multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other. \fig{techref:macromolMultimer} illustrates the glyph.
\glyphLabel As monomer
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[width = 3.5in]{images/macromolMultimer}
\caption{The \PD glyph for \glyph{macromolecule multimer}, shown plain and
unadorned on the left, and with an additional state variable and a
unit of information in the right and the cloned form on the right.}
- \label{fig:macromolMultimer}
+ \label{fig:techref:macromolMultimer}
\end{figure}
\paragraph{Usage Examples}
-\label{sec:CplxEPNs}
+\label{sec:techref:CplxEPNs}
In this section, we provide examples of Entity Pool Node representations drawn using the \SBGNPDLone glyphs described above.
-\fig{example-camkii} represents calcium/calmodulin kinase II, with phosphorylation on the sites threonine 286 and 306, as well as catalytic and autoinhibitory domains. Note the use of \emph{units of information} and \emph{state variables}.
+\fig{techref:example-camkii} represents calcium/calmodulin kinase II, with phosphorylation on the sites threonine 286 and 306, as well as catalytic and autoinhibitory domains. Note the use of \emph{units of information} and \emph{state variables}.
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{examples/macromolecule-CaMKII}
\caption{An example representation of calcium/calmodulin kinase II.}
- \label{fig:example-camkii}
+ \label{fig:techref:example-camkii}
\end{figure}
-\fig{example-glur} represents the glutamate receptor in the open state, with both phosphorylation and glycosylation. The entity carries two functional domains, the ligand-binding domain and the ion pore, and its chemical nature is precided.
+\fig{techref:example-glur} represents the glutamate receptor in the open state, with both phosphorylation and glycosylation. The entity carries two functional domains, the ligand-binding domain and the ion pore, and its chemical nature is precided.
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{examples/macromolecule-GluR}
\caption{An example of a glutamate receptor in the open state.}
- \label{fig:example-glur}
+ \label{fig:techref:example-glur}
\end{figure}
@@ -1243,7 +1243,7 @@
No changes from the previous version.
\subsection{NucleicAcidFeature}
-\label{sec:genetic}
+\label{sec:techref:genetic}
The \sbgnclass{NucleicAcidFeature} represents a fragment of a
macromolecule carrying genetic information. A common use for this
@@ -1282,18 +1282,18 @@
\begin{glyphDescription}
\glyphSboTerm SBO:0000354 ! informational molecule segment
-\glyphContainer A \glyph{nucleic acid feature} is represented by a rectangular container whose bottom half has rounded corners, as shown in \fig{genetic}.
+\glyphContainer A \glyph{nucleic acid feature} is represented by a rectangular container whose bottom half has rounded corners, as shown in \fig{techref:genetic}.
\glyphLabel The identity of a particular \glyph{Nucleic acid feature} is established by a label placed in an unordered box containing a string of characters. The characters may be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[width = 3.5in]{images/genetic}
\caption{The \PD glyph for \glyph{nucleic acid feature monomer}, shown plain and
unadorned on the left and with an additional state variable and a
unit of information in the middle and the cloned form on the right.}
- \label{fig:genetic}
+ \label{fig:techref:genetic}
\end{figure}
\paragraph{Glyph: \glyph{Nucleic acid feature multimer}}
@@ -1304,19 +1304,19 @@
\glyphSboTerm SBO:0000419 ! multimer of informational molecule segments
-\glyphContainer A \glyph{Nucleic acid feature multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other. \fig{genetic-multimer} illustrates the glyph.
+\glyphContainer A \glyph{Nucleic acid feature multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other. \fig{techref:genetic-multimer} illustrates the glyph.
\glyphLabel As monomer glyph.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[width = 3.5in]{images/geneticMultimer}
\caption{The \PD glyph for \glyph{nucleic acid feature multimer}, shown plain and
unadorned on the left and with an additional state variable and a
unit of information in the middle and the cloned form on the right.}
- \label{fig:genetic-multimer}
+ \label{fig:techref:genetic-multimer}
\end{figure}
\subsubsection{Changes from Previous Version}
@@ -1327,15 +1327,15 @@
%%%% Complex
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Complex}\label{sec:complex}
+\subsection{Complex}\label{sec:techref:complex}
\label{defn:Complex}
A \sbgnclass{Complex} represents a biochemical entity composed of
other biochemical entities, whether macromolecules, simple chemicals,
multimers, or other complexes (figure
-\ref{fig:complexsubunituml}). The \sbgnclass{Complex} can described
+\ref{fig:techref:complexsubunituml}). The \sbgnclass{Complex} can described
its composition by the set of \sbgnclass{Subunit}s it contains (see
-figure \ref{sec:subunits}). This description is entirely optional and
+figure \ref{sec:techref:subunits}). This description is entirely optional and
is their to assist the user with a visual shorthand about the
composition of the complex.
@@ -1346,7 +1346,7 @@
associated \sbgnclass{subunit}s. In particular this describes organisation
of the state variables that belong to both the subunit, but also
the complex.}
- \label{fig:complexsubunituml}
+ \label{fig:techref:complexsubunituml}
\end{figure}
\subsubsection{Generalisations}
@@ -1400,11 +1400,11 @@
optimise the clarity and avoid overlapping.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[width=3.5in]{images/complexGlyph}
\caption{The \glyph{complex} glyph.}
- \label{fig:complex}
+ \label{fig:techref:complex}
\end{figure}
@@ -1414,16 +1414,16 @@
\glyphSboTerm SBO:0000418 ! multimer of complexes
\glyphContainer A \glyph{Complex Multimer} is represented by two
identical \glyph{Complex} containers shifted horizontally and
-vertically and stacked one on top of the other. \fig{complexMultimer}
+vertically and stacked one on top of the other. \fig{techref:complexMultimer}
illustrates the glyph.
\glyphLabel As monomer
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[width = 3.5in]{images/complexMultimerGlyph}
\caption{The \glyph{Complex Multimer} glyph.}
- \label{fig:complexMultimer}
+ \label{fig:techref:complexMultimer}
\end{figure}
\subsubsection{Layout Rules and Guidelines}
@@ -1446,7 +1446,7 @@
\end{itemize}
\subsection{Subunit}
-\label{defn:Subunit}\label{sec:subunits}
+\label{defn:Subunit}\label{sec:techref:subunits}
The \sbgnclass{Subunit}\query{The principles of the subunit have been
agreed, but the details of this implementation should be
@@ -1454,7 +1454,7 @@
\classref{Complex}. A complex can optionally be decorated with one or
more subunits, which represent the types of \classref{EntityPoolNode}
that may aggregate to form a complex. As we can see from the UML
-representation (figure \ref{fig:complexsubunituml}) the
+representation (figure \ref{fig:techref:complexsubunituml}) the
\sbgnclass{Subunit} is an auxiliary unit that decorates the
\sbgnclass{Complex} and does not represent an entity pool directly. In
addition it does not mimic the \sbgnclass{EntityPoolNode} class
@@ -1515,7 +1515,7 @@
available are equivalent to those used by the EPN glyphs including the
\glyph{complex}. Therefore it is possible to describe complexes within
complexes. The mapping between these and the symbol used is shown
-table \ref{tab:subunit types}. Not that subunits may contain labels
+table \ref{tab:techref:subunit types}. Not that subunits may contain labels
corresponding to their \attrib{name}.
\begin{center}
@@ -1523,7 +1523,7 @@
\attrib{cardinality} values of \sbgnclass{Subunit} and the glyphs
used to represent it. These are essentially the EPN glyphs
described in this document.}
-\label{tab:subunit types}
+\label{tab:techref:subunit types}
%\begin{footnotesize}
\tablefirsthead{\toprule
\attrib{subunit\_type} & \attrib{cardinality} $=0$ & \attrib{cardinality} $>0$ \\\midrule}
@@ -1550,7 +1550,7 @@
%\end{footnotesize}
\end{center}
-The example in figure \ref{fig:complexSubunits} illustrates the use of
+The example in figure \ref{fig:techref:complexSubunits} illustrates the use of
subunits in a complex. It also shows an equivalent compex without
subunits. This is an import point. For every \glyph{Complex} drawn
with subunits it will always be possible to drawn an equivalent
@@ -1559,13 +1559,13 @@
actually belong to the complex. Either this or we enforce a rule
that all state vars must be named uniquely.}.
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[width = 3.0in]{images/complex}
\caption{Both these complex glyphs are equivalent. The one on the
left is described using subunit decorators, the one on the right
describes the same thing without them.}
- \label{fig:complexSubunits}
+ \label{fig:techref:complexSubunits}
\end{figure}
\subsubsection{Changes from Previous Version}
@@ -1576,10 +1576,10 @@
paradigms of the \PDl. This is corrected in the current version and
subunits are now adornments of the \sbgnclass{Complex}.
-\subsection{ProcessNode}\label{sec:PNs}
+\subsection{ProcessNode}\label{sec:techref:PNs}
\label{defn:ProcessNode}
-The \sbgnclass{Process} (figure \ref{fig:processumlview}) represents a
+The \sbgnclass{Process} (figure \ref{fig:techref:processumlview}) represents a
process that transforms one or more entity pools into one or more
entity pools, that are identical or different. A process may be used
to represent or summarise more than one known process.
@@ -1591,7 +1591,7 @@
associated subclasses. Note that the \sbgnclass{Process} extends
\sbgnclass{SBGNNode} so all its descendants can potentially be
nodes in a directed graph.}
- \label{fig:processumlview}
+ \label{fig:techref:processumlview}
\end{figure}
@@ -1618,7 +1618,7 @@
\item This was not explicitly defined in the previous version, but
this version did define a glyph called \glyph{Process}. To avoid
ambiguity this glyph has now been renamed \glyph{Stoichiometric
- Process} (see section \ref{sec:stoichiometricprocess}).
+ Process} (see section \ref{sec:techref:stoichiometricprocess}).
\item Previous specifications stated that processed could be
duplicated when all associated EPNs were cloned. This behaviour has
been changed the current status where all processes are unique in a \PDm.
@@ -1628,7 +1628,7 @@
\label{defn:NonStoichiometricProcess}
The \sbgnclass{NonStoichiometricProcess}\query{This has been discussed
- and agreed in past meetings} (figure \ref{fig:nonstoichprocessuml})
+ and agreed in past meetings} (figure \ref{fig:techref:nonstoichprocessuml})
is a type of process. It does not necessarily result in a measurable
change of entity pools, nor does it necessarily have a defined start
and end point. In many cases the process is not well defined. This may
@@ -1640,7 +1640,7 @@
\includegraphics[width = 0.45\textwidth]{images/nonstoichprocessuml}
\caption{The UML definition of the \sbgnclass{NonStoichiometricProcess} and its
associated subclasses.}
- \label{fig:nonstoichprocessuml}
+ \label{fig:techref:nonstoichprocessuml}
\end{figure}
\subsubsection{Generalisation}
@@ -1670,7 +1670,7 @@
A biochemical network can generate phenotypes or affect biological
processes. Such processes can take place at different levels and are
independent of the biochemical network itself. To represent these
-processes in a map, SBGN defines the \sbgnclass{Phenotype} (figure \ref{fig:nonstoichprocessuml}).
+processes in a map, SBGN defines the \sbgnclass{Phenotype} (figure \ref{fig:techref:nonstoichprocessuml}).
\subsubsection{Generalisation}
@@ -1707,14 +1707,14 @@
\subsubsection{Notation}
\paragraph{Glyph: \glyph{Phenotype}}
-\label{sec:phenotype}
+\label{sec:techref:phenotype}
\begin{glyphDescription}
\glyphSboTerm SBO:0000358 ! phenotype
\glyphContainer A \glyph{phenotype} is represented by an elongated
-hexagon, as illustrated in \fig{phenotype}.
+hexagon, as illustrated in \fig{techref:phenotype}.
\glyphLabel A \glyph{phenotype} is identified by a label placed in an
unbordered box containing a string of characters. The characters can be
@@ -1723,11 +1723,11 @@
\glyph{phenotype} container. The label may spill outside of the container.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{images/phenotype}
\caption{The \PD glyph for \glyph{phenotype}.}
- \label{fig:phenotype}
+ \label{fig:techref:phenotype}
\end{figure}
@@ -1739,27 +1739,27 @@
\subsection{SubmapNode}
-\label{sec:submap}\label{defn:SubmapNode}
+\label{sec:techref:submap}\label{defn:SubmapNode}
The \sbgnclass{SubmapNode}\query{This name change has not been
discussed at the time of writing. The aim is to provide clarity
- between the submap and this glyph.} (figure \ref{fig:submapnodeuml}) is a
+ between the submap and this glyph.} (figure \ref{fig:techref:submapnodeuml}) is a
placeholder for another process and is used when one wishes to hide
the detail of this process from the \PDm, but make it available to the
reader as a separate related map. The \sbgnclass{Submap} is not
equivalent to an \sbgnclass{OmittedProcess} (section
-\ref{sec:omitted}). The \sbgnclass{Submap} allows the detail of
+\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
\sbgnclass{SubmapNode}, which acts as a place-holder. This is
-described in section \ref{sec:map} and the semantics of submap linking
-is defined in section \ref{sec:submaplinkingsemantics}.
+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}
\caption{The UML definition of the \sbgnclass{SubmapNode} and its
relationship to its submap, tags etc.}
- \label{fig:submapnodeuml}
+ \label{fig:techref:submapnodeuml}
\end{figure}
\subsubsection{Generalisation}
@@ -1815,7 +1815,7 @@
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.22]{images/submapglyph}
\caption{The \PD glyph for \glyph{submap}. (a) the basic glyph
@@ -1823,7 +1823,7 @@
would normally be associated with it. (b) The glyph as it would
typically be used within a map --- associated with EPN glyphs and
containing \glyph{submap terminals}.}
- \label{fig:submap}
+ \label{fig:techref:submap}
\end{figure}
\subsubsection{Changes from Previous Version}
@@ -1833,17 +1833,17 @@
so this glyph is now referred to as the SubmapNode to distinguish it.
\subsection{LogicalOperator}
-\label{sec:logic}
+\label{sec:techref:logic}
\label{defn:LogicalOperator}
\begin{figure}[htb]
\centering
\includegraphics[width = 0.5\textwidth]{images/logicaloperatoruml}
\caption{The UML definition of the \sbgnclass{LogicalOperator}.}
- \label{fig:logicaloperatoruml}
+ \label{fig:techref:logicaloperatoruml}
\end{figure}
- The \sbgnclass{LogicalOperator} (figure \ref{fig:logicaloperatoruml} performs a Boolean operation on one or
+ The \sbgnclass{LogicalOperator} (figure \ref{fig:techref:logicaloperatoruml} performs a Boolean operation on one or
more inputs to give a binary output. The input must be a Boolean
value, and are obtained from the \classref{LogicArc} connected to the
\sbgnclass{LogicOperator}. The output a two-value quantity, 0 for False and positive
@@ -1901,48 +1901,48 @@
Three glyphs are used to represent the different operator types. The
glyphs are names after the corresponding type.
-\paragraph{Glyph: \glyph{And}}\label{sec:and}
+\paragraph{Glyph: \glyph{And}}\label{sec:techref:and}
\begin{glyphDescription}
\glyphSboTerm SBO:0000173 ! and.
\glyphNode \glyph{And} is represented by a circle carrying the word ``AND''.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.5]{images/and}
\caption{The \PD glyph for \glyph{and}. Only two inputs are represented, but more would be allowed.}
- \label{fig:and}
+ \label{fig:techref:and}
\end{figure}
-\paragraph{Glyph: \glyph{Or}}\label{sec:or}
+\paragraph{Glyph: \glyph{Or}}\label{sec:techref:or}
\begin{glyphDescription}
\glyphSboTerm SBO:0000174 ! or.
\glyphNode \glyph{Or} is represented by a circle carrying the word ``OR''.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.5]{images/or}
\caption{The \PD glyph for \glyph{or}. Only two inputs are represented, but more would be allowed.}
- \label{fig:or}
+ \label{fig:techref:or}
\end{figure}
-\paragraph{Glyph: \glyph{Not}}\label{sec:not}
+\paragraph{Glyph: \glyph{Not}}\label{sec:techref:not}
\begin{glyphDescription}
\glyphSboTerm SBO:0000238 ! not.
\glyphNode \glyph{Not} is represented by a circle carrying the word ``NOT''.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.5]{images/not}
\caption{The \PD glyph for \glyph{not}.}
- \label{fig:not}
+ \label{fig:techref:not}
\end{figure}
\subsubsection{Changes from Previous Version}
@@ -1952,7 +1952,7 @@
\subsection{StoichiometricProcess}
-\label{defn:StoichiometricProcess}\label{sec:stoichiometricprocess}
+\label{defn:StoichiometricProcess}\label{sec:techref:stoichiometricprocess}
\begin{figure}[htb]
\centering
@@ -1960,7 +1960,7 @@
\caption{The UML definition of the
\sbgnclass{StiochiometricProcess}. The class interacts with
subclasses of \sbgnclass{FluxArc} and \sbgnclass{ModulationArc}.}
- \label{fig:stoichprocessuml}
+ \label{fig:techref:stoichprocessuml}
\end{figure}
A stoichiometric process\query{New concept, but discussed in previous
@@ -1983,17 +1983,17 @@
``right-hand-side'' (RHS) of the process\footnote{Note this
designation is purely for grouping and is used even then the sides
of the reaction are above and below the process.} (figure
-\ref{fig:process-sidedness}).
+\ref{fig:techref:process-sidedness}).
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.4]{images/process_sidedness}
\caption{An illustration of the ``sidedness'' of a process. The designation of LHS and RHS is essentially arbitrary.}
- \label{fig:process-sidedness}
+ \label{fig:techref:process-sidedness}
\end{figure}
In the \PDl this is represented by the
-\sbgnclass{StoichiometricProcess} (figure \ref{fig:stoichprocessuml}). It
+\sbgnclass{StoichiometricProcess} (figure \ref{fig:techref:stoichprocessuml}). It
can be one of several different types, which indicate the amount that
is known about the process or in some cases the nature of the process,
for example association and dissociation. The permitted values for
@@ -2014,7 +2014,7 @@
reason the \classref{FluxArc} has an \attrib{stoichiometry} attribute
and each \classref{EntityPoolNode} has a cardinality, which should be
balanced in a valid \PDm. This is especially important where there is
-potential ambiguity in the stoichiometry of the process (figure \ref{fig:prod-card}).
+potential ambiguity in the stoichiometry of the process (figure \ref{fig:techref:prod-card}).
@@ -2025,25 +2025,25 @@
required to clarify potentially ambiguous stoichiometry. In the
top example there is more than one possible solution, which can
only be made clear using the stoichiometry labels in the bottom examples.}
- \label{fig:prod-card}
+ \label{fig:techref:prod-card}
\end{figure}
-\label{sec: semantics reversible procs}
+\label{sec:techref: semantics reversible procs}
A stoichiometric process is deemed to be reversible its
\attrib{in\_arcs} are \sbgnclass{FluxArc}s of type `reversible' (see
-figure \ref{fig:process-reversibility}). Semantically, this permits a
+figure \ref{fig:techref:process-reversibility}). Semantically, this permits a
reversible flow of entities through the process. Modulation of a
reversible process affects the rate of flux through the process, but
does not directly affect the direction of that flow.
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.4]{images/reversible_process}
\caption{A valid reversible process. A process is reversible if its LHS and RHS contain only \glyph{production} arcs.}
- \label{fig:process-reversibility}
+ \label{fig:techref:process-reversibility}
\end{figure}
\subsubsection{Generalisation}
@@ -2125,7 +2125,7 @@
\subsubsection{Notation}
\paragraph{Glyph: \glyph{Process}}
-\label{sec:process}
+\label{sec:techref:process}
\begin{glyphDescription}
@@ -2139,76 +2139,76 @@
perpendicular to the process and does it need to be a straight line?
How should it be used when the arc connecting to it is curved.}. The
flux arcs arcs are linked to the ends of the lugs as shown in figure
-\ref{fig:process}. The lug's purpose is to 'gather' the flux arcs
+\ref{fig:techref:process}. The lug's purpose is to 'gather' the flux arcs
together before meeting the process node proper and in doing so they
emphasis the 'sides' of the reaction. Therefore the lug must have a
visually appreciable length\query{Undefined previously, but if we
define it then it should be visible.} and must be placed on opposite sides
of the process square. The modulatory arcs (section
-\ref{sec:modulation}) point to the other two sides of the box.
+\ref{sec:techref:modulation}) point to the other two sides of the box.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.4]{images/process}
\caption{The \PD glyph for \glyph{process}.}
- \label{fig:process}
+ \label{fig:techref:process}
\end{figure}
-The example in \fig{trans-phos} illustrates the use of a \glyph{process} node to represent the phosphorylation of a protein in a \PD.
+The example in \fig{techref:trans-phos} illustrates the use of a \glyph{process} node to represent the phosphorylation of a protein in a \PD.
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{examples/process-phosphorylation}
\caption{Phosphorylation of the protein MAP kinase.}
- \label{fig:trans-phos}
+ \label{fig:techref:trans-phos}
\end{figure}
-The example in \fig{trans-react} illustrates the use of a \glyph{process} node to represent a reaction between two reactants that generates three products.
+The example in \fig{techref:trans-react} illustrates the use of a \glyph{process} node to represent a reaction between two reactants that generates three products.
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{examples/process-reaction}
\caption{Reaction between ATP and fructose-6-phosphate to produce fructose-1,6-biphosphate, ADP and a proton.}
- \label{fig:trans-react}
+ \label{fig:techref:trans-react}
\end{figure}
-The example in \fig{trans-trans} illustrates the use of a \glyph{process} node to represent a translocation. The large round-cornered rectangle represents a compartment border (see \sect{compartment}).
+The example in \fig{techref:trans-trans} illustrates the use of a \glyph{process} node to represent a translocation. The large round-cornered rectangle represents a compartment border (see \sect{compartment}).
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{examples/process-translocation}
\caption{Translocation of calcium ion out of the endoplasmic reticulum. Note that the \glyph{process} does not have to be located on the boundary of the \glyph{compartment}. A \glyph{process} is not attached to any \glyph{compartment}.}
- \label{fig:trans-trans}
+ \label{fig:techref:trans-trans}
\end{figure}
-The example in \fig{trans-reverse} illustrates the use of a \glyph{process} node to represent the reversible opening and closing of an ionic channel in a \PD.
+The example in \fig{techref:trans-reverse} illustrates the use of a \glyph{process} node to represent the reversible opening and closing of an ionic channel in a \PD.
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{examples/process-reversible}
\caption{Reversible opening and closing of an ionic channel.}
- \label{fig:trans-reverse}
+ \label{fig:techref:trans-reverse}
\end{figure}
-When such a reversible process is asymmetrically modulated, it must be represented by two different processes in a \PD. \fig{trans-mod} illustrates the use of two \glyph{process} nodes to represent the reversible activation of a G-protein coupled receptor. In the absence of any effector, an equilibrium exists between the inactive and active forms. The agonist stabilises the active form, while the inverse agonist stabilises the inactive form.
+When such a reversible process is asymmetrically modulated, it must be represented by two different processes in a \PD. \fig{techref:trans-mod} illustrates the use of two \glyph{process} nodes to represent the reversible activation of a G-protein coupled receptor. In the absence of any effector, an equilibrium exists between the inactive and active forms. The agonist stabilises the active form, while the inverse agonist stabilises the inactive form.
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{examples/process-modulated}
\caption{The reversible activation of a G-protein coupled receptor.}
- \label{fig:trans-mod}
+ \label{fig:techref:trans-mod}
\end{figure}
-The example in \fig{trans-dim} presents the conversion of two galactoses into a lactose. Galactoses are represented by only one \glyph{simple chemical}, the cardinality being carried by the \glyph{consumption} arc.
+The example in \fig{techref:trans-dim} presents the conversion of two galactoses into a lactose. Galactoses are represented by only one \glyph{simple chemical}, the cardinality being carried by the \glyph{consumption} arc.
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.3]{examples/process-dimerisation}
\caption{Conversion of two galactoses into a lactose.}
- \label{fig:trans-dim}
+ \label{fig:techref:trans-dim}
\end{figure}
@@ -2216,7 +2216,7 @@
%% Omitted Process
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\paragraph{Glyph: \glyph{Omitted process}}\label{sec:omitted}
+\paragraph{Glyph: \glyph{Omitted process}}\label{sec:techref:omitted}
\begin{glyphDescription}
@@ -2225,11 +2225,11 @@
\glyphNode An \glyph{omitted process} is represented by a \glyph{process} in which the square box contains a two parallel slanted lines oriented northwest-to-southeast and separated by an empty space.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.5]{images/omitted}
\caption{The \PD glyph for \glyph{omitted process}.}
- \label{fig:omitted}
+ \label{fig:techref:omitted}
\end{figure}
@@ -2237,18 +2237,18 @@
%% Uncertain Process
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\paragraph{Glyph: \glyph{Uncertain process}}\label{sec:uncertain}
+\paragraph{Glyph: \glyph{Uncertain process}}\label{sec:techref:uncertain}
\begin{glyphDescription}
\glyphSboTerm SBO:0000396 ! uncertain process.
\glyphNode An \glyph{uncertain process} is represented by a \glyph{process} which square box contains a question mark.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0.5]{images/uncertain}
\caption{The \PD glyph for an \glyph{uncertain process}.}
- \label{fig:uncertain}
+ \label{fig:techref:uncertain}
\end{figure}
@@ -2256,7 +2256,7 @@
%% Association
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\paragraph{Glyph: \glyph{Association}}\label{sec:association}
+\paragraph{Glyph: \glyph{Association}}\label{sec:techref:association}
\begin{glyphDescription}
@@ -2264,45 +2264,45 @@
\glyphNode An \glyph{association} between several entities is represented by a filled disc linked to two connectors, small arcs attached on point separated by 180 degrees. The consumption (\sect{consumption}) and production (\sect{production}) arcs are linked to the extremities of those connectors.
\end{glyphDescription}
-\begin{figure}[H]
+\begin{figure}[htb]
\centering
\includegraphics[scale = 0...
[truncated message content] |
|
From: <lp...@us...> - 2013-04-25 17:10:22
|
Revision: 862
http://sourceforge.net/p/sbgn/code/862
Author: lptolik
Date: 2013-04-25 17:10:19 +0000 (Thu, 25 Apr 2013)
Log Message:
-----------
fix ticket #26
Modified Paths:
--------------
EntityRelationship/trunk/sources/stateVariable.tex
EntityRelationship/trunk/sources/variableValue.tex
Modified: EntityRelationship/trunk/sources/stateVariable.tex
===================================================================
--- EntityRelationship/trunk/sources/stateVariable.tex 2013-03-22 15:52:38 UTC (rev 861)
+++ EntityRelationship/trunk/sources/stateVariable.tex 2013-04-25 17:10:19 UTC (rev 862)
@@ -27,7 +27,7 @@
\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 state variable, vertical state variable, \glyph{location}, \glyph{existence}.}
\label{fig:state-var}
\end{figure}
Modified: EntityRelationship/trunk/sources/variableValue.tex
===================================================================
--- EntityRelationship/trunk/sources/variableValue.tex 2013-03-22 15:52:38 UTC (rev 861)
+++ EntityRelationship/trunk/sources/variableValue.tex 2013-04-25 17:10:19 UTC (rev 862)
@@ -21,7 +21,7 @@
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/variableValue}
- \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{variable value}.}
\label{fig:var-value}
\end{figure}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fal...@us...> - 2013-03-22 15:52:40
|
Revision: 861
http://sourceforge.net/p/sbgn/code/861
Author: falkschreiber
Date: 2013-03-22 15:52:38 +0000 (Fri, 22 Mar 2013)
Log Message:
-----------
Added Paths:
-----------
ProcessDiagram/trunk/UserManual/images/Fig12.png
ProcessDiagram/trunk/UserManual/images/Fig12.sbgn
ProcessDiagram/trunk/UserManual/images/Fig13.png
ProcessDiagram/trunk/UserManual/images/Fig13.sbgn
ProcessDiagram/trunk/UserManual/images/Fig14.png
ProcessDiagram/trunk/UserManual/images/Fig14.sbgn
ProcessDiagram/trunk/UserManual/images/Fig15.png
ProcessDiagram/trunk/UserManual/images/Fig15.sbgn
Added: ProcessDiagram/trunk/UserManual/images/Fig12.png
===================================================================
(Binary files differ)
Index: ProcessDiagram/trunk/UserManual/images/Fig12.png
===================================================================
--- ProcessDiagram/trunk/UserManual/images/Fig12.png 2013-03-16 18:27:16 UTC (rev 860)
+++ ProcessDiagram/trunk/UserManual/images/Fig12.png 2013-03-22 15:52:38 UTC (rev 861)
Property changes on: ProcessDiagram/trunk/UserManual/images/Fig12.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: ProcessDiagram/trunk/UserManual/images/Fig12.sbgn
===================================================================
--- ProcessDiagram/trunk/UserManual/images/Fig12.sbgn (rev 0)
+++ ProcessDiagram/trunk/UserManual/images/Fig12.sbgn 2013-03-22 15:52:38 UTC (rev 861)
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+ <map language="process description">
+ <glyph id="glyph1" class="simple chemical">
+ <label text="S1"/>
+ <bbox y="180.0" x="100.0" h="40.0" w="40.0"/>
+ </glyph>
+ <glyph id="glyph3" class="simple chemical">
+ <label text="S2"/>
+ <bbox y="240.0" x="100.0" h="40.0" w="40.0"/>
+ </glyph>
+ <glyph id="glyph2" class="simple chemical">
+ <label text="P1"/>
+ <bbox y="210.0" x="240.0" h="40.0" w="40.0"/>
+ </glyph>
+ <glyph id="glyph0" class="macromolecule">
+ <label text="E"/>
+ <bbox y="130.0" x="160.0" h="40.0" w="60.0"/>
+ </glyph>
+ <glyph id="glyph4" class="process">
+ <bbox y="222.5" x="182.5" h="15.0" w="15.0"/>
+ <port y="230.0" x="175.0" id="glyph4.1"/>
+ <port y="230.0" x="205.0" id="glyph4.2"/>
+ </glyph>
+ <arc target="glyph4.1" source="glyph1" id="arc0" class="consumption">
+ <start y="209.57704" x="137.5579"/>
+ <end y="230.0" x="175.0"/>
+ </arc>
+ <arc target="glyph4.1" source="glyph3" id="arc1" class="consumption">
+ <start y="250.42296" x="137.5579"/>
+ <end y="230.0" x="175.0"/>
+ </arc>
+ <arc target="glyph2" source="glyph4.2" id="arc2" class="production">
+ <start y="230.0" x="205.0"/>
+ <end y="230.0" x="240.0"/>
+ </arc>
+ <arc target="glyph4" source="glyph0" id="arc3" class="catalysis">
+ <start y="170.0" x="190.0"/>
+ <end y="222.5" x="190.0"/>
+ </arc>
+ </map>
+</sbgn>
Added: ProcessDiagram/trunk/UserManual/images/Fig13.png
===================================================================
(Binary files differ)
Index: ProcessDiagram/trunk/UserManual/images/Fig13.png
===================================================================
--- ProcessDiagram/trunk/UserManual/images/Fig13.png 2013-03-16 18:27:16 UTC (rev 860)
+++ ProcessDiagram/trunk/UserManual/images/Fig13.png 2013-03-22 15:52:38 UTC (rev 861)
Property changes on: ProcessDiagram/trunk/UserManual/images/Fig13.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: ProcessDiagram/trunk/UserManual/images/Fig13.sbgn
===================================================================
--- ProcessDiagram/trunk/UserManual/images/Fig13.sbgn (rev 0)
+++ ProcessDiagram/trunk/UserManual/images/Fig13.sbgn 2013-03-22 15:52:38 UTC (rev 861)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+ <map language="process description">
+ <glyph id="glyph1" class="macromolecule">
+ <label text="X"/>
+ <bbox y="380.0" x="100.0" h="40.0" w="60.0"/>
+ </glyph>
+ <glyph id="glyph3" class="macromolecule">
+ <label text="Y"/>
+ <bbox y="460.0" x="100.0" h="40.0" w="60.0"/>
+ </glyph>
+ <glyph id="glyph5" class="association">
+ <bbox y="428.0" x="208.0" h="24.0" w="24.0"/>
+ <port y="440.0" x="196.0" id="glyph5.1"/>
+ <port y="440.0" x="244.0" id="glyph5.2"/>
+ </glyph>
+ <glyph id="glyph0" class="complex">
+ <bbox y="380.0" x="265.0" h="120.0" w="90.0"/>
+ <glyph id="glyph4" class="macromolecule">
+ <label text="X"/>
+ <bbox y="390.0" x="280.0" h="40.0" w="60.0"/>
+ </glyph>
+ <glyph id="glyph2" class="macromolecule">
+ <label text="Y"/>
+ <bbox y="450.0" x="280.0" h="40.0" w="60.0"/>
+ </glyph>
+ </glyph>
+ <arc target="glyph5.1" source="glyph1" id="arc0" class="consumption">
+ <start y="418.18182" x="160.0"/>
+ <end y="440.0" x="196.0"/>
+ </arc>
+ <arc target="glyph5.1" source="glyph3" id="arc1" class="consumption">
+ <start y="461.81818" x="160.0"/>
+ <end y="440.0" x="196.0"/>
+ </arc>
+ <arc target="glyph0" source="glyph5.2" id="arc2" class="production">
+ <start y="440.0" x="244.0"/>
+ <end y="440.0" x="265.0"/>
+ </arc>
+ </map>
+</sbgn>
Added: ProcessDiagram/trunk/UserManual/images/Fig14.png
===================================================================
(Binary files differ)
Index: ProcessDiagram/trunk/UserManual/images/Fig14.png
===================================================================
--- ProcessDiagram/trunk/UserManual/images/Fig14.png 2013-03-16 18:27:16 UTC (rev 860)
+++ ProcessDiagram/trunk/UserManual/images/Fig14.png 2013-03-22 15:52:38 UTC (rev 861)
Property changes on: ProcessDiagram/trunk/UserManual/images/Fig14.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: ProcessDiagram/trunk/UserManual/images/Fig14.sbgn
===================================================================
--- ProcessDiagram/trunk/UserManual/images/Fig14.sbgn (rev 0)
+++ ProcessDiagram/trunk/UserManual/images/Fig14.sbgn 2013-03-22 15:52:38 UTC (rev 861)
@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+ <map language="process description">
+ <glyph id="glyph0" class="macromolecule">
+ <label text="X"/>
+ <bbox y="380.0" x="100.0" h="40.0" w="60.0"/>
+ <glyph id="glyph0a" class="unit of information">
+ <label text="ct:gene"/>
+ <bbox y="372.0" x="89.5" h="16.0" w="51.0"/>
+ </glyph>
+ </glyph>
+ <glyph id="glyph1" class="macromolecule">
+ <label text="TF"/>
+ <bbox y="460.0" x="100.0" h="40.0" w="60.0"/>
+ <glyph id="glyph1a" class="unit of information">
+ <label text="mt:prot"/>
+ <bbox y="452.0" x="91.0" h="16.0" w="48.0"/>
+ </glyph>
+ </glyph>
+ <glyph id="glyph4" class="source and sink">
+ <bbox y="360.0" x="290.0" h="40.0" w="40.0"/>
+ </glyph>
+ <glyph id="glyph2" class="nucleic acid feature">
+ <label text="X"/>
+ <bbox y="480.0" x="280.0" h="40.0" w="60.0"/>
+ </glyph>
+ <glyph id="glyph3" class="and">
+ <bbox y="419.0" x="189.0" h="42.0" w="42.0"/>
+ <port y="440.0" x="168.0" id="glyph3.1"/>
+ <port y="440.0" x="252.0" id="glyph3.2"/>
+ </glyph>
+ <glyph id="glyph5" orientation="vertical" class="process">
+ <bbox y="432.5" x="302.5" h="15.0" w="15.0"/>
+ <port y="425.0" x="310.0" id="glyph5.1"/>
+ <port y="455.0" x="310.0" id="glyph5.2"/>
+ </glyph>
+ <arc target="glyph3.1" source="glyph0" id="arc0" class="logic arc">
+ <start y="420.0" x="149.0"/>
+ <end y="440.0" x="168.0"/>
+ </arc>
+ <arc target="glyph3.1" source="glyph1" id="arc1" class="logic arc">
+ <start y="460.0" x="149.0"/>
+ <end y="440.0" x="168.0"/>
+ </arc>
+ <arc target="glyph5.1" source="glyph4" id="arc2" class="consumption">
+ <start y="400.0" x="310.0"/>
+ <end y="425.0" x="310.0"/>
+ </arc>
+ <arc target="glyph2" source="glyph5.2" id="arc3" class="production">
+ <start y="455.0" x="310.0"/>
+ <end y="480.0" x="310.0"/>
+ </arc>
+ <arc target="glyph5" source="glyph3.2" id="arc4" class="necessary stimulation">
+ <start y="440.0" x="252.0"/>
+ <end y="440.0" x="302.5"/>
+ </arc>
+ </map>
+</sbgn>
Added: ProcessDiagram/trunk/UserManual/images/Fig15.png
===================================================================
(Binary files differ)
Index: ProcessDiagram/trunk/UserManual/images/Fig15.png
===================================================================
--- ProcessDiagram/trunk/UserManual/images/Fig15.png 2013-03-16 18:27:16 UTC (rev 860)
+++ ProcessDiagram/trunk/UserManual/images/Fig15.png 2013-03-22 15:52:38 UTC (rev 861)
Property changes on: ProcessDiagram/trunk/UserManual/images/Fig15.png
___________________________________________________________________
Added: svn:mime-type
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+application/octet-stream
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Added: ProcessDiagram/trunk/UserManual/images/Fig15.sbgn
===================================================================
--- ProcessDiagram/trunk/UserManual/images/Fig15.sbgn (rev 0)
+++ ProcessDiagram/trunk/UserManual/images/Fig15.sbgn 2013-03-22 15:52:38 UTC (rev 861)
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+ <map language="process description">
+ <glyph compartmentOrder="-5.0" id="glyph0" class="compartment">
+ <label text=" cytosol"/>
+ <bbox y="340.0" x="25.0" h="200.0" w="370.0"/>
+ </glyph>
+ <glyph compartmentOrder="-4.0" id="glyph1" class="compartment">
+ <label text="nucleus">
+ <bbox y="388.0" x="263.5" h="16.0" w="53.0"/>
+ </label>
+ <bbox y="380.0" x="215.0" h="120.0" w="150.0"/>
+ </glyph>
+ <glyph id="glyph2" class="macromolecule">
+ <label text="X"/>
+ <bbox y="420.0" x="60.0" h="40.0" w="60.0"/>
+ </glyph>
+ <glyph id="glyph4" class="process">
+ <bbox y="432.5" x="232.5" h="15.0" w="15.0"/>
+ <port y="440.0" x="225.0" id="glyph4.1"/>
+ <port y="440.0" x="255.0" id="glyph4.2"/>
+ </glyph>
+ <glyph id="glyph3" class="macromolecule">
+ <label text="X"/>
+ <bbox y="420.0" x="280.0" h="40.0" w="60.0"/>
+ </glyph>
+ <arc target="glyph4.1" source="glyph2" id="arc0" class="consumption">
+ <start y="440.0" x="120.0"/>
+ <end y="440.0" x="225.0"/>
+ </arc>
+ <arc target="glyph3" source="glyph4.2" id="arc1" class="production">
+ <start y="440.0" x="255.0"/>
+ <end y="440.0" x="280.0"/>
+ </arc>
+ </map>
+</sbgn>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <stu...@us...> - 2013-03-16 18:27:23
|
Revision: 860
http://sbgn.svn.sourceforge.net/sbgn/?rev=860&view=rev
Author: stumoodie
Date: 2013-03-16 18:27:16 +0000 (Sat, 16 Mar 2013)
Log Message:
-----------
Added ignires and updated pdf
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
Property Changed:
----------------
ProcessDiagram/trunk/Specification/
Property changes on: ProcessDiagram/trunk/Specification
___________________________________________________________________
Added: svn:ignore
+ sbgn_PD-level1.aux
sbgn_PD-level1.bbl
sbgn_PD-level1.blg
sbgn_PD-level1.fdb_latexmk
sbgn_PD-level1.log
sbgn_PD-level1.out
sbgn_PD-level1.toc
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <stu...@us...> - 2013-03-16 18:23:19
|
Revision: 859
http://sbgn.svn.sourceforge.net/sbgn/?rev=859&view=rev
Author: stumoodie
Date: 2013-03-16 18:23:05 +0000 (Sat, 16 Mar 2013)
Log Message:
-----------
Reoganised spec. Merged in parts of manual
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/Makefile
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
ProcessDiagram/trunk/Specification/sources/concepts.tex
ProcessDiagram/trunk/Specification/sources/front-page.tex
ProcessDiagram/trunk/Specification/sources/glyphs.tex
ProcessDiagram/trunk/Specification/sources/grammar.tex
ProcessDiagram/trunk/Specification/sources/introduction.tex
ProcessDiagram/trunk/Specification/sources/latex-macros.tex
ProcessDiagram/trunk/Specification/sources/latex-style.tex
ProcessDiagram/trunk/Specification/sources/revision_history.tex
ProcessDiagram/trunk/Specification/sources/toc.tex
Added Paths:
-----------
ProcessDiagram/trunk/Specification/images/Fig12.svg
ProcessDiagram/trunk/Specification/images/Fig13.svg
ProcessDiagram/trunk/Specification/images/Fig14.svg
ProcessDiagram/trunk/Specification/images/Fig15.svg
ProcessDiagram/trunk/Specification/images/MAPK-only.svg
ProcessDiagram/trunk/Specification/le_images/
ProcessDiagram/trunk/Specification/le_images/Fig12.pdf
ProcessDiagram/trunk/Specification/le_images/Fig12.svg
ProcessDiagram/trunk/Specification/le_images/Fig13.pdf
ProcessDiagram/trunk/Specification/le_images/Fig13.svg
ProcessDiagram/trunk/Specification/le_images/Fig14.pdf
ProcessDiagram/trunk/Specification/le_images/Fig14.svg
ProcessDiagram/trunk/Specification/le_images/Fig15.pdf
ProcessDiagram/trunk/Specification/le_images/Fig15.svg
ProcessDiagram/trunk/Specification/le_images/MAPK-NoVar.pdf
ProcessDiagram/trunk/Specification/le_images/MAPK-NoVar.svg
ProcessDiagram/trunk/Specification/le_images/MAPK-OneVar.pdf
ProcessDiagram/trunk/Specification/le_images/MAPK-OneVar.svg
ProcessDiagram/trunk/Specification/le_images/MAPK-TwoVar.pdf
ProcessDiagram/trunk/Specification/le_images/MAPK-TwoVar.svg
ProcessDiagram/trunk/Specification/le_images/MAPK-only.pdf
ProcessDiagram/trunk/Specification/le_images/MAPK-only.svg
ProcessDiagram/trunk/Specification/le_images/Makefile
ProcessDiagram/trunk/Specification/le_images/NucAcidFeat-examples.pdf
ProcessDiagram/trunk/Specification/le_images/NucAcidFeat-examples.svg
ProcessDiagram/trunk/Specification/le_images/and.pdf
ProcessDiagram/trunk/Specification/le_images/and.svg
ProcessDiagram/trunk/Specification/le_images/association-MPF.pdf
ProcessDiagram/trunk/Specification/le_images/association-MPF.svg
ProcessDiagram/trunk/Specification/le_images/association-multimerisation.pdf
ProcessDiagram/trunk/Specification/le_images/association-multimerisation.svg
ProcessDiagram/trunk/Specification/le_images/association-unamed.pdf
ProcessDiagram/trunk/Specification/le_images/association-unamed.svg
ProcessDiagram/trunk/Specification/le_images/association.pdf
ProcessDiagram/trunk/Specification/le_images/association.svg
ProcessDiagram/trunk/Specification/le_images/catalysis-MAPK.pdf
ProcessDiagram/trunk/Specification/le_images/catalysis-MAPK.svg
ProcessDiagram/trunk/Specification/le_images/catalysis.pdf
ProcessDiagram/trunk/Specification/le_images/catalysis.svg
ProcessDiagram/trunk/Specification/le_images/compartment.pdf
ProcessDiagram/trunk/Specification/le_images/compartment.svg
ProcessDiagram/trunk/Specification/le_images/complex-examples.pdf
ProcessDiagram/trunk/Specification/le_images/complex-examples.svg
ProcessDiagram/trunk/Specification/le_images/complex.pdf
ProcessDiagram/trunk/Specification/le_images/complex.svg
ProcessDiagram/trunk/Specification/le_images/consumption.pdf
ProcessDiagram/trunk/Specification/le_images/consumption.svg
ProcessDiagram/trunk/Specification/le_images/dissociation-ribosome.pdf
ProcessDiagram/trunk/Specification/le_images/dissociation-ribosome.svg
ProcessDiagram/trunk/Specification/le_images/dissociation.pdf
ProcessDiagram/trunk/Specification/le_images/dissociation.svg
ProcessDiagram/trunk/Specification/le_images/equivalence.pdf
ProcessDiagram/trunk/Specification/le_images/equivalence.svg
ProcessDiagram/trunk/Specification/le_images/genetic-plain.pdf
ProcessDiagram/trunk/Specification/le_images/genetic-plain.svg
ProcessDiagram/trunk/Specification/le_images/genetic.pdf
ProcessDiagram/trunk/Specification/le_images/genetic.svg
ProcessDiagram/trunk/Specification/le_images/hemoglobin-complex.pdf
ProcessDiagram/trunk/Specification/le_images/hemoglobin-complex.svg
ProcessDiagram/trunk/Specification/le_images/hemoglobin-macromolecule.pdf
ProcessDiagram/trunk/Specification/le_images/hemoglobin-macromolecule.svg
ProcessDiagram/trunk/Specification/le_images/hemoglobin-multimer.pdf
ProcessDiagram/trunk/Specification/le_images/hemoglobin-multimer.svg
ProcessDiagram/trunk/Specification/le_images/inhibition.pdf
ProcessDiagram/trunk/Specification/le_images/inhibition.svg
ProcessDiagram/trunk/Specification/le_images/labeledCloneMarker.pdf
ProcessDiagram/trunk/Specification/le_images/labeledCloneMarker.svg
ProcessDiagram/trunk/Specification/le_images/logicArc.pdf
ProcessDiagram/trunk/Specification/le_images/logicArc.svg
ProcessDiagram/trunk/Specification/le_images/macromolecule-examples.pdf
ProcessDiagram/trunk/Specification/le_images/macromolecule-examples.svg
ProcessDiagram/trunk/Specification/le_images/macromolecule-plain.pdf
ProcessDiagram/trunk/Specification/le_images/macromolecule-plain.svg
ProcessDiagram/trunk/Specification/le_images/macromolecule.pdf
ProcessDiagram/trunk/Specification/le_images/macromolecule.svg
ProcessDiagram/trunk/Specification/le_images/modulation-VOC.pdf
ProcessDiagram/trunk/Specification/le_images/modulation-VOC.svg
ProcessDiagram/trunk/Specification/le_images/modulation-nAChR.pdf
ProcessDiagram/trunk/Specification/le_images/modulation-nAChR.svg
ProcessDiagram/trunk/Specification/le_images/modulation.pdf
ProcessDiagram/trunk/Specification/le_images/modulation.svg
ProcessDiagram/trunk/Specification/le_images/multimer-examples.pdf
ProcessDiagram/trunk/Specification/le_images/multimer-examples.svg
ProcessDiagram/trunk/Specification/le_images/multimer.pdf
ProcessDiagram/trunk/Specification/le_images/multimer.svg
ProcessDiagram/trunk/Specification/le_images/necessary_stim-genetic.pdf
ProcessDiagram/trunk/Specification/le_images/necessary_stim-genetic.svg
ProcessDiagram/trunk/Specification/le_images/necessary_stim-transport.pdf
ProcessDiagram/trunk/Specification/le_images/necessary_stim-transport.svg
ProcessDiagram/trunk/Specification/le_images/necessary_stim.pdf
ProcessDiagram/trunk/Specification/le_images/necessary_stim.svg
ProcessDiagram/trunk/Specification/le_images/not.pdf
ProcessDiagram/trunk/Specification/le_images/not.svg
ProcessDiagram/trunk/Specification/le_images/omitted.pdf
ProcessDiagram/trunk/Specification/le_images/omitted.svg
ProcessDiagram/trunk/Specification/le_images/or.pdf
ProcessDiagram/trunk/Specification/le_images/or.svg
ProcessDiagram/trunk/Specification/le_images/perturbing_agent.pdf
ProcessDiagram/trunk/Specification/le_images/perturbing_agent.svg
ProcessDiagram/trunk/Specification/le_images/phenotype-MPF.pdf
ProcessDiagram/trunk/Specification/le_images/phenotype-MPF.svg
ProcessDiagram/trunk/Specification/le_images/phenotype.pdf
ProcessDiagram/trunk/Specification/le_images/phenotype.svg
ProcessDiagram/trunk/Specification/le_images/process-dimerisation.pdf
ProcessDiagram/trunk/Specification/le_images/process-dimerisation.svg
ProcessDiagram/trunk/Specification/le_images/process-modulated.pdf
ProcessDiagram/trunk/Specification/le_images/process-modulated.svg
ProcessDiagram/trunk/Specification/le_images/process-phosphorylation.pdf
ProcessDiagram/trunk/Specification/le_images/process-phosphorylation.svg
ProcessDiagram/trunk/Specification/le_images/process-reaction.pdf
ProcessDiagram/trunk/Specification/le_images/process-reaction.svg
ProcessDiagram/trunk/Specification/le_images/process-reversible.pdf
ProcessDiagram/trunk/Specification/le_images/process-reversible.svg
ProcessDiagram/trunk/Specification/le_images/process-translocation.pdf
ProcessDiagram/trunk/Specification/le_images/process-translocation.svg
ProcessDiagram/trunk/Specification/le_images/process.pdf
ProcessDiagram/trunk/Specification/le_images/process.svg
ProcessDiagram/trunk/Specification/le_images/production.pdf
ProcessDiagram/trunk/Specification/le_images/production.svg
ProcessDiagram/trunk/Specification/le_images/refcard.pdf
ProcessDiagram/trunk/Specification/le_images/refcard.svg
ProcessDiagram/trunk/Specification/le_images/simpleChemical-examples.pdf
ProcessDiagram/trunk/Specification/le_images/simpleChemical-examples.svg
ProcessDiagram/trunk/Specification/le_images/simpleChemical.pdf
ProcessDiagram/trunk/Specification/le_images/simpleChemical.svg
ProcessDiagram/trunk/Specification/le_images/simpleCloneMarker.pdf
ProcessDiagram/trunk/Specification/le_images/simpleCloneMarker.svg
ProcessDiagram/trunk/Specification/le_images/sourceSink.pdf
ProcessDiagram/trunk/Specification/le_images/sourceSink.svg
ProcessDiagram/trunk/Specification/le_images/stateVariable.pdf
ProcessDiagram/trunk/Specification/le_images/stateVariable.svg
ProcessDiagram/trunk/Specification/le_images/stimulation-reversible.pdf
ProcessDiagram/trunk/Specification/le_images/stimulation-reversible.svg
ProcessDiagram/trunk/Specification/le_images/stimulation.pdf
ProcessDiagram/trunk/Specification/le_images/stimulation.svg
ProcessDiagram/trunk/Specification/le_images/submap-dissociated.pdf
ProcessDiagram/trunk/Specification/le_images/submap-dissociated.svg
ProcessDiagram/trunk/Specification/le_images/submap-folded.pdf
ProcessDiagram/trunk/Specification/le_images/submap-folded.svg
ProcessDiagram/trunk/Specification/le_images/submap-unfolded.pdf
ProcessDiagram/trunk/Specification/le_images/submap-unfolded.svg
ProcessDiagram/trunk/Specification/le_images/submap.pdf
ProcessDiagram/trunk/Specification/le_images/submap.svg
ProcessDiagram/trunk/Specification/le_images/uncertain.pdf
ProcessDiagram/trunk/Specification/le_images/uncertain.svg
ProcessDiagram/trunk/Specification/le_images/unitInformation.pdf
ProcessDiagram/trunk/Specification/le_images/unitInformation.svg
ProcessDiagram/trunk/Specification/le_images/unspecified.pdf
ProcessDiagram/trunk/Specification/le_images/unspecified.svg
ProcessDiagram/trunk/Specification/sources/language_overview.tex
ProcessDiagram/trunk/Specification/sources/worked_examples.tex
Modified: ProcessDiagram/trunk/Specification/Makefile
===================================================================
--- ProcessDiagram/trunk/Specification/Makefile 2013-03-16 16:00:58 UTC (rev 858)
+++ ProcessDiagram/trunk/Specification/Makefile 2013-03-16 18:23:05 UTC (rev 859)
@@ -15,6 +15,7 @@
all default: images examples
$(MAKE) -C examples
$(MAKE) -C images
+ $(MAKE) -C le_images
$(LATEX) $(MAIN).tex
$(LATEX) $(MAIN).tex
$(BIBTEX) $(MAIN)
Added: ProcessDiagram/trunk/Specification/images/Fig12.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/images/Fig12.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/images/Fig13.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/images/Fig13.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/images/Fig14.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/images/Fig14.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/images/Fig15.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/images/Fig15.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/images/MAPK-only.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/images/MAPK-only.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/le_images/Fig12.pdf
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/Fig12.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/pdf
Added: ProcessDiagram/trunk/Specification/le_images/Fig12.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/Fig12.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/le_images/Fig13.pdf
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/Fig13.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/pdf
Added: ProcessDiagram/trunk/Specification/le_images/Fig13.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/Fig13.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/le_images/Fig14.pdf
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/Fig14.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/pdf
Added: ProcessDiagram/trunk/Specification/le_images/Fig14.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/Fig14.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/le_images/Fig15.pdf
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/Fig15.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/pdf
Added: ProcessDiagram/trunk/Specification/le_images/Fig15.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/Fig15.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/le_images/MAPK-NoVar.pdf
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/MAPK-NoVar.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/pdf
Added: ProcessDiagram/trunk/Specification/le_images/MAPK-NoVar.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/MAPK-NoVar.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/le_images/MAPK-OneVar.pdf
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/MAPK-OneVar.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/pdf
Added: ProcessDiagram/trunk/Specification/le_images/MAPK-OneVar.svg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/Specification/le_images/MAPK-OneVar.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg+xml
Added: ProcessDiagram/trunk/Specification/le_images/MAPK-TwoVar.pdf
===================================================================
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Added: ProcessDiagram/trunk/Specification/le_images/Makefile
===================================================================
--- ProcessDiagram/trunk/Specification/le_images/Makefile (rev 0)
+++ ProcessDiagram/trunk/Specification/le_images/Makefile 2013-03-16 18:23:05 UTC (rev 859)
@@ -0,0 +1,20 @@
+.PHONY: clean
+
+SVG_FILES := $(wildcard *.svg)
+
+PDF_FILES := $(patsubst %.svg,%.pdf, $(SVG_FILES))
+
+%.pdf : %.svg
+ inkscape -D -z --file=$< --export-pdf=$@
+
+all: $(PDF_FILES)
+# echo $(PDF_FILES)
+
+
+
+
+
+clean:
+ -rm -f *.pdf
+
+
Added: ProcessDiagram/trunk/Specification/le_images/NucAcidFeat-examples.pdf
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