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From: <tcz...@us...> - 2015-07-16 04:13:22
|
Revision: 934
http://sourceforge.net/p/sbgn/code/934
Author: tczauderna
Date: 2015-07-16 04:13:19 +0000 (Thu, 16 Jul 2015)
Log Message:
-----------
fixed a typo in affiliation
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 2015-07-16 04:07:53 UTC (rev 933)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2015-07-16 04:13:19 UTC (rev 934)
@@ -1,48 +1,410 @@
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From: <tcz...@us...> - 2015-07-16 04:07:55
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Revision: 933
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From: <tcz...@us...> - 2015-07-16 03:43:23
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Revision: 932
http://sourceforge.net/p/sbgn/code/932
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From: <hua...@us...> - 2015-07-15 18:44:37
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Revision: 931
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From: <hua...@us...> - 2015-07-15 18:43:23
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Revision: 930
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-@Book{DiBattista:1998,
- author = {{D}i {B}attista, G. and Eades, P. and Tamassia, R. and Tollis, I.~G.},
- title = {Graph Drawing: Algorithms for the Visualization of Graphs},
- year = {1998},
- publisher = {Prentice Hall},
- address = {New Jersey},
-}
-
-@Book{Kaufmann:2001,
- author = {Kaufmann, M. and Wagner, D.},
- title = {Drawing Graphs: Methods and Models},
- year = {2001},
- volume = {2025},
- series = {Lecture Notes in Computer Science Tutorial},
- publisher = {Springer},
-}
-
-@article{Hucka:2003,
- AUTHOR = {Hucka, M. and Finney, A. and Sauro, H.~M. and Bolouri, H. and Doyle, J.~C. and Kitano, H. and Arkin, A.~P.
- and Bornstein, B.~J. and Bray, D. and Cornish-Bowden, A. and Cuellar, A.~A. and Dronov, S. and Gilles, E.~D.
- and Ginkel, M. and Gor, V. and Goryanin, I.~I. and Hedley, W.~J. and Hodgman, T.~C. and Hofmeyr, J.-H.
- and Hunter, P.~J. and Juty, N.~S. and Kasberger, J.~L. and Kremling, A. and Kummer, U. and Le Nov\`{e}re, N.
- and Loew, L.~M. and Lucio, D. and Mendes, P. and Minch, E. and Mjolsness, E.~D. and Nakayama, Y. and Nelson, M.~R.
- and Nielsen, P.~F. and Sakurada, T. and Schaff, J.~C. and Shapiro, B.~E. and Shimizu, T.~S. and Spence, H.~D.
- and Stelling, J. and Takahashi, K. and Tomita, M. and Wagner, J. and Wang, J.},
- TITLE = {The {S}ystems {B}iology {M}arkup {L}anguage ({SBML}): A Medium for Representation and Exchange of Biochemical Network Models},
- JOURNAL = {Bioinformatics},
- VOLUME = {19},
- NUMBER = {4},
- PAGES = {524--531},
- YEAR = {2003},
-}
-
-@TechReport{Lenov:2008,
- author = {Le Nov\`{e}re, N. and Moodie, S. and Sorokin, A. and Hucka, M. and Schreiber, F. and Demir, E. and Mi, H. and Matsuoka, Y.
- and Wegner, K. and Kitano, H.},
- title = {Systems Biology Graphical Notation: Process Diagram Level 1},
- institution = {},
- year = {2008},
- type = {Nature Precedings},
- doi = {10101/npre.2008.2320.1}
-}
-
-@Article{Adorno:2009,
- author = {M. Adorno and M. Cordenonsi and M. Montagner and S. Dupont and C. Wong and B. Hann and A. Solari and
- S. Bobisse and M.~B. Rondina and V. Guzzardo and A.~R. Parenti and A. Rosato and S. Bicciato and A. Balmain and S. Piccolo},
- title = {A Mutant-p53/Smad complex opposes p63 to empower {TGF}beta-induced metastasis},
- journal = {Cell},
- year = {2009},
- volume = {137},
- number = {1},
- pages = {87--98}
-}
-
-@Article{Pan:2009,
- author = {D. Pan and M. Fujimoto and A. Lopes and Y. Wang},
- title = {Twist-1 Is a {PPAR}$\delta$-Inducible, Negative-Feedback Regulator of {PGC}-1$\alpha$ in Brown Fat Metabolism },
- journal = {Cell},
- year = {2009},
- volume = {137},
- number = {1},
- pages = {73--86}
-}
-
-@Article{Massague:1998,
- author = {J. Massague},
- title = {{TGF}-beta signal transduction},
- journal = {Annual Review Biochemistry},
- year = {1998},
- volume = {67},
- pages = {753--791}
-}
-
-@Article{Derynck:2001,
- author = {R. Derynck and R.~J. Akhurst and A. Balmain},
- title = {{TGF}-beta signaling in tumor suppression and cancer progression},
- journal = {Nature Genetics},
- year = {2001},
- volume = {29},
- number = {2},
- 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.}
-}
-
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <hua...@us...> - 2015-07-15 18:39:15
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Revision: 929
http://sourceforge.net/p/sbgn/code/929
Author: huaiyumi
Date: 2015-07-15 18:39:13 +0000 (Wed, 15 Jul 2015)
Log Message:
-----------
update AF tag
Removed Paths:
-------------
ActivityFlow/tags/L1R1.2/examples/
ActivityFlow/tags/L1R1.2/images/
ActivityFlow/tags/L1R1.2/sources/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
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From: <hua...@us...> - 2015-07-15 17:43:02
|
Revision: 928
http://sourceforge.net/p/sbgn/code/928
Author: huaiyumi
Date: 2015-07-15 17:42:59 +0000 (Wed, 15 Jul 2015)
Log Message:
-----------
Update acknowledgments
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/acknowledgments.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2015-07-15 17:34:58 UTC (rev 927)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2015-07-15 17:42:59 UTC (rev 928)
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
...
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From: <hua...@us...> - 2015-07-15 17:35:02
|
Revision: 927
http://sourceforge.net/p/sbgn/code/927
Author: huaiyumi
Date: 2015-07-15 17:34:58 +0000 (Wed, 15 Jul 2015)
Log Message:
-----------
Update authors list, correct typos, and update financial support acknowledgment.
Modified Paths:
--------------
ActivityFlow/trunk/sbgn_AF-level1.pdf
ActivityFlow/trunk/sources/acknowledgments.tex
ActivityFlow/trunk/sources/delay.tex
ActivityFlow/trunk/sources/front-page.tex
ActivityFlow/trunk/sources/revision_history.tex
Modified: ActivityFlow/trunk/sbgn_AF-level1.pdf
===================================================================
--- ActivityFlow/trunk/sbgn_AF-level1.pdf 2015-05-05 18:53:18 UTC (rev 926)
+++ ActivityFlow/trunk/sbgn_AF-level1.pdf 2015-07-15 17:34:58 UTC (rev 927)
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|
From: <lp...@us...> - 2015-05-05 18:53:21
|
Revision: 926
http://sourceforge.net/p/sbgn/code/926
Author: lptolik
Date: 2015-05-05 18:53:18 +0000 (Tue, 05 May 2015)
Log Message:
-----------
fix the figure 2.15
Modified Paths:
--------------
EntityRelationship/trunk/images/interaction.pdf
EntityRelationship/trunk/images/interaction.png
EntityRelationship/trunk/images/interaction.svg
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/interaction.tex
Modified: EntityRelationship/trunk/images/interaction.pdf
===================================================================
--- EntityRelationship/trunk/images/interaction.pdf 2015-04-23 17:43:34 UTC (rev 925)
+++ EntityRelationship/trunk/images/interaction.pdf 2015-05-05 18:53:18 UTC (rev 926)
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Modified: EntityRelationship/trunk/images/interaction.png
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Modified: EntityRelationship/trunk/images/interaction.svg
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--- EntityRelationship/trunk/images/interaction.svg 2015-04-23 17:43:34 UTC (rev 925)
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Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
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Modified: EntityRelationship/trunk/sources/interaction.tex
===================================================================
--- EntityRelationship/trunk/sources/interaction.tex 2015-04-23 17:43:34 UTC (rev 925)
+++ EntityRelationship/trunk/sources/interaction.tex 2015-05-05 18:53:18 UTC (rev 926)
@@ -1,3 +1,4 @@
+% !TEX root = ../sbgn_ER-level1.tex
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Interaction
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <stu...@us...> - 2015-04-23 17:43:37
|
Revision: 925
http://sourceforge.net/p/sbgn/code/925
Author: stumoodie
Date: 2015-04-23 17:43:34 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Added validation rules now.
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/images/nonstoichprocessuml.svg
ProcessDiagram/trunk/Specification/images/sbgn_model_revised/128173
ProcessDiagram/trunk/Specification/images/sbgn_model_revised/128173.diagram
ProcessDiagram/trunk/Specification/images/sbgn_model_revised/134957.diagram
ProcessDiagram/trunk/Specification/images/sbgn_model_revised/154925.diagram
ProcessDiagram/trunk/Specification/images/sbgn_model_revised/161453.diagram
ProcessDiagram/trunk/Specification/images/sbgn_model_revised/168365.diagram
ProcessDiagram/trunk/Specification/images/sbgn_model_revised/45.session
ProcessDiagram/trunk/Specification/images/sbgnumloverview.svg
ProcessDiagram/trunk/Specification/images/submapnodeuml.svg
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
ProcessDiagram/trunk/Specification/sources/glyphs.tex
Added Paths:
-----------
ProcessDiagram/trunk/Specification/images/submap-unfolded.svg
Modified: ProcessDiagram/trunk/Specification/images/nonstoichprocessuml.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/nonstoichprocessuml.svg 2015-04-23 15:53:19 UTC (rev 924)
+++ ProcessDiagram/trunk/Specification/images/nonstoichprocessuml.svg 2015-04-23 17:43:34 UTC (rev 925)
@@ -1,69 +1,69 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Created with Bouml (http://bouml.free.fr/) -->
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<svg width="937" height="296" version="1.1" xmlns="http://www.w3.org/2000/svg">
+<svg width="948" height="299" version="1.1" xmlns="http://www.w3.org/2000/svg">
<g>
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="611" y="111" width="3" height="35" />
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="409" y="143" width="205" height="3" />
- <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="405" y="107" width="206" height="36" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="508" y="124">NonStoichiometricProcess</text>
- <line stroke="black" stroke-opacity="1" x1="405" y1="127" x2="611" y2="127" />
- <line stroke="black" stroke-opacity="1" x1="405" y1="135" x2="611" y2="135" />
+ <rect fill="#cbcbcb" stroke="none" stroke-opacity="1" x="441" y="236" width="3" height="45" />
+ <rect fill="#cbcbcb" stroke="none" stroke-opacity="1" x="351" y="278" width="93" height="3" />
+ <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="347" y="232" width="94" height="46" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="394" y="249">Submap</text>
+ <line stroke="black" stroke-opacity="1" x1="347" y1="251" x2="441" y2="251" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="351" y="268">name : string</text>
+ <line stroke="black" stroke-opacity="1" x1="347" y1="270" x2="441" y2="270" />
</g>
<g>
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="457" y="236" width="3" height="47" />
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="351" y="280" width="109" height="3" />
- <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="347" y="232" width="110" height="48" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="402" y="249">SubmapNode</text>
- <line stroke="black" stroke-opacity="1" x1="347" y1="252" x2="457" y2="252" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="351" y="269">name : string</text>
- <line stroke="black" stroke-opacity="1" x1="347" y1="272" x2="457" y2="272" />
+ <rect fill="#cbcbcb" stroke="none" stroke-opacity="1" x="603" y="111" width="3" height="33" />
+ <rect fill="#cbcbcb" stroke="none" stroke-opacity="1" x="409" y="141" width="197" height="3" />
+ <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="405" y="107" width="198" height="34" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="504" y="124">NonStoichiometricProcess</text>
+ <line stroke="black" stroke-opacity="1" x1="405" y1="126" x2="603" y2="126" />
+ <line stroke="black" stroke-opacity="1" x1="405" y1="134" x2="603" y2="134" />
</g>
<g>
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="678" y="236" width="3" height="47" />
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="586" y="280" width="95" height="3" />
- <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="582" y="232" width="96" height="48" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="630" y="249">Phenotype</text>
- <line stroke="black" stroke-opacity="1" x1="582" y1="252" x2="678" y2="252" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="586" y="269">name : string</text>
- <line stroke="black" stroke-opacity="1" x1="582" y1="272" x2="678" y2="272" />
+ <rect fill="#cbcbcb" stroke="none" stroke-opacity="1" x="676" y="236" width="3" height="45" />
+ <rect fill="#cbcbcb" stroke="none" stroke-opacity="1" x="586" y="278" width="93" height="3" />
+ <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="582" y="232" width="94" height="46" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="629" y="249">Phenotype</text>
+ <line stroke="black" stroke-opacity="1" x1="582" y1="251" x2="676" y2="251" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="586" y="268">name : string</text>
+ <line stroke="black" stroke-opacity="1" x1="582" y1="270" x2="676" y2="270" />
</g>
<g>
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="921" y="235" width="3" height="47" />
- <rect fill="#808080" stroke="none" stroke-opacity="1" x="753" y="279" width="171" height="3" />
- <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="749" y="231" width="172" height="48" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="835" y="248">ModulationArc</text>
- <line stroke="black" stroke-opacity="1" x1="749" y1="251" x2="921" y2="251" />
- <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="753" y="268">modulation_type : enum</text>
- <line stroke="black" stroke-opacity="1" x1="749" y1="271" x2="921" y2="271" />
+ <rect fill="#cbcbcb" stroke="none" stroke-opacity="1" x="932" y="241" width="3" height="45" />
+ <rect fill="#cbcbcb" stroke="none" stroke-opacity="1" x="768" y="283" width="167" height="3" />
+ <rect fill="#ffffff" stroke="black" stroke-width="1" stroke-opacity="1" x="764" y="237" width="168" height="46" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" font-weight="bold" text-anchor="middle" x="848" y="254">ModulationArc</text>
+ <line stroke="black" stroke-opacity="1" x1="764" y1="256" x2="932" y2="256" />
+ <text font-family="Helvetica" font-size="15" fill="#000000" xml:space="preserve" x="768" y="273">modulation_type : enum</text>
+ <line stroke="black" stroke-opacity="1" x1="764" y1="275" x2="932" y2="275" />
</g>
<g>
- <line stroke="black" stroke-opacity="1" x1="404" y1="231" x2="404" y2="189" />
+ <line stroke="#000000" stroke-opacity="1" x1="631" y1="188" x2="506" y2="188" />
</g>
<g>
- <line stroke="black" stroke-opacity="1" x1="404" y1="189" x2="510" y2="189" />
+ <line stroke="#000000" stroke-opacity="1" x1="506" y1="188" x2="506" y2="151" />
+ <line stroke="#000000" stroke-opacity="1" x1="506" y1="145" x2="500" y2="151" />
+ <line stroke="#000000" stroke-opacity="1" x1="506" y1="145" x2="512" y2="151" />
+ <line stroke="#000000" stroke-opacity="1" x1="500" y1="151" x2="512" y2="151" />
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<g>
- <line stroke="black" stroke-opacity="1" x1="510" y1="189" x2="510" y2="153" />
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- <line stroke="black" stroke-opacity="1" x1="510" y1="147" x2="516" y2="153" />
- <line stroke="black" stroke-opacity="1" x1="504" y1="153" x2="516" y2="153" />
+ <line stroke="#000000" stroke-opacity="1" x1="631" y1="231" x2="631" y2="188" />
</g>
<g>
- <line stroke="black" stroke-opacity="1" x1="632" y1="231" x2="632" y2="189" />
+ <line stroke="#000000" stroke-opacity="1" x1="396" y1="188" x2="506" y2="188" />
</g>
<g>
- <line stroke="black" stroke-opacity="1" x1="632" y1="189" x2="510" y2="189" />
+ <line stroke="#000000" stroke-opacity="1" x1="506" y1="188" x2="506" y2="151" />
+ <line stroke="#000000" stroke-opacity="1" x1="506" y1="145" x2="500" y2="151" />
+ <line stroke="#000000" stroke-opacity="1" x1="506" y1="145" x2="512" y2="151" />
+ <line stroke="#000000" stroke-opacity="1" x1="500" y1="151" x2="512" y2="151" />
</g>
<g>
- <line stroke="black" stroke-opacity="1" x1="510" y1="189" x2="510" y2="153" />
- <line stroke="black" stroke-opacity="1" x1="510" y1="147" x2="504" y2="153" />
- <line stroke="black" stroke-opacity="1" x1="510" y1="147" x2="516" y2="153" />
- <line stroke="black" stroke-opacity="1" x1="504" y1="153" x2="516" y2="153" />
+ <line stroke="#000000" stroke-opacity="1" x1="396" y1="231" x2="396" y2="188" />
</g>
<g>
- <line stroke="black" stroke-opacity="1" x1="748" y1="257" x2="742" y2="251" />
- <line stroke="black" stroke-opacity="1" x1="748" y1="257" x2="742" y2="263" />
- <line stroke-dasharray="4,4" stroke="black" stroke-opacity="1" x1="682" y1="257" x2="748" y2="257" />
+ <line stroke="black" stroke-opacity="1" x1="763" y1="258" x2="757" y2="251" />
+ <line stroke="black" stroke-opacity="1" x1="763" y1="258" x2="756" y2="263" />
+ <line stroke-dasharray="4,4" stroke="black" stroke-opacity="1" x1="680" y1="257" x2="763" y2="258" />
</g>
</svg>
Modified: ProcessDiagram/trunk/Specification/images/sbgn_model_revised/128173
===================================================================
--- ProcessDiagram/trunk/Specification/images/sbgn_model_revised/128173 2015-04-23 15:53:19 UTC (rev 924)
+++ ProcessDiagram/trunk/Specification/images/sbgn_model_revised/128173 2015-04-23 17:43:34 UTC (rev 925)
@@ -1,185 +1,185 @@
-format 75
+format 207
"org.sbgn.level1" // org.sbgn.level1
- revision 20
+ revision 21
modified_by 45 "smoodie"
// class settings
- //class diagram settings
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
- //use case diagram settings
- package_name_in_tab default show_context default auto_label_position default draw_all_relations default class_drawing_mode default shadow default show_stereotype_properties default
- //sequence diagram settings
- show_full_operations_definition default write_horizontally default class_drawing_mode default drawing_language default draw_all_relations default shadow default show_stereotype_properties default show_class_context_mode default show_msg_context_mode default
- //collaboration diagram settings
- show_full_operations_definition default show_hierarchical_rank default write_horizontally default drawing_language default package_name_in_tab default show_context default show_msg_context default draw_all_relations default shadow default show_stereotype_properties default
- //object diagram settings
- write_horizontally default package_name_in_tab default show_context default auto_label_position default draw_all_relations default shadow default show_stereotype_properties default
- //component diagram settings
- package_name_in_tab default show_context default auto_label_position default draw_all_relations default shadow default
- draw_component_as_icon default show_component_req_prov default show_component_rea default show_stereotype_properties default
- //deployment diagram settings
- package_name_in_tab default show_context default write_horizontally default auto_label_position default draw_all_relations default shadow default
- draw_component_as_icon default show_component_req_prov default show_component_rea default show_stereotype_properties default
- //state diagram settings
- package_name_in_tab default show_context default auto_label_position default write_trans_label_horizontally default show_trans_definition default draw_all_relations default shadow default
- show_activities default region_horizontally default drawing_language default show_stereotype_properties default
- //activity diagram settings
- package_name_in_tab default show_context default show_opaque_action_definition default auto_label_position default write_flow_label_horizontally default draw_all_relations default shadow default
- show_infonote default drawing_language default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
+
+ usecasediagramsettings end
+
+ sequencediagramsettings end
+
+ collaborationdiagramsettings end
+
+ objectdiagramsettings end
+
+ componentdiagramsettings
+ end
+
+ deploymentdiagramsettings
+ end
+
+ statediagramsettings
+ end
+
+ activitydiagramsettings
+ end
+
class_color white
classview 128173 "Class View"
- //class diagram settings
- draw_all_relations yes hide_attributes no hide_operations default hide_getset_operations default show_members_full_definition yes show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers yes member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language uml show_context_mode default auto_label_position yes show_relation_modifiers yes show_relation_visibility default show_infonote default shadow yes show_stereotype_properties default
- //collaboration diagram settings
- show_full_operations_definition default show_hierarchical_rank default write_horizontally default drawing_language default package_name_in_tab default show_context default show_msg_context default draw_all_relations default shadow default show_stereotype_properties default
- //object diagram settings
- write_horizontally default package_name_in_tab default show_context default auto_label_position default draw_all_relations default shadow default show_stereotype_properties default
- //sequence diagram settings
- show_full_operations_definition default write_horizontally default class_drawing_mode default drawing_language default draw_all_relations default shadow default show_stereotype_properties default show_class_context_mode default show_msg_context_mode default
- //state diagram settings
- package_name_in_tab default show_context default auto_label_position default write_trans_label_horizontally default show_trans_definition default draw_all_relations default shadow default
- show_activities default region_horizontally default drawing_language default show_stereotype_properties default
- //class settings
- //activity diagram settings
- package_name_in_tab default show_context default show_opaque_action_definition default auto_label_position default write_flow_label_horizontally default draw_all_relations default shadow default
- show_infonote default drawing_language default show_stereotype_properties default
+
+ classdiagramsettings draw_all_relations yes hide_attributes no show_members_full_definition yes show_attribute_modifiers yes member_max_width 0 drawing_language uml auto_label_position yes show_relation_modifiers yes shadow yes end
+
+ collaborationdiagramsettings end
+
+ objectdiagramsettings end
+
+ sequencediagramsettings end
+
+ statediagramsettings
+ end
+
+
+ activitydiagramsettings
+ end
classdiagram 128173 "MainView"
- draw_all_relations no hide_attributes yes hide_operations yes hide_getset_operations yes show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow no show_stereotype_properties default
+ classdiagramsettings draw_all_relations no hide_attributes yes hide_operations yes hide_getset_operations yes member_max_width 0 shadow no end
size A2-Landscape
end
classdiagram 175021 "StoichiometricProcessView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 168109 "AuxiliaryUnitView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 174893 "LogicalOperatorView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 168365 "SubmapNodeView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 134701 "MapView"
- draw_all_relations no hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings draw_all_relations no member_max_width 0 end
size A4-Landscape
end
classdiagram 134829 "GlyphAuxView"
- draw_all_relations yes hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings draw_all_relations yes member_max_width 0 end
size A4-Landscape
end
classdiagram 134957 "EntityPoolNodeView"
- draw_all_relations no hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings draw_all_relations no member_max_width 0 end
size A0-Landscape
end
classdiagram 135085 "StatelessEPNView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 141613 "StatefulEPNView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 141741 "EmptySetView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 141869 "ComplexView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 148397 "ProcessView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 154925 "NonStoichiometricProcessView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 161453 "SBGNArcsView"
- draw_all_relations yes hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings draw_all_relations yes member_max_width 0 end
size A4-Landscape
end
classdiagram 168237 "CrossreferenceView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 175149 "CompartmentView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 181677 "AttributeValueView"
- draw_all_relations no hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings draw_all_relations no member_max_width 0 end
size A4-Landscape
end
classdiagram 188205 "StateVariableView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 194733 "AnnotationView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 194861 "TagView"
- draw_all_relations no hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings draw_all_relations no member_max_width 0 end
size A4-Landscape
end
classdiagram 201389 "CloneMarkerView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 201517 "FluxArcView"
- draw_all_relations no hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings draw_all_relations no member_max_width 0 end
size A4-Landscape
end
classdiagram 201645 "ModulationArcView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 201773 "LogicArcView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 208301 "EquivalenceArcView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 208429 "EntityDefinitionView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
classdiagram 214957 "SBGNNodeView"
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
size A4-Landscape
end
@@ -193,6 +193,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
attribute 134701 "id"
private explicit_type "identifier"
@@ -202,6 +203,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
end
@@ -215,6 +218,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 137389 // elements (<composition>)
relation 136749 *---
@@ -259,6 +263,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 137517 // owning_map (<composition>)
relation_ref 136749 // <composition>
@@ -283,6 +288,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 128173 // <generalisation>
relation 128173 ---|>
@@ -311,6 +317,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 128301 // <generalisation>
relation 128301 ---|>
@@ -355,6 +362,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 128557 // <generalisation>
relation 128557 ---|>
@@ -373,6 +381,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
classrelation 142765 // <composition>
@@ -421,6 +431,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 138029 // <generalisation>
relation 137261 ---|>
@@ -453,6 +464,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 138157 // <generalisation>
relation 137389 ---|>
@@ -473,6 +485,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 142637 // epns (<composition>)
relation 140589 *---
@@ -503,6 +516,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
attribute 156077 "natures"
@@ -514,6 +529,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
classrelation 209069 // displayed_attributes (<directional composition>)
@@ -536,6 +553,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 138285 // <generalisation>
relation 137517 ---|>
@@ -575,6 +593,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 138541 // owning_epn (<composition>)
relation_ref 137645 // <composition>
@@ -589,6 +608,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
classrelation 138797 // <generalisation>
@@ -619,6 +640,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 138669 // <generalisation>
relation 137773 ---|>
@@ -639,6 +661,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 142253 // <generalisation>
relation 140205 ---|>
@@ -666,6 +689,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 139053 // <generalisation>
relation 138157 ---|>
@@ -686,6 +710,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 139181 // <generalisation>
relation 138285 ---|>
@@ -704,6 +729,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
end
@@ -717,6 +744,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 139309 // <generalisation>
relation 138413 ---|>
@@ -735,6 +763,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
end
@@ -748,6 +778,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 140077 // <generalisation>
relation 138925 ---|>
@@ -773,6 +804,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
end
@@ -786,6 +819,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
attribute 155693 "operator_type"
private explicit_type "enum"
@@ -796,6 +830,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
classrelation 194989 // <generalisation>
@@ -831,6 +867,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 141741 // <generalisation>
relation 139821 ---|>
@@ -865,6 +902,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 142125 // <generalisation>
relation 140077 ---|>
@@ -885,6 +923,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 142381 // <generalisation>
relation 140333 ---|>
@@ -905,6 +944,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 143021 // <generalisation>
relation 140845 ---|>
@@ -925,6 +965,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 143149 // <generalisation>
relation 140973 ---|>
@@ -945,6 +986,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 143277 // <generalisation>
relation 141101 ---|>
@@ -965,6 +1007,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 143533 // owning_epn (<composition>)
relation_ref 141229 // <composition>
@@ -989,6 +1032,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 143661 // <generalisation>
relation 141357 ---|>
@@ -1009,6 +1053,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 143789 // <generalisation>
relation 141485 ---|>
@@ -1027,6 +1072,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
end
@@ -1040,6 +1087,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
attribute 141869 "code"
private explicit_type "string"
@@ -1050,6 +1098,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
attribute 141997 "value"
@@ -1061,6 +1111,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
classrelation 188333 // <generalisation>
@@ -1082,6 +1134,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 151085 // <generalisation>
relation 148653 ---|>
@@ -1100,6 +1153,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
attribute 142509 "natures"
@@ -1111,6 +1166,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
attribute 142381 "subunit_type"
@@ -1121,6 +1178,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
classrelation 151597 // states (<aggregation>)
@@ -1168,6 +1227,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 151469 // <generalisation>
relation 148909 ---|>
@@ -1192,6 +1252,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 166189 // <generalisation>
relation 162989 ---|>
@@ -1202,7 +1263,7 @@
end
end
- class 158509 "SubmapNode"
+ class 158509 "Submap"
visibility package
cpp_decl ""
java_decl "${comment}${@}${visibility}${final}${abstract}class ${name}${extends}${implements} {
@@ -1212,6 +1273,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 172717 // <generalisation>
relation 169517 ---|>
@@ -1251,6 +1313,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
end
@@ -1264,6 +1328,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 172845 // <generalisation>
relation 169645 ---|>
@@ -1275,7 +1340,7 @@
classrelation 179629 // <dependency>
relation 176429 -_->
- a default
+ a package
classrelation_ref 179629 // <dependency>
b parent class_ref 137005 // ModulationArc
end
@@ -1289,6 +1354,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
end
@@ -1302,6 +1369,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 179501 // <generalisation>
relation 176301 ---|>
@@ -1322,6 +1390,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 179373 // <generalisation>
relation 176173 ---|>
@@ -1342,6 +1411,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 180141 // owning_submap_node (<composition>)
relation_ref 176685 // <composition>
@@ -1374,6 +1444,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 180653 // <generalisation>
relation 177069 ---|>
@@ -1415,6 +1486,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 181037 // <generalisation>
relation 177325 ---|>
@@ -1443,6 +1515,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
attribute 149037 "reference_id"
private explicit_type "string"
@@ -1453,6 +1526,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
classrelation 249645 // equivalence (<aggregation>)
@@ -1474,6 +1549,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 215597 // <generalisation>
relation 211757 ---|>
@@ -1492,6 +1568,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
classrelation 215725 // annotated_glyph (<unidirectional association>)
@@ -1514,6 +1592,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
attribute 175789 "name"
private explicit_type "string"
@@ -1524,6 +1603,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
attribute 175917 "natures"
@@ -1535,6 +1616,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
classrelation 229421 // state_definitions (<composition>)
@@ -1564,6 +1647,7 @@
python_2_2 python_decl ""
idl_decl ""
explicit_switch_type ""
+ mysql_decl ""
classrelation 229549 // owning_entity_type (<composition>)
relation_ref 225581 // <composition>
@@ -1578,6 +1662,8 @@
php_decl ""
python_decl ""
idl_decl ""
+ mysql_decl ""
+ MysqlColumn
end
end
end
Modified: ProcessDiagram/trunk/Specification/images/sbgn_model_revised/128173.diagram
===================================================================
--- ProcessDiagram/trunk/Specification/images/sbgn_model_revised/128173.diagram 2015-04-23 15:53:19 UTC (rev 924)
+++ ProcessDiagram/trunk/Specification/images/sbgn_model_revised/128173.diagram 2015-04-23 17:43:34 UTC (rev 925)
@@ -1,161 +1,161 @@
-format 75
+format 207
classcanvas 128045 class_ref 128173 // SBGNGlyph
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
- xyz 1456.09 137.436 2000
+ classdiagramsettings member_max_width 0 end
+ xyz 1456.67 137.876 2000
end
classcanvas 128173 class_ref 128301 // SBGNNode
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
- xyz 1425.63 265.949 2000
+ classdiagramsettings member_max_width 0 end
+ xyz 1425.97 265.469 2000
end
classcanvas 128301 class_ref 128429 // SBGNArc
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
- xyz 2057.97 266.756 2000
+ classdiagramsettings member_max_width 0 end
+ xyz 2057.67 266.136 2000
end
classcanvas 128941 class_ref 128685 // EntityPoolNode
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
+ classdiagramsettings member_max_width 0 end
color white
- xyz 970.304 396.279 2000
+ xyz 970.104 396.459 2000
end
classcanvas 129197 class_ref 128813 // Complex
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
- xyz 638.577 616.083 2000
+ classdiagramsettings member_max_width 0 end
+ xyz 638.357 616.463 2000
end
classcanvas 129453 class_ref 128941 // Macromolecule
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
- xyz 771.613 619.089 2000
+ classdiagramsettings member_max_width 0 end
+ xyz 772.553 619.049 2000
end
classcanvas 130989 class_ref 129325 // Map
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
- xyz 1079.56 135.133 2000
+ classdiagramsettings member_max_width 0 end
+ xyz 1078.7 135.853 2000
end
classcanvas 132781 class_ref 135981 // SBGNElement
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
- xyz 1043.06 27.1676 2000
+ classdiagramsettings member_max_width 0 end
+ xyz 1043.34 27.0076 2000
end
classcanvas 133933 class_ref 136109 // StatefulEPN
- draw_all_relations default hide_attributes default hide_operations default hide_getset_operations default show_members_full_definition default show_members_visibility default show_members_stereotype default show_members_context default show_members_multiplicity default show_members_initialization default show_attribute_modifiers default member_max_width 0 show_parameter_dir default show_parameter_name default package_name_in_tab default class_drawing_mode default drawing_language default show_context_mode default auto_label_position default show_relation_modifiers default show_relation_visibility default show_infonote default shadow default show_stereotype_properties default
- xyz 784.749 478.112 2000
+ classdiagramsettings member_max_width 0 end
+ xyz 784.409 478.812 2000
end
classcanvas 135085 class_ref 136237 // StateVariable
- draw_all_relations default hide_attributes default hide_op...
[truncated message content] |
|
From: <lp...@us...> - 2015-04-23 15:53:28
|
Revision: 924
http://sourceforge.net/p/sbgn/code/924
Author: lptolik
Date: 2015-04-23 15:53:19 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
added acknowledements for funding workshops
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/acknowledgments.tex
ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/trunk/sources/acknowledgments.tex
===================================================================
--- EntityRelationship/trunk/sources/acknowledgments.tex 2015-04-23 14:46:54 UTC (rev 923)
+++ EntityRelationship/trunk/sources/acknowledgments.tex 2015-04-23 15:53:19 UTC (rev 924)
@@ -17,5 +17,20 @@
\section{Financial support}
-The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, \url{http://www.nedo.go.jp/}). The Okinawa Institute of Science and Technology (OIST, \url{http://www.oist.jp/}), the AIST Computational Biology Research Center (AIST CBRC, \url{http://www.cbrc.jp/index.eng.html}), the British Biotechnology and Biological Sciences Research Council (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award, the European Media Laboratory (EML Research gGmbH, \url{http://www.eml.org/english/}), the Beckman Institute at the California Institute of Technology (\url{http://bnmc.caltech.edu}), Ontario National Science Foundation (NSF, \url{http://www.nsf.gov/}), USC Norris Comprehensive Cancer Center (\url{http://uscnorriscancer.usc.edu/}), Martin Luther University Halle-Wittenberg (\url{http://www.uni-halle.de/}), Monash University (\url{http://www.monash.edu.au/}), IPK Gatersleben (\url{http://www.ipk-gatersleben.de/en/}), University of Rostock (\url{http://www.uni-rostock.de/}) and German Federal Ministry of Research and Education (\url{http://www.bmbf.de/}) provided additional support for SBGN workshops. Some help was provided by the Japan Science and Technology Agency (JST, \url{http://www.jst.go.jp/}) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp/}) for the development of the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
+The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, \url{http://www.nedo.go.jp/}).
+The Okinawa Institute of Science and Technology (OIST, \url{http://www.oist.jp/}),
+the AIST Computational Biology Research Center (AIST CBRC, \url{http://www.cbrc.jp/index.eng.html}),
+the British Biotechnology and Biological Sciences Research Council (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award,
+the European Media Laboratory (EML Research gGmbH, \url{http://www.eml.org/english/}),
+the Beckman Institute at the California Institute of Technology (\url{http://bnmc.caltech.edu}),
+Ontario Institute for Cancer Research (OICR, \url{http://oicr.on.ca/}),
+Ontario Genomics Institute (OGI, \url{http://www.ontariogenomics.ca/}),
+National Science Foundation (NSF, \url{http://www.nsf.gov/}),
+USC Norris Comprehensive Cancer Center (\url{http://uscnorriscancer.usc.edu/}),
+Martin Luther University Halle-Wittenberg (\url{http://www.uni-halle.de/}),
+Monash University (\url{http://www.monash.edu.au/}),
+IPK Gatersleben (\url{http://www.ipk-gatersleben.de/en/}),
+University of Rostock (\url{http://www.uni-rostock.de/}) and
+German Federal Ministry of Research and Education (\url{http://www.bmbf.de/}) provided additional support for SBGN workshops.
+Some help was provided by the Japan Science and Technology Agency (JST, \url{http://www.jst.go.jp/}) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp/}) for the development of the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
Modified: ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-04-23 14:46:54 UTC (rev 923)
+++ ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-04-23 15:53:19 UTC (rev 924)
@@ -44,4 +44,22 @@
\section{Financial Support}
-The development of SBGN was mainly supported by a grant from the Japanese \emph{New Energy and Industrial Technology Development Organization} (NEDO, \url{http://www.nedo.go.jp/}). The \emph{Okinawa Institute of Science and Technology} (OIST, \url{http://www.oist.jp/}), the \emph{AIST Computational Biology Research Center} (AIST CBRC, \url{http://www.cbrc.jp/index.eng.html}) the British \emph{Biotechnology and Biological Sciences Research Council} (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award, the European Media Laboratory (EML Research gGmbH, \url{http://www.eml-r.org/}), and the Beckman Institute at the California Institute of Technology (\url{http://bnmc.caltech.edu}) provided additional support for SBGN workshops. Some help was provided by the \emph{Japan Science and Technology Agency} (JST, \url{http://www.jst.go.jp/}) and the \emph{Genome Network Project} of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp/}) for the development of the gene regulation network aspect of SBGN, and from the \emph{Engineering and Physical Sciences Research Council} (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
+The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, \url{http://www.nedo.go.jp/}).
+The Okinawa Institute of Science and Technology (OIST, \url{http://www.oist.jp/}),
+the AIST Computational Biology Research Center (AIST CBRC, \url{http://www.cbrc.jp/index.eng.html}),
+the British Biotechnology and Biological Sciences Research Council (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award,
+the European Media Laboratory (EML Research gGmbH, \url{http://www.eml.org/english/}),
+the Beckman Institute at the California Institute of Technology (\url{http://bnmc.caltech.edu}),
+Ontario Institute for Cancer Research (OICR, \url{http://oicr.on.ca/}),
+Ontario Genomics Institute (OGI, \url{http://www.ontariogenomics.ca/}),
+National Science Foundation (NSF, \url{http://www.nsf.gov/}),
+USC Norris Comprehensive Cancer Center (\url{http://uscnorriscancer.usc.edu/}),
+Martin Luther University Halle-Wittenberg (\url{http://www.uni-halle.de/}),
+Monash University (\url{http://www.monash.edu.au/}),
+IPK Gatersleben (\url{http://www.ipk-gatersleben.de/en/}),
+University of Rostock (\url{http://www.uni-rostock.de/}) and
+German Federal Ministry of Research and Education (\url{http://www.bmbf.de/}) provided additional support for SBGN workshops.
+Some help was provided by the Japan Science and Technology Agency (JST, \url{http://www.jst.go.jp/}) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp/}) for the development of the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
+
+
+%The development of SBGN was mainly supported by a grant from the Japanese \emph{New Energy and Industrial Technology Development Organization} (NEDO, \url{http://www.nedo.go.jp/}). The \emph{Okinawa Institute of Science and Technology} (OIST, \url{http://www.oist.jp/}), the \emph{AIST Computational Biology Research Center} (AIST CBRC, \url{http://www.cbrc.jp/index.eng.html}) the British \emph{Biotechnology and Biological Sciences Research Council} (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award, the European Media Laboratory (EML Research gGmbH, \url{http://www.eml-r.org/}), and the Beckman Institute at the California Institute of Technology (\url{http://bnmc.caltech.edu}) provided additional support for SBGN workshops. Some help was provided by the \emph{Japan Science and Technology Agency} (JST, \url{http://www.jst.go.jp/}) and the \emph{Genome Network Project} of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp/}) for the development of the gene regulation network aspect of SBGN, and from the \emph{Engineering and Physical Sciences Research Council} (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <stu...@us...> - 2015-04-23 14:46:56
|
Revision: 923
http://sourceforge.net/p/sbgn/code/923
Author: stumoodie
Date: 2015-04-23 14:46:54 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Done submap tidied up.
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/images/submapglyph.svg
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/glyphs.tex
ProcessDiagram/trunk/Specification/sources/whatsnew.tex
Modified: ProcessDiagram/trunk/Specification/images/submapglyph.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/submapglyph.svg 2015-04-23 11:16:17 UTC (rev 922)
+++ ProcessDiagram/trunk/Specification/images/submapglyph.svg 2015-04-23 14:46:54 UTC (rev 923)
@@ -9,11 +9,11 @@
xmlns="http://www.w3.org/2000/svg"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- width="1581.266"
- height="304.9599"
+ width="1589.26"
+ height="820.79865"
id="svg2"
sodipodi:version="0.32"
- inkscape:version="0.48.2 r9819"
+ inkscape:version="0.48.5 r10040"
version="1.0"
sodipodi:docname="submapglyph.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape">
@@ -54,6 +54,41 @@
transform="matrix(-0.8,0,0,-0.8,-10,0)"
inkscape:connector-curvature="0" />
</marker>
+ <marker
+ style="overflow:visible"
+ id="Arrow1Lend-5"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="Arrow1Lend">
+ <path
+ inkscape:connector-curvature="0"
+ transform="matrix(-0.8,0,0,-0.8,-10,0)"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ id="path2978-8" />
+ </marker>
+ <marker
+ style="overflow:visible"
+ id="Arrow1Mend-0"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="Arrow1Mend">
+ <path
+ inkscape:connector-curvature="0"
+ transform="matrix(-0.4,0,0,-0.4,-4,0)"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ id="path2972-5" />
+ </marker>
+ <inkscape:perspective
+ id="perspective71-4"
+ inkscape:persp3d-origin="526.18109 : 248.03149 : 1"
+ inkscape:vp_z="1052.3622 : 372.04724 : 1"
+ inkscape:vp_y="0 : 1000 : 0"
+ inkscape:vp_x="0 : 372.04724 : 1"
+ sodipodi:type="inkscape:persp3d" />
</defs>
<sodipodi:namedview
id="base"
@@ -65,17 +100,17 @@
objecttolerance="10"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
- inkscape:zoom="0.44657596"
- inkscape:cx="1220.7873"
- inkscape:cy="-217.60112"
+ inkscape:zoom="0.37528474"
+ inkscape:cx="775.20069"
+ inkscape:cy="134.51417"
inkscape:document-units="px"
inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
- inkscape:window-width="1680"
- inkscape:window-height="995"
- inkscape:window-x="1343"
- inkscape:window-y="169"
+ inkscape:window-width="1573"
+ inkscape:window-height="818"
+ inkscape:window-x="115"
+ inkscape:window-y="41"
showguides="true"
inkscape:guide-bbox="true"
showgrid="false"
@@ -86,15 +121,15 @@
fit-margin-bottom="0">
<sodipodi:guide
orientation="vertical"
- position="1205.5852,-182.2275"
+ position="1205.5852,333.61124"
id="guide2990" />
<sodipodi:guide
orientation="vertical"
- position="883.98293,-374.64997"
+ position="883.98293,141.18877"
id="guide3405" />
<sodipodi:guide
orientation="horizontal"
- position="1176.3334,-187.25517"
+ position="1176.3334,328.58357"
id="guide3518" />
<inkscape:grid
type="xygrid"
@@ -102,7 +137,9 @@
empspacing="5"
visible="true"
enabled="true"
- snapvisiblegridlinesonly="true" />
+ snapvisiblegridlinesonly="true"
+ originx="-3.75e-06px"
+ originy="515.83874px" />
</sodipodi:namedview>
<metadata
id="metadata7">
@@ -120,6 +157,21 @@
id="layer2"
inkscape:label="final"
transform="translate(583.98297,-64.48465)">
+ <path
+ id="path5199-3"
+ d="m 715.95408,622.57716 c -51.6188,0 -51.6188,0 -51.6188,0"
+ style="fill:none;stroke:#969696;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:none;stroke:#969696;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ d="m 715.95408,784.57717 c -51.6188,0 -51.6188,0 -51.6188,0"
+ id="path5219-6"
+ inkscape:connector-curvature="0" />
+ <path
+ id="path3799-7"
+ d="m -287.21072,702.28591 c -51.6188,0 -51.6188,0 -51.6188,0"
+ style="fill:none;stroke:#969696;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ inkscape:connector-curvature="0" />
<rect
style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:5;stroke-linecap:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
id="rect3545"
@@ -304,5 +356,287 @@
height="69.669441"
x="-177.34041"
y="23.051073" /></flowRegion><flowPara
- id="flowPara4970">b)</flowPara></flowRoot> </g>
+ id="flowPara4970">b)</flowPara></flowRoot> <rect
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+ id="rect3545-4"
+ width="948.16382"
+ height="356.3046"
+ x="-288.39587"
+ y="526.4787"
+ rx="0"
+ ry="0" />
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+ d="m 659.43898,768.00314 -28.6308,0.12742 -18.9364,21.66223 18.8718,21.40738 28.6954,0 0,-43.19703 z"
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+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:none;stroke:#000000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
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Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-04-23 11:16:17 UTC (rev 922)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-04-23 14:46:54 UTC (rev 923)
@@ -293,11 +293,9 @@
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: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:techref:mapsubmaps}. The \attrib{elements} held should be
-logically unique and conform to the identity rules in section
-\ref{sec:techref:uniquenessdefinition}.
+holds all the glyphs (\classref{SBGNGlyph}) drawn in a \PDm. The
+\attrib{elements} held should be logically unique and conform to the
+identity rules in section \ref{sec:techref:uniquenessdefinition}.
\subsubsection{Generalisation}
@@ -1782,7 +1780,7 @@
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
+unordered 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
\glyph{phenotype} container. The label may spill outside of the container.
@@ -1803,26 +1801,34 @@
unique.
-\umlclasshead{SubmapNode}
-\label{sec:techref:submap}\label{defn:SubmapNode}
+\umlclasshead{Submap}
+\label{sec:techref:submap}\label{defn:Submap}
-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: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:techref:omitted}). The \sbgnclass{Submap} allows the detail of
-the section of the \PDm to be exported to another \PDm and replaced by the
-\sbgnclass{SubmapNode}, which acts as a place-holder. This is
-described in section \ref{sec:techref:map} and the semantics of submap linking
-is defined in section \ref{sec:techref:submaplinkingsemantics}.
+The \sbgnclass{Submap} (figure \ref{fig:techref:submapnodeuml})
+represents a process or set of processes and is a mechanism for hiding
+the detail of a portion of a \PDm. The \sbgnclass{Submap} can be
+'collapsed', in which case it acts as a placeholder in the map for the
+information it is hiding, or 'expanded' when the content of the submap
+is displayed. The node is linked to EPNs outside the submap that are
+also in the \sbgnclass{Submap}. It is anticipated that a software tool
+will use these forms as a convenient way to hide and show portions of
+a large SBGN map.
+% is a placeholder for another process
+% and is used when one wishes to hide the detail of this process from
+% the \PDm. The \sbgnclass{Submap} is not equivalent to an
+% \sbgnclass{OmittedProcess} (section \ref{sec:techref:omitted}),
+% because it does not necessarily have inputs and outputs. The
+% \sbgnclass{Submap} allows the detail of the section of the \PDm to be
+% exported to another \PDm and replaced by the \sbgnclass{Submap},
+% which acts as a place-holder. This is described in section
+% \ref{sec:techref:map} and the semantics of submap linking is defined
+% in section \ref{sec:techref:submaplinkingsemantics}.
+
\begin{figure}[htb]
\centering
\includegraphics[width = \textwidth]{images/submapnodeuml}
- \caption{The UML definition of the \sbgnclass{SubmapNode} and its
+ \caption{The UML definition of the \sbgnclass{Submap} and its
relationship to its submap, tags etc.}
\label{fig:techref:submapnodeuml}
\end{figure}
@@ -1867,7 +1873,7 @@
\subsubsection{Notation}
-\paragraph{Glyph: \glyph{Submap Node}}
+\paragraph{Glyph: \glyph{Submap}}
\begin{glyphDescription}
@@ -1887,15 +1893,16 @@
symbol, without the \glyph{submap terminal} auxiliary units that
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}.}
+ containing \glyph{submap terminals}. (c) An expanded view of the
+ submap showing its content.}
\label{fig:techref:submap}
\end{figure}
\subsubsection{Changes from Previous Version}
This glyph was called \glyph{Submap} in previous version of the \PD
-specification. This is confusing when talking about the Submap itself
-so this glyph is now referred to as the SubmapNode to distinguish it.
+specification. The semantics of the Submap have been clarified and the
+ability of submaps to be independent of the main map has been removed.
\umlclasshead{LogicalOperator}
\label{sec:techref:logic}
@@ -2825,7 +2832,11 @@
via a callout (see figure \ref{fig:techref:ex-annotation}. The callout should
overlap with the object it is annotating.
-\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.
+\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.
\end{glyphDescription}
@@ -2839,7 +2850,11 @@
\begin{figure}[htb]
\centering
\includegraphics[scale = 0.5]{examples/ex-annotation}
- \caption{Example of \glyph{annotations} adding information to the description of the trans-phosphorylation of CaMKII. Note that three different types of links are used between annotation nodes and annotated elements. However, it is recommended to use a consistent scheme whithin a map.}
+ \caption{Example of \glyph{annotations} adding information to the
+ description of the trans-phosphorylation of CaMKII. Note that
+ three different types of links are used between annotation nodes
+ and annotated elements. However, it is recommended to use a
+ consistent scheme whithin a map.}
\label{fig:techref:ex-annotation}
\end{figure}
@@ -2893,7 +2908,7 @@
\begin{itemize}
\item Two or more instances of \sbgnclass{CrossReference} with the
same \attrib{reference\_id} value are pointing to the same element.
-\item The above rules applies within a \PDm's namespace (see section \ref{sec:techref:mapsubmaps}).
+%\item The above rules applies within a \PDm's namespace (see section \ref{sec:techref:mapsubmaps}).
\end{itemize}
\subsubsection{Changes from Previous Version}
@@ -2906,8 +2921,8 @@
A \sbgnclass{SubmapTerminal}\query{Not properly defined in previous
versions of the spec. The rules described here are consistent with
accepted usage.} (figure \ref{fig:techref:submapnodeuml}) is a named reference that is part of a
-\classref{SubmapNode}. It provides the reference that is the link to a
-tag in the submap that the \sbgnclass{SubmapNode} refers to.
+\classref{Submap}. It provides the reference that is the link to a
+tag in the submap that the \sbgnclass{Submap} refers to.
\subsubsection{Generalisation}
@@ -4049,8 +4064,6 @@
\label{sec:techref:epnuniqueness}
\label{sec:techref:uniquenessdefinition}
-\textbf{Add something about process identity}
-
By definition all glyphs drawn on a \PDl are unique. They are shapes
that are distinct from other shapes drawn on the map. However, in some
cases the glyphs can represent the same concepts. The \PDl has a
@@ -4148,111 +4161,70 @@
\label{fig:techref:cloningrules-eg}
\end{figure}
-\section{Map and Submap Linking}
-\label{sec:techref:mapsubmaps}
-\label{sec:techref:submaplinkingsemantics}
+% \section{Map and Submap Linking}
+% \label{sec:techref:mapsubmaps}
+% \label{sec:techref:submaplinkingsemantics}
-The submap is a visual device that allows the detail of an \PD map to
-be exported into another \PD map and replaced by a
-\classref{SubmapNode}, which acts as a place-holder. In the case of an
-SBGN description that is made available through a software tool, the
-content of a \sbgnclass{SubmapNode} may be available to the tool. A
-user could then ask the tool to expand it, for instance by clicking on
-the \glyph{submap node} glyph. The tool might then expand and show
-its submap within the same map, or it might display it as a separate
-map. In the case of an SBGN description made available in a book or a
-website, the content of the \glyph{submap node} may be available on another
-page, possibly accessible via a hyperlink.\query{Currently we can't
- name a map so linking between supermaps and submaps is problematic.}
+% The submap is a visual device that allows the detail of an \PD map to
+% be exported into another \PD map and replaced by a
+% \classref{Submap}, which acts as a place-holder. In the case of an
+% SBGN description that is made available through a software tool, the
+% content of a \sbgnclass{Submap} may be available to the tool. A
+% user could then ask the tool to expand it, for instance by clicking on
+% the \glyph{submap node} glyph. The tool might then expand and show
+% its submap within the same map, or it might display it as a separate
+% map. In the case of an SBGN description made available in a book or a
+% website, the content of the \glyph{submap node} may be available on another
+% page, possibly accessible via a hyperlink.\query{Currently we can't
+% name a map so linking between supermaps and submaps is problematic.}
-As you can see the rules relating to the submap concept range wider
-than those applying to the \sbgnclass{SubmapNode} so we will detail
-these rules here. The concepts and nomenclature here can get confusing, so we will use
- the following nomenclature in the rest of this section\query{This
- nomenclature has not been used previously. The previous
- nomenclature was a bit confusing and didn't capture the hierarchy
- of maps well.}:
-\begin{description}
-\item[supermap] The map that owns the submap and so contains the submap glyph referring to it.
-\item[submap] The map that contains the detail summarised by the submap glyph in the super-map.
-\item[\attrib{reference\_id}] the value displayed by the tag and
- submap terminal. These must be the same to indicate equivalence
- between map and submap.
-\end{description}
+% As you can see the rules relating to the submap concept range wider
+% than those applying to the \sbgnclass{Submap} so we will detail
+% these rules here. The concepts and nomenclature here can get confusing, so we will use
+% the following nomenclature in the rest of this section\query{This
+% nomenclature has not been used previously. The previous
+% nomenclature was a bit confusing and didn't capture the hierarchy
+% of maps well.}:
+% \begin{description}
+% \item[supermap] The map that owns the submap and so contains the submap glyph referring to it.
+% \item[submap] The map that contains the detail summarised by the submap glyph in the super-map.
+% \item[\attrib{reference\_id}] the value displayed by the tag and
+% submap terminal. These must be the same to indicate equivalence
+% between map and submap.
+% \end{description}
-\fig{techref:submap-folded} represents a \glyph{submap node} that transforms
-glucose into fructose-6-phosphate.
-%The \glyph{submap node} carries five terminals, four linked to EPNs and one linked
-%to a \glyph{compartment}. The latter is particularly important in the case of EPNs
-%present only in a \glyph{compartment} enclosed in a \glyph{submap node}, and that
-%are not linked to terminals themselves.
-The \glyph{submap node} carries four terminals linked to EPNs.
-Note that the terminals do not define a ``direction'', such as input or
-output. The flux of the reactions is determined by the context.
+% \fig{techref:submap-folded} represents a \glyph{submap node} that transforms
+% glucose into fructose-6-phosphate.
+% %The \glyph{submap node} carries five terminals, four linked to EPNs and one linked
+% %to a \glyph{compartment}. The latter is particularly important in the case of EPNs
+% %present only in a \glyph{compartment} enclosed in a \glyph{submap node}, and that
+% %are not linked to terminals themselves.
+% The \glyph{submap} carries four terminals linked to EPNs.
+% Note that the terminals do not define a ``direction'', such as input or
+% output. The flux of the reactions is determined by the context.
-\begin{figure}[htb]
- \centering
- \includegraphics[scale = 0.4]{examples/submap-folded}
- \caption{Example of a submap with contents elided.}
- \label{fig:techref:submap-folded}
-\end{figure}
+% \begin{figure}[htb]
+% \centering
+% \includegraphics[scale = 0.4]{examples/submap-folded}
+% \caption{Example of a submap with contents elided.}
+% \label{fig:techref:submap-folded}
+% \end{figure}
-The map in \fig{techref:submap-unfolded} represents an unfolded version of a
-\glyph{submap}. Here, anything outside the \glyph{submap node} has
-disappeared, and the internal \glyph{tags} are not linked to the
-corresponding external \glyph{submap terminals}.\query{This example
-in the previous version of the spec included compartment
-tagging. This has been removed, but the example may need refinement as
-a result.}
+% The map in \fig{techref:submap-unfolded} represents an unfolded version of a
+% \glyph{submap}. Here, anything outside the \glyph{submap} has
+% disappeared, and the internal \glyph{tags} are not linked to the
+% corresponding external \glyph{submap terminals}.\query{This example
+% in the previous version of the spec included compartment
+% tagging. This has been removed, but the example may need refinement as
+% a result.}
-\begin{figure}[htb]
- \centering
- \includegraphics[scale = 0.35]{examples/submap-dissociated}
- \caption{Example of an unfolded submap. The unfolded submap corresponds to the folded submap of \fig{techref:submap-folded}.}
- \label{fig:techref:submap-unfolded}
-\end{figure}
+% \begin{figure}[htb]
+% \centering
+% \includegraphics[scale = 0.35]{examples/submap-dissociated}
+% \caption{Example of an unfolded submap. The unfolded submap corresponds to the folded submap of \fig{techref:submap-folded}.}
+% \label{fig:techref:submap-unfolded}
+% \end{figure}
-\subsection{Namespace and the relationship between maps}
-
-The following rules apply to the use of the \sbgnclass{SubmapNode} and
-submaps in the \PDl\query{These rules are taken from the previous
- version of the spec, but rules about the depth of submap `recursion',
- the uniqueness of reference\_id values and cloning between maps are not}.
-
-
-\begin{itemize}
-\item Submaps can contain \sbgnclass{SubmapNode} instances so submaps
- can contain submaps - there is no limit on the depth of this.
-\item Submaps share the same namespace as their supermap. Therefore submaps of
- submaps share the top-most map's namespace.
-\item Compartment's can be replicated across submaps and they all
- refer to the same compartment if they share the same name.
-\item Subclasses of \sbgnclass{EntityPoolNode} replicated in both map
- and its immediate submap must be
- associated with a subclass of \sbgnclass{CrossReference}
- (\sbgnclass{SubmapTerminal} for the supermap and \sbgnclass{Tag} for
- the submap).
-\item Subclasses of \sbgnclass{EntityPoolNode} may be replicated
- between submaps separated by one or more other submaps, i.e. those
- not affected by the above rule.
-\item All \attrib{reference\_id}s used must be unique within a given
- map namespace.
-\item submap folding: all tagged nodes in submap merge with those
- linked to terminals in super-map. If either node is cloned then all
- equivalent nodes in merged map must share the appropriate clone
- marker.
-\item For a valid mapping between subclasses of \sbgnclass{EntityPoolNode} in a supermap and submap to
- exist, the \sbgnclass{EntityPoolNode} subclasses must be logically
- identical and the \attrib{reference\_id} in their associated \sbgnclass{CrossReference} must be identical.
-\item A \sbgnclass{SubmapNode} which does not have a corresponding
- submap is valid.
-\item Submaps without a corresponding supermap are invalid\query{We
- need to sort out mapping between super and sub maps to get this
- working. I propose naming the maps}.
-\item Subclasses of \sbgnclass{EntityPoolNode} with the same name must
- share the same \sbgnclass{EntityType}.
-\end{itemize}
-
\subsection{Compartment spanning}
An \glyph{EPN} cannot \emph{belong} to more than one
Modified: ProcessDiagram/trunk/Specification/sources/whatsnew.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/whatsnew.tex 2015-04-23 11:16:17 UTC (rev 922)
+++ ProcessDiagram/trunk/Specification/sources/whatsnew.tex 2015-04-23 14:46:54 UTC (rev 923)
@@ -36,10 +36,10 @@
\begin{description}
\item[Process Duplication] The specification was unclear about whether a process could be duplicated. This situation could possibly arise if two processes were drawn that involved the same inputs, outputs and modulators. This is now clarified and all processes drawn in a map are unique and should be interpreted as describing different processes.
-\item[Phenotype Duplication] The phenotype has, in previous specifications, been described as having a clone marker. This was inconsistent with the concept that a phenotype as a process, which cannot be cloned (see above). The specification has been revised accordingly (section~\ref{sec:techref:epnuniqueness}).
+\item[Phenotype Duplication] The phenotype has, in previous specifications, been described as having a clone marker. This was inconsistent with the concept that a phenotype as a process, which cannot be cloned (see above). The specification has been revised accordingly (section~\ref{sec:techref:process}).
\item[Clarified Identity Semantics] The specification was vague on when an author needed to use a clone marker. Especially when a macromolecule of the same name had material type or cardinality units of information. These rules have been expanded and the role of the cardinality and material type clarified. See section~\ref{sec:techref:epnuniqueness}.
\item[Subunits are not EPNs] Previous specifications treated the subunit of a complex as a EPN. This was a mistake as the complex itself is the EPN and the subunits provide an illustrative guide of its composition. The specification has been revised to reflect this new understanding of the complex and its subunit decoration (see section~\ref{sec:techref:subunits}).
\item[Complex Identity] There was an open question about how a complex was to be identified. This was important because the decision about whether to use a clone marker correctly relies on this. The complex is now identified solely by its name and states and the its subunit composition is ignored (see section~\ref{defn:Complex}).
\item[Stoichiometry] In the previous specification it was possible to define a stoichiometry as unknown and also it was assumed that the stoichiometry was unknown if it was not displayed. The current specification revises this rule so that the stoichiometry is assumed to be one if not displayed and also if specified the stoichiometry must be an integer (see section~\ref{defn:stoichlabel}).
-\item[Submap rules simplified] In previous specifications the submap was described as being an independent map, which shared the same namespace as its parent map. The rules for consistency checking between maps were under-defined there, but attempts to enumerate the rules led to an unacceptable increase in complexity. To simplify this situation the submap is now assumed to be a mechanism to be used by software to collapse a region of detail in a given map. See section~\ref{sec:techref:mapsubmaps}.
+\item[Submap rules simplified] In previous specifications the submap was described as being an independent map, which shared the same namespace as its parent map. The rules for consistency checking between maps were under-defined there, but attempts to enumerate the rules led to an unacceptable increase in complexity. To simplify this situation the submap is now assumed to be a mechanism to be used by software to collapse a region of detail in a given map. See section~\ref{sec:techref:submap}.
\end{description}
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|
|
From: <lp...@us...> - 2015-04-23 11:16:19
|
Revision: 922
http://sourceforge.net/p/sbgn/code/922
Author: lptolik
Date: 2015-04-23 11:16:17 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
nonASCII symbols are fixed
Modified Paths:
--------------
EntityRelationship/trunk/sources/acknowledgments.tex
Modified: EntityRelationship/trunk/sources/acknowledgments.tex
===================================================================
--- EntityRelationship/trunk/sources/acknowledgments.tex 2015-04-23 11:12:54 UTC (rev 921)
+++ EntityRelationship/trunk/sources/acknowledgments.tex 2015-04-23 11:16:17 UTC (rev 922)
@@ -11,11 +11,11 @@
Here is a more comprehensive list of people who have been actively involved in SBGN development, either by their help designing the languages, their comments on the specification, help with development infrastructure or any other useful input. We aim this list to be rather complete. We are very sorry if we forgot someone, and will be grateful if you notified us of any omission.
-Mirit Aladjem, Frank Bergmann, Michael Blinov, Bernard de Bono, Sarah Boyd, Laurence Calzone, Melanie Courtot, David Croft, Tobias Czauderna, Emek Demir, Johannes W. Dietrich, Ugur Dogrusoz, Damien Fleury, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Samik Ghosh, Igor Goryanin, Anja Hartmann, Robin Haw, Michael Hucka, Matthias Jeschke, Mathias John, Akiya Jouraku, Astrid Junker, Hideya Kawaji, Douglas Kell, Sohyoung Kim, Hiroaki Kitano, Christian Klukas, Kurt Kohn, Fedor Kolpakov, Nicolas Le Nov\`{e}re, Lu Li, Augustin Luna, Yukiko Matsuoka, Carsten Maus, Alexander Mazein, Huaiyu Mi, Stuart Moodie, Ulrike Münzner, Anushya Muruganujan, Michael Pedersen, Jacqueline Quinn, Stefan Rybacki, Sven Sahle, Chris Sander, Herbert Sauro, Esther Schmidt, Falk Schreiber, Jacky Snoep, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Carolyn Talcott, Lin Uhrmacher, Martijn van Iersel, Alice Vill\'{e}ger, Stephen Waterson, Steven Watterson, Katja Wegner, Katja Wengler, Sarala Wimalaratne (Dissanayake), Guanming Wu, Röbbe Wünschiers.
+Mirit Aladjem, Frank Bergmann, Michael Blinov, Bernard de Bono, Sarah Boyd, Laurence Calzone, Melanie Courtot, David Croft, Tobias Czauderna, Emek Demir, Johannes W. Dietrich, Ugur Dogrusoz, Damien Fleury, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Samik Ghosh, Igor Goryanin, Anja Hartmann, Robin Haw, Michael Hucka, Matthias Jeschke, Mathias John, Akiya Jouraku, Astrid Junker, Hideya Kawaji, Douglas Kell, Sohyoung Kim, Hiroaki Kitano, Christian Klukas, Kurt Kohn, Fedor Kolpakov, Nicolas Le Nov\`{e}re, Lu Li, Augustin Luna, Yukiko Matsuoka, Carsten Maus, Alexander Mazein, Huaiyu Mi, Stuart Moodie, Ulrike M\"unzner, Anushya Muruganujan, Michael Pedersen, Jacqueline Quinn, Stefan Rybacki, Sven Sahle, Chris Sander, Herbert Sauro, Esther Schmidt, Falk Schreiber, Jacky Snoep, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Carolyn Talcott, Lin Uhrmacher, Martijn van Iersel, Alice Vill\'{e}ger, Steven Watterson, Katja Wegner (Wengler), Sarala Wimalaratne (Dissanayake), Guanming Wu, R\"obbe W\"unschiers.
The authors are also grateful to all the attendees of the SBGN meetings, as well as to the subscribers of the sbg...@ca... mailing list.
\section{Financial support}
-The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, \url{http://www.nedo.go.jp/}). The Okinawa Institute of Science and Technology (OIST, \url{http://www.oist.jp/}), the AIST Computational Biology Research Center (AIST CBRC, \url{http://www.cbrc.jp/index.eng.html}), the British Biotechnology and Biological Sciences Research Council (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award, the European Media Laboratory (EML Research gGmbH, \url{http://www.eml.org/english/}), and the Beckman Institute at the California Institute of Technology (\url{http://bnmc.caltech.edu}) provided additional support for SBGN workshops. Some help was provided by the Japan Science and Technology Agency (JST, \url{http://www.jst.go.jp/}) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp/}) for the development of the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
+The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, \url{http://www.nedo.go.jp/}). The Okinawa Institute of Science and Technology (OIST, \url{http://www.oist.jp/}), the AIST Computational Biology Research Center (AIST CBRC, \url{http://www.cbrc.jp/index.eng.html}), the British Biotechnology and Biological Sciences Research Council (BBSRC, \url{http://www.bbsrc.ac.uk/}) through a Japan Partnering Award, the European Media Laboratory (EML Research gGmbH, \url{http://www.eml.org/english/}), the Beckman Institute at the California Institute of Technology (\url{http://bnmc.caltech.edu}), Ontario National Science Foundation (NSF, \url{http://www.nsf.gov/}), USC Norris Comprehensive Cancer Center (\url{http://uscnorriscancer.usc.edu/}), Martin Luther University Halle-Wittenberg (\url{http://www.uni-halle.de/}), Monash University (\url{http://www.monash.edu.au/}), IPK Gatersleben (\url{http://www.ipk-gatersleben.de/en/}), University of Rostock (\url{http://www.uni-rostock.de/}) and German Federal Ministry of Research and Education (\url{http://www.bmbf.de/}) provided additional support for SBGN workshops. Some help was provided by the Japan Science and Technology Agency (JST, \url{http://www.jst.go.jp/}) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, \url{http://www.mext.go.jp/}) for the development of the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EPSRC, \url{http://www.epsrc.ac.uk}) during the redaction of the specification.
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|
|
From: <tcz...@us...> - 2015-04-23 11:13:01
|
Revision: 921
http://sourceforge.net/p/sbgn/code/921
Author: tczauderna
Date: 2015-04-23 11:12:54 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
added list of contributors provided by Anatoly (ER L1V2.0)
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
Modified: ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-04-23 10:01:49 UTC (rev 920)
+++ ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-04-23 11:12:54 UTC (rev 921)
@@ -36,7 +36,7 @@
Here is a more comprehensive list of people who have been actively involved in SBGN development, either by their help designing the languages, their comments on the specification, help with development infrastructure or any other useful input. We intend this list to be complete. We are very sorry if we forgot someone, and would be grateful if you could notify us of any omission.
-Mirit Aladjemm, Frank Bergmann, Sarah Boyd, Laurence Calzone, Melanie Courtot, Tobias Czauderna, Emek Demir, Ugur Dogrusoz, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Samik Ghosh, Igor Goryanin, Michael Hucka, Akiya Jouraku, Hideya Kawaji, Douglas Kell, Sohyoung Kim, Hiroaki Kitano, Kurt Kohn, Fedor Kolpakov, Nicolas \lenov{}, Lu Li, Augustin Luna, Yukiko Matsuoka, Huaiyu Mi, Stuart Moodie, Sven Sahle, Chris Sander, Herbert Sauro, Esther Schmidt, Falk Schreiber, Jacky Snoep, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Steven Watterson, Alice Vill\'{e}ger, Katja Wegner, Sarala Wimalaratne, Guanming Wu.
+Mirit Aladjem, Frank Bergmann, Michael Blinov, Bernard de Bono, Sarah Boyd, Laurence Calzone, Melanie Courtot, David Croft, Tobias Czauderna, Emek Demir, Johannes W. Dietrich, Ugur Dogrusoz, Damien Fleury, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Samik Ghosh, Igor Goryanin, Anja Hartmann, Robin Haw, Michael Hucka, Matthias Jeschke, Mathias John, Akiya Jouraku, Astrid Junker, Hideya Kawaji, Douglas Kell, Sohyoung Kim, Hiroaki Kitano, Christian Klukas, Kurt Kohn, Fedor Kolpakov, Nicolas Le Nov\`{e}re, Lu Li, Augustin Luna, Yukiko Matsuoka, Carsten Maus, Alexander Mazein, Huaiyu Mi, Stuart Moodie, Ulrike M\"unzner, Anushya Muruganujan, Michael Pedersen, Jacqueline Quinn, Stefan Rybacki, Sven Sahle, Chris Sander, Herbert Sauro, Esther Schmidt, Falk Schreiber, Jacky Snoep, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Carolyn Talcott, Lin Uhrmacher, Martijn van Iersel, Alice Vill\'{e}ger, Steven Watterson, Katja Wegner (Wengler), Sarala Wimalaratne (Dissanayake), Guanming Wu, R\"obbe W\"unschiers.
The authors are also grateful to all the attendees of the SBGN meetings, as
well as to the subscribers of the \mailto{sbg...@ca...} mailing list.
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|
|
From: <tcz...@us...> - 2015-04-23 10:01:56
|
Revision: 920
http://sourceforge.net/p/sbgn/code/920
Author: tczauderna
Date: 2015-04-23 10:01:49 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
added contributions to PD L1V2.0
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
Modified: ProcessDiagram/trunk/Specification/sources/acknowledgments.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-04-23 09:48:11 UTC (rev 919)
+++ ProcessDiagram/trunk/Specification/sources/acknowledgments.tex 2015-04-23 10:01:49 UTC (rev 920)
@@ -18,19 +18,19 @@
\section{Level 1 Release 1.1}
-The specification of SBGN PD Level 1.1 was written by Stuart Moodie and Nicolas \lenov{}, with contributions from (in alphabetical order) Frank Bergmann, Sarah Boyd, Emek Demir, Sarala Wimalaratne, Yukiko Matsuoka, Huaiyu Mi, Falk Schreiber, Anatoly Sorokin, and Alice Vill\'{e}ger.
+The specification of SBGN PD Level 1 Release 1.1 was written by Stuart Moodie and Nicolas \lenov{}, with contributions from (in alphabetical order) Frank Bergmann, Sarah Boyd, Emek Demir, Sarala Wimalaratne, Yukiko Matsuoka, Huaiyu Mi, Falk Schreiber, Anatoly Sorokin, and Alice Vill\'{e}ger.
\section{Level 1 Release 1.2}
-The specification of SBGN PD Level 1.2 was modified by Stuart Moodie, with contributions from (in alphabetical order) Sarah Boyd, Nicolas \lenov{}, and Huaiyu Mi.
+The specification of SBGN PD Level 1 Release 1.2 was modified by Stuart Moodie, with contributions from (in alphabetical order) Sarah Boyd, Nicolas \lenov{}, and Huaiyu Mi.
\section{Level 1 Release 1.3}
-The specification of SBGN PD Level 1.3 was modified by Stuart Moodie, with contributions from (in alphabetical order), Tobias Czauderna, Nicolas \lenov{}, and Anatoly Sorokin.
+The specification of SBGN PD Level 1 Release 1.3 was modified by Stuart Moodie, with contributions from (in alphabetical order), Tobias Czauderna, Nicolas \lenov{}, and Anatoly Sorokin.
\section{Level 1 Release 2.0}
-PUT SOME ACKNOWLEDGEMENTS HERE!
+The specification of SBGN PD Level 1 Release 2.0 was modified by Stuart Moodie, with contributions from (in alphabetical order), Tobias Czauderna, Nicolas \lenov{}, Huaiyu Mi, Falk Schreiber, Anatoly Sorokin and Alice Vill\'{e}ger.
\section{Comprehensive list of acknowledgements}
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|
|
From: <lp...@us...> - 2015-04-23 09:48:13
|
Revision: 919
http://sourceforge.net/p/sbgn/code/919
Author: lptolik
Date: 2015-04-23 09:48:11 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
list of meeting attendies is fixed
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/acknowledgments.tex
EntityRelationship/trunk/sources/front-page.tex
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/trunk/sources/acknowledgments.tex
===================================================================
--- EntityRelationship/trunk/sources/acknowledgments.tex 2015-04-23 09:35:35 UTC (rev 918)
+++ EntityRelationship/trunk/sources/acknowledgments.tex 2015-04-23 09:48:11 UTC (rev 919)
@@ -11,7 +11,7 @@
Here is a more comprehensive list of people who have been actively involved in SBGN development, either by their help designing the languages, their comments on the specification, help with development infrastructure or any other useful input. We aim this list to be rather complete. We are very sorry if we forgot someone, and will be grateful if you notified us of any omission.
-Mirit Aladjemm, Frank Bergmann, Michael Blinov, Sarah Boyd, Laurence Calzone, Melanie Courtot, Tobias Czauderna, Emek Demir, Ugur Dogrusoz, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Samik Ghosh, Igor Goryanin, Michael Hucka, Akiya Jouraku, Hideya Kawaji, Douglas Kell, Sohyoung Kim, Hiroaki Kitano, Kurt Kohn, Fedor Kolpakov , Nicolas Le Nov\`{e}re, Lu Li, Augustin Luna, Yukiko Matsuoka, Huaiyu Mi, Stuart Moodie, Sven Sahle, Chris Sander, Herbert Sauro, Esther Schmidt, Falk Schreiber, Jacky Snoep, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Steven Watterson, Martijn van Iersel, Alice Vill\'{e}ger, Katja Wegner, Sarala Wimalaratne, Guanming Wu.
+Mirit Aladjem, Frank Bergmann, Michael Blinov, Bernard de Bono, Sarah Boyd, Laurence Calzone, Melanie Courtot, David Croft, Tobias Czauderna, Emek Demir, Johannes W. Dietrich, Ugur Dogrusoz, Damien Fleury, Tom Freeman, Akira Funahashi, Ralph Gauges, Peter Ghazal, Samik Ghosh, Igor Goryanin, Anja Hartmann, Robin Haw, Michael Hucka, Matthias Jeschke, Mathias John, Akiya Jouraku, Astrid Junker, Hideya Kawaji, Douglas Kell, Sohyoung Kim, Hiroaki Kitano, Christian Klukas, Kurt Kohn, Fedor Kolpakov, Nicolas Le Nov\`{e}re, Lu Li, Augustin Luna, Yukiko Matsuoka, Carsten Maus, Alexander Mazein, Huaiyu Mi, Stuart Moodie, Ulrike Münzner, Anushya Muruganujan, Michael Pedersen, Jacqueline Quinn, Stefan Rybacki, Sven Sahle, Chris Sander, Herbert Sauro, Esther Schmidt, Falk Schreiber, Jacky Snoep, Anatoly Sorokin, Jessica Stephens, Linda Taddeo, Carolyn Talcott, Lin Uhrmacher, Martijn van Iersel, Alice Vill\'{e}ger, Stephen Waterson, Steven Watterson, Katja Wegner, Katja Wengler, Sarala Wimalaratne (Dissanayake), Guanming Wu, Röbbe Wünschiers.
The authors are also grateful to all the attendees of the SBGN meetings, as well as to the subscribers of the sbg...@ca... mailing list.
Modified: EntityRelationship/trunk/sources/front-page.tex
===================================================================
--- EntityRelationship/trunk/sources/front-page.tex 2015-04-23 09:35:35 UTC (rev 918)
+++ EntityRelationship/trunk/sources/front-page.tex 2015-04-23 09:48:11 UTC (rev 919)
@@ -16,7 +16,7 @@
\vspace*{0.5in}
\Large
-\textbf{Version 2}\\[0.1in]
+\textbf{Version 2.0}\\[0.1in]
\large
%Date: \sbgndate\\[0.25in]
Date: \today\\[0.25in]
@@ -35,7 +35,7 @@
Augustin Luna & \emph{Memorial Sloan-Kettering Institute, USA}\\
Tobias Czauderna & \emph{Monash University, Australia}\\
Emek Demir & \emph{Memorial Sloan-Kettering Institute, USA}\\
-Robin Haw & \emph{Othario Institute for Cancer Research, Canada}\\
+Robin Haw & \emph{Ontario Institute for Cancer Research, Canada}\\
Huaiyu Mi & \emph{University of Southern California, USA}\\
Stuart Moodie & \emph{Eight Pillars Ltd, UK}\\
Falk Schreiber & \emph{Monash University, Australia \& MLU Halle, Germany}\\
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|
|
From: <stu...@us...> - 2015-04-23 09:35:37
|
Revision: 918
http://sourceforge.net/p/sbgn/code/918
Author: stumoodie
Date: 2015-04-23 09:35:35 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Changed so glossary now has a useful heading name
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/Makefile
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
ProcessDiagram/trunk/Specification/sources/glyphs.tex
ProcessDiagram/trunk/Specification/sources/validation.tex
Modified: ProcessDiagram/trunk/Specification/Makefile
===================================================================
--- ProcessDiagram/trunk/Specification/Makefile 2015-04-23 07:47:04 UTC (rev 917)
+++ ProcessDiagram/trunk/Specification/Makefile 2015-04-23 09:35:35 UTC (rev 918)
@@ -12,6 +12,7 @@
LATEX = pdflatex
BIBTEX = bibtex
MKIDX = makeindex
+MKGLOS = makeglossaries
all default: images examples
$(MAKE) -C examples
@@ -20,8 +21,10 @@
$(LATEX) $(MAIN).tex
$(LATEX) $(MAIN).tex
$(MKIDX) $(MAIN)
+ $(MKGLOS) $(MAIN)
$(BIBTEX) $(MAIN)
$(LATEX) $(MAIN).tex
+ $(LATEX) $(MAIN).tex
clean:
$(MAKE) -C images clean
@@ -32,11 +35,16 @@
-rm -f *.dvi
-rm -f *.toc
-rm -f *.aux
+ -rm -f *.fls
-rm -f *.log
-rm -f *.tmp
-rm -f *.prv
-rm -f *.idx
+ -rm -f *.ind
+ -rm -f *.ist
-rm -f sbgn_PD-level1.fdb_latexmk
+ -rm -f *.gl*
+ -rm -f *.ilg
dist_clean: clean
-rm -f *.pdf
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2015-04-23 07:47:04 UTC (rev 917)
+++ ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2015-04-23 09:35:35 UTC (rev 918)
@@ -32,6 +32,7 @@
\usepackage[olditem,oldenum]{paralist}
\usepackage{fourier}
\usepackage{multicol}
+\usepackage[toc,section=chapter,numberedsection]{glossaries}
%\usepackage{layouts}
\usepackage[pdftex]{graphicx}
@@ -67,12 +68,27 @@
%\input{sources/latex-style}
\input{sources/latex-macros}
+\makeglossaries
+
\makeindex
+\renewcommand{\glsglossarymark}[1]{}
+
%% ----------------------------------------------------------------------------
\begin{document}
%% ----------------------------------------------------------------------------
+
+\newenvironment{valrules}{\begin{description}}{\end{description}}
+
+\newcommand{\defrule}[2]{\newglossaryentry{#1}
+{
+ name=#1,
+ description={#2}
+}
+\item[\gls{#1}] #2
+}
+
\newcommand{\umlclasshead}[1]{\subsection{\index{#1}#1}}
\renewenvironment*{theindex}{\begin{itemize}[label={}]\tightlist\setlength{\itemindent}{-25pt}\nolinenumbers\begin{multicols}{2}}{\end{multicols}\end{itemize}}
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-04-23 07:47:04 UTC (rev 917)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-04-23 09:35:35 UTC (rev 918)
@@ -557,15 +557,38 @@
\subsubsection{Rule and Constraints}
-\begin{itemize}
-\item All instances of \sbgnclass{EntityPoolNode} associated with a
- particular \sbgnclass{EntityType} must be of the same class.
-\item If an instance of \sbgnclass{EntityType} contains one or more
+
+
+\begin{valrules}
+% \newglossaryentry{Rule001}
+% {
+% name=Rule001,
+% description={All instances of \sbgnclass{EntityPoolNode} associated with a
+% particular \sbgnclass{EntityType} must be of the same class.}
+% }
+% \item[\gls{Rule001}] All instances of \sbgnclass{EntityPoolNode} associated with a
+% particular \sbgnclass{EntityType} must be of the same class.
+\defrule{Rule001}{All instances of \sbgnclass{EntityPoolNode} associated with a
+ particular \sbgnclass{EntityType} must be of the same class.}
+\defrule{Rule002}{If an instance of \sbgnclass{EntityType} contains one or more
instances of \sbgnclass{StateVariableDefinition} then the
\sbgnclass{EntityPoolNode}s associated with it must be subclasses of
- \sbgnclass{StatefulEPN}.
-\end{itemize}
+ \sbgnclass{StatefulEPN}.}
+% \newglossaryentry{Rule002}
+% {
+% name=Rule002,
+% description={If an instance of \sbgnclass{EntityType} contains one or more
+% instances of \sbgnclass{StateVariableDefinition} then the
+% \sbgnclass{EntityPoolNode}s associated with it must be subclasses of
+% \sbgnclass{StatefulEPN}.}
+% }
+% \item[\gls{Rule002}] If an instance of \sbgnclass{EntityType} contains one or more
+% instances of \sbgnclass{StateVariableDefinition} then the
+% \sbgnclass{EntityPoolNode}s associated with it must be subclasses of
+% \sbgnclass{StatefulEPN}.
+\end{valrules}
+
\subsubsection{Notation}
Although there is no direct graphical representation of this class,
Modified: ProcessDiagram/trunk/Specification/sources/validation.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/validation.tex 2015-04-23 07:47:04 UTC (rev 917)
+++ ProcessDiagram/trunk/Specification/sources/validation.tex 2015-04-23 09:35:35 UTC (rev 918)
@@ -1,16 +1,20 @@
-\chapter{Validation and consistency rules}
+%\chapter{Validation and consistency rules}
-\newcommand{\validationRule} [1]{\item[#1.~]\input{validation-rules/#1.tex}}
+% \newcommand{\validationRule} [1]{\item[#1.~]\input{validation-rules/#1.tex}}
-This section describes criteria that must be met by the diagram (or SBGN-ML diagram description) to conform
-\SBGNPDLone specification.
+% This section describes criteria that must be met by the diagram (or SBGN-ML diagram description) to conform
+% \SBGNPDLone specification.
-This is still to be completed. However, the plan is to extract the
-rules itemised throughput the specification and duplicate them
-here. Extraction will be carried out using a script so although the
-information will be redundant it will be easy to keep this section
-consistent with the rest of the specification.
+% This is still to be completed. However, the plan is to extract the
+% rules itemised throughput the specification and duplicate them
+% here. Extraction will be carried out using a script so although the
+% information will be redundant it will be easy to keep this section
+% consistent with the rest of the specification.
+%\clearpage
+
+\printglossary[title=Validation and consistency rules]
+
% All criteria has unique and perennial numbering. In the case when modification of the specification makes a rule
% irrelevant it will be deleted but the number of the rule will not be taken, so there will be gaps in rule numbering.
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|
|
From: <stu...@us...> - 2015-04-23 07:47:07
|
Revision: 917
http://sourceforge.net/p/sbgn/code/917
Author: stumoodie
Date: 2015-04-23 07:47:04 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Build index from makefile now
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/Makefile
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
Modified: ProcessDiagram/trunk/Specification/Makefile
===================================================================
--- ProcessDiagram/trunk/Specification/Makefile 2015-04-23 07:39:52 UTC (rev 916)
+++ ProcessDiagram/trunk/Specification/Makefile 2015-04-23 07:47:04 UTC (rev 917)
@@ -11,6 +11,7 @@
LATEX = pdflatex
BIBTEX = bibtex
+MKIDX = makeindex
all default: images examples
$(MAKE) -C examples
@@ -18,6 +19,7 @@
$(MAKE) -C le_images
$(LATEX) $(MAIN).tex
$(LATEX) $(MAIN).tex
+ $(MKIDX) $(MAIN)
$(BIBTEX) $(MAIN)
$(LATEX) $(MAIN).tex
@@ -33,6 +35,7 @@
-rm -f *.log
-rm -f *.tmp
-rm -f *.prv
+ -rm -f *.idx
-rm -f sbgn_PD-level1.fdb_latexmk
dist_clean: clean
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
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|
|
From: <stu...@us...> - 2015-04-23 07:39:59
|
Revision: 916
http://sourceforge.net/p/sbgn/code/916
Author: stumoodie
Date: 2015-04-23 07:39:52 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Updated revision appendix
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/front-page.tex
ProcessDiagram/trunk/Specification/sources/revision_history.tex
ProcessDiagram/trunk/Specification/sources/whatsnew.tex
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/front-page.tex 2015-04-23 07:21:13 UTC (rev 915)
+++ ProcessDiagram/trunk/Specification/sources/front-page.tex 2015-04-23 07:39:52 UTC (rev 916)
@@ -27,12 +27,6 @@
Level~1 Version 2.0 specification. It is not a normative document.
\end{minipage}}
-% \cornersize{0.3}\ovalbox{\begin{minipage}{4.9in}\color{DarkRed}
-% Disclaimer: This is a release candiate of the SBGN \PDl
-% Level~1 Release 1.3 specification. Please report any errors to the issues tracker at \url{http://sourceforge.net/projects/sbgn/develop}.
-% It is not a normative document.
-% \end{minipage}}
-
\vspace{0.5in}
% Acknowledgements
Modified: ProcessDiagram/trunk/Specification/sources/revision_history.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/revision_history.tex 2015-04-23 07:21:13 UTC (rev 915)
+++ ProcessDiagram/trunk/Specification/sources/revision_history.tex 2015-04-23 07:39:52 UTC (rev 916)
@@ -118,3 +118,8 @@
Fixed typo in item on catalysis in section on modulation semantics. & \\\hline
State variables figure 2.6 V1.2 & 3090543 \\\hline\end{supertabular}
\end{center}
+
+\section{Version 1.3 to Version 2.0}
+
+The changes incorporated into Version 2.0 of the \SBGNPDLone are
+summarised in chapter~\ref{chap:whatsnew}.
Modified: ProcessDiagram/trunk/Specification/sources/whatsnew.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/whatsnew.tex 2015-04-23 07:21:13 UTC (rev 915)
+++ ProcessDiagram/trunk/Specification/sources/whatsnew.tex 2015-04-23 07:39:52 UTC (rev 916)
@@ -1,4 +1,5 @@
\chapter{What's New}
+\label{chap:whatsnew}
\section{Introduction}
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|
|
From: <stu...@us...> - 2015-04-23 07:21:15
|
Revision: 915
http://sourceforge.net/p/sbgn/code/915
Author: stumoodie
Date: 2015-04-23 07:21:13 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Updated tite page etc
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/le_images/process-dimerisation.pdf
ProcessDiagram/trunk/Specification/le_images/submap-dissociated.pdf
ProcessDiagram/trunk/Specification/le_images/submap-folded.pdf
ProcessDiagram/trunk/Specification/le_images/submap-unfolded.pdf
ProcessDiagram/trunk/Specification/le_images/submap.pdf
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/front-page.tex
ProcessDiagram/trunk/Specification/sources/glyphs.tex
ProcessDiagram/trunk/Specification/sources/whatsnew.tex
Modified: ProcessDiagram/trunk/Specification/le_images/process-dimerisation.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/le_images/submap-dissociated.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/le_images/submap-folded.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/le_images/submap-unfolded.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/le_images/submap.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/front-page.tex 2015-04-22 15:10:03 UTC (rev 914)
+++ ProcessDiagram/trunk/Specification/sources/front-page.tex 2015-04-23 07:21:13 UTC (rev 915)
@@ -35,13 +35,20 @@
\vspace{0.5in}
+% Acknowledgements
+
\textbf{\sffamily Editors}:\\[7pt]
\begin{tabular}{l>{\hspace*{15pt}}r}
Stuart Moodie & \emph{Eight Pillars Ltd, UK}\\
Tobias Czauderna & \emph{Monash University, Australia}\\
+Emek Demir & \emph{Memorial Sloan-Kettering Institute, USA}\\
+Robin Haw & \emph{Othario Institute for Cancer Research, Canada}\\
+Augustin Luna & \emph{Memorial Sloan-Kettering Institute, USA}\\
+Huaiyu Mi & \emph{University of Southern California, USA}\\
+Nicolas \lenov & \emph{Babraham Institute, UK}\\
Falk Schreiber & \emph{Monash University, Australia \& MLU Halle, Germany}\\
-Anatoly Sorokin & \emph{Institute of Cell Biophysics RAS, Russia}\\
-Huaiyu Mi & \emph{University of Southern California, USA}\\
+Anatoly Sorokin & \emph{Institute of Cell Biophysics RAS, RU}\\
+Alice Vill\'{e}ger & \emph{Freelance IT Consultant, UK}
\end{tabular}
% \vspace*{1em}
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-04-22 15:10:03 UTC (rev 914)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2015-04-23 07:21:13 UTC (rev 915)
@@ -107,7 +107,6 @@
value that is a integer.
\end{description}
%
-%
\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.9\textwidth]{images/exampleuml}
@@ -764,6 +763,7 @@
\umlclasshead{EmptySet}
\label{sec:techref:sourceSink}
+\label{defn:emptySet}
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
@@ -3139,6 +3139,7 @@
\paragraph{Glyph: \glyph{Stoichiometry Label}}
+\label{defn:stoichlabel}
The stoichiometry label is part of the \glyph{consumption arc} and
\glyph{production arc} glyphs see below (sections
@@ -4025,6 +4026,8 @@
\label{sec:techref:epnuniqueness}
\label{sec:techref:uniquenessdefinition}
+\textbf{Add something about process identity}
+
By definition all glyphs drawn on a \PDl are unique. They are shapes
that are distinct from other shapes drawn on the map. However, in some
cases the glyphs can represent the same concepts. The \PDl has a
Modified: ProcessDiagram/trunk/Specification/sources/whatsnew.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/whatsnew.tex 2015-04-22 15:10:03 UTC (rev 914)
+++ ProcessDiagram/trunk/Specification/sources/whatsnew.tex 2015-04-23 07:21:13 UTC (rev 915)
@@ -23,8 +23,22 @@
\begin{description}
\item[Annotation (New)] This version sees the introduction of the annotation glyph. This makes the \PDl consistent with the other SBGN languages. The glyph provides a mechanisms to annotate parts of an SBGN map and does not affect the meaning of the map. See section~\ref{defn:Annotation}.
\item[State Variable] The symbol used for this glyph has been modified to use the stadium (or capsule) glyph. This replaces the elipse although the circle is preserved (it can be though of as a special form of the stadium symbol with no straight edges). More details can be found in section~\ref{defn:StateVariable}.
-\item[Small Molecule]
+\item[Small Molecule] The small molecule glyph has been changed from a circle to a stadium symbol. The circle had the drawback of taking up a lot of space if the author wanted to draw the label inside the shape. Also if the circle was deformed it became an oval, which is the symbol of a Unspecified Entity. The new glyph does not have either of these problems and can also adopt a circle shape if the straight lined have zero length. See section~\ref{sec:techref:simpleChemical}.
+\item[Empty Set] The empty set glyph is a rationalisation of the source and sink glyphs, which both have the same symbol. They are now represented by the same glyph and the usage rules have been relaxed. More details can be found in section~\ref{defn:emptySet}.
\end{description}
-\section{Semantics}
+%\begin{figure}
+%\includegraphics[width=0.9\textwidth]{images/new_glyphs}
+%\end{figure}
+\section{Rule Changes and Clarifications}
+
+\begin{description}
+\item[Process Duplication] The specification was unclear about whether a process could be duplicated. This situation could possibly arise if two processes were drawn that involved the same inputs, outputs and modulators. This is now clarified and all processes drawn in a map are unique and should be interpreted as describing different processes.
+\item[Phenotype Duplication] The phenotype has, in previous specifications, been described as having a clone marker. This was inconsistent with the concept that a phenotype as a process, which cannot be cloned (see above). The specification has been revised accordingly (section~\ref{sec:techref:epnuniqueness}).
+\item[Clarified Identity Semantics] The specification was vague on when an author needed to use a clone marker. Especially when a macromolecule of the same name had material type or cardinality units of information. These rules have been expanded and the role of the cardinality and material type clarified. See section~\ref{sec:techref:epnuniqueness}.
+\item[Subunits are not EPNs] Previous specifications treated the subunit of a complex as a EPN. This was a mistake as the complex itself is the EPN and the subunits provide an illustrative guide of its composition. The specification has been revised to reflect this new understanding of the complex and its subunit decoration (see section~\ref{sec:techref:subunits}).
+\item[Complex Identity] There was an open question about how a complex was to be identified. This was important because the decision about whether to use a clone marker correctly relies on this. The complex is now identified solely by its name and states and the its subunit composition is ignored (see section~\ref{defn:Complex}).
+\item[Stoichiometry] In the previous specification it was possible to define a stoichiometry as unknown and also it was assumed that the stoichiometry was unknown if it was not displayed. The current specification revises this rule so that the stoichiometry is assumed to be one if not displayed and also if specified the stoichiometry must be an integer (see section~\ref{defn:stoichlabel}).
+\item[Submap rules simplified] In previous specifications the submap was described as being an independent map, which shared the same namespace as its parent map. The rules for consistency checking between maps were under-defined there, but attempts to enumerate the rules led to an unacceptable increase in complexity. To simplify this situation the submap is now assumed to be a mechanism to be used by software to collapse a region of detail in a given map. See section~\ref{sec:techref:mapsubmaps}.
+\end{description}
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|
|
From: <tcz...@us...> - 2015-04-22 15:10:14
|
Revision: 914
http://sourceforge.net/p/sbgn/code/914
Author: tczauderna
Date: 2015-04-22 15:10:03 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
removed empty set from EPNs
added annotation
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/images/refcard.svg
Modified: ProcessDiagram/trunk/Specification/images/refcard.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/refcard.svg 2015-04-22 12:48:47 UTC (rev 913)
+++ ProcessDiagram/trunk/Specification/images/refcard.svg 2015-04-22 15:10:03 UTC (rev 914)
@@ -41,8 +41,8 @@
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
inkscape:zoom="0.6227328"
- inkscape:cx="600.08383"
- inkscape:cy="360.64355"
+ inkscape:cx="271.75091"
+ inkscape:cy="212.39561"
inkscape:document-units="px"
inkscape:current-layer="g3382"
width="1052.3622px"
@@ -89,22 +89,12 @@
inkscape:label="Sections"
inkscape:groupmode="layer"
id="layer1"
- style="display:inline"
- sodipodi:insensitive="true">
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- rx="10.47941"
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- x="251.19485"
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- style="fill:#fafafa;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" />
+ style="display:inline">
<path
style="fill:#fafafa;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
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+ d="M 36.186528,19.836966 C 30.245884,20.02123 26.167877,24.293614 25.991101,30.477894 l 0.353553,521.497586 c 0,5.0787 3.901228,10.0849 8.781214,10.08489 l 427.115682,2.3e-4 c 4.91297,-0.24655 9.83109,-4.17869 9.77227,-10.08512 l 0,-195.19669 c -0.0568,-5.48178 -4.02366,-9.48908 -9.31628,-9.46972 -35.54196,0.004 -167.74405,0.31153 -203.38055,0.7915 -15.80096,0.21282 -15.80096,-12.95508 -15.80096,-12.94125 l 0.42331,-304.767749 c 0,-5.078699 -3.78877,-10.186077 -9.19908,-10.370341 z"
id="rect3279"
- sodipodi:nodetypes="ccccccccccccscccc"
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inkscape:connector-curvature="0" />
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style="fill:#fafafa;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
@@ -207,19 +197,6 @@
sodipodi:role="line"
style="font-size:14px">Auxiliary Units</tspan></text>
<text
- id="text3275"
- y="593.4942"
- x="266.77542"
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- y="593.4942"
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- sodipodi:role="line"
- style="font-size:14px">Reference Nodes</tspan></text>
- <text
id="text3168-4"
y="557.88354"
x="718.59338"
@@ -231,6 +208,25 @@
id="tspan3170-4"
sodipodi:role="line"
style="font-size:13.99983406px">Logical Operators</tspan></text>
+ <path
+ style="display:inline;fill:#fafafa;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
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+ xml:space="preserve"
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+ inkscape:transform-center-y="5.4174805"><tspan
+ y="593.4942"
+ x="41.571575"
+ id="tspan3277"
+ sodipodi:role="line"
+ style="font-size:14px">Reference Nodes</tspan></text>
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id="g3382"
@@ -238,21 +234,21 @@
inkscape:label="Gyphs"
style="display:inline">
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- transform="translate(552.14295,537.71915)"
+ transform="translate(326.9391,547.71915)"
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sodipodi:nodetypes="cccccccc"
id="path3428"
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+ style="font-style:normal;font-weight:normal;font-size:12px;font-family:'Bitstream Vera Sans';fill:#000000;fill-opacity:1;stroke:none"
xml:space="preserve"><tspan
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@@ -307,7 +303,7 @@
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
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From: <tcz...@us...> - 2015-04-22 13:17:50
|
Revision: 913
http://sourceforge.net/p/sbgn/code/913
Author: tczauderna
Date: 2015-04-22 12:48:47 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
fixed some problems on reference card
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/images/refcard.svg
Modified: ProcessDiagram/trunk/Specification/images/refcard.svg
===================================================================
--- ProcessDiagram/trunk/Specification/images/refcard.svg 2015-04-22 12:42:59 UTC (rev 912)
+++ ProcessDiagram/trunk/Specification/images/refcard.svg 2015-04-22 12:48:47 UTC (rev 913)
@@ -13,7 +13,7 @@
height="744.09448"
id="svg2"
sodipodi:version="0.32"
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+ inkscape:version="0.91 r13725"
version="1.0"
sodipodi:docname="refcard.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape"
@@ -40,17 +40,17 @@
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inkscape:pageshadow="2"
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+ inkscape:zoom="0.6227328"
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inkscape:document-units="px"
inkscape:current-layer="g3382"
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+ style="fill:#fafafa;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" />
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xml:space="preserve"
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+ style="font-style:normal;font-weight:normal;font-size:12px;font-family:'Bitstream Vera Sans';fill:#000000;fill-opacity:1;stroke:none"
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y="37.582188"
id="text3156"><tspan
@@ -161,21 +161,21 @@
id="tspan3158"
x="42.206646"
y="37.582188"
- style="font-size:14px">Entity Pool Nodes</tspan></text>
+ style="font-size:14px">Entity Pool Nodes (EPN)</tspan></text>
<text
id="text3160"
y="443.76596"
x="504.41101"
- style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;font-family:Bitstream Vera Sans"
+ style="font-style:normal;font-weight:normal;font-size:12px;font-family:'Bitstream Vera Sans';fill:#000000;fill-opacity:1;stroke:none"
xml:space="preserve"><tspan
y="443.76596"
x="504.41101"
id="tspan3162"
sodipodi:role="line"
- style="font-size:14px">Container Nodes</tspan></text>
+ style="font-size:14px">Container Nodes (CN)</tspan></text>
<text
xml:space="preserve"
- style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;font-family:Bitstream Vera Sans"
+ style="font-style:normal;font-weight:normal;font-size:12px;font-family:'Bitstream Vera Sans';fill:#000000;fill-opacity:1;stroke:none"
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@@ -183,23 +183,23 @@
id="tspan3166"
x="492.10843"
y="37.582188"
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+ style="font-size:14px">Process Nodes (PN)</tspan></text>
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x="718.60211"
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xml:space="preserve"><tspan
y="37.582188"
x="718.60211"
id="tspan3170"
sodipodi:role="line"
- style="font-size:14px">Connecting arcs</tspan></text>
+ style="font-size:14px">Connecting Arcs</tspan></text>
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@@ -219,6 +219,18 @@
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sodipodi:role="line"
style="font-size:14px">Reference Nodes</tspan></text>
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2015-04-22 12:43:01
|
Revision: 912
http://sourceforge.net/p/sbgn/code/912
Author: lptolik
Date: 2015-04-22 12:42:59 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
editor list is fixed
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 2015-04-22 12:38:45 UTC (rev 911)
+++ EntityRelationship/trunk/sources/front-page.tex 2015-04-22 12:42:59 UTC (rev 912)
@@ -35,6 +35,7 @@
Augustin Luna & \emph{Memorial Sloan-Kettering Institute, USA}\\
Tobias Czauderna & \emph{Monash University, Australia}\\
Emek Demir & \emph{Memorial Sloan-Kettering Institute, USA}\\
+Robin Haw & \emph{Othario Institute for Cancer Research, Canada}\\
Huaiyu Mi & \emph{University of Southern California, USA}\\
Stuart Moodie & \emph{Eight Pillars Ltd, UK}\\
Falk Schreiber & \emph{Monash University, Australia \& MLU Halle, Germany}\\
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2015-04-22 12:38:53
|
Revision: 911
http://sourceforge.net/p/sbgn/code/911
Author: lptolik
Date: 2015-04-22 12:38:45 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
version for review
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/ENs.tex
EntityRelationship/trunk/sources/acknowledgments.tex
EntityRelationship/trunk/sources/er-overview.tex
EntityRelationship/trunk/sources/front-page.tex
EntityRelationship/trunk/sources/introduction.tex
EntityRelationship/trunk/sources/outcome.tex
EntityRelationship/trunk/sources/revision_history.tex
EntityRelationship/trunk/sources/semantics.tex
EntityRelationship/trunk/sources/working.tex
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/trunk/sources/ENs.tex
===================================================================
--- EntityRelationship/trunk/sources/ENs.tex 2015-04-22 12:33:50 UTC (rev 910)
+++ EntityRelationship/trunk/sources/ENs.tex 2015-04-22 12:38:45 UTC (rev 911)
@@ -1,3 +1,4 @@
+% !TEX root = ../sbgn_ER-level1.tex
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% Entity nodes
@@ -25,12 +26,14 @@
\subsection{Logical operators}\label{sec:logic}
-A \glyph{logical operator} allows to combine elements of truth into another element of truth (if A exists and B exits, then A AND B exists) in order to apply influences. \SBGNERLone{} provides three \glyph{logical operators}, \glyph{and}, \glyph{or}, and \glyph{not}. %\SBGNERLone{} provides four \glyph{logical operators}, \glyph{and}, \glyph{or}, \glyph{not} and \glyph{delay}.
+A \glyph{logical operator} allows to combine elements of truth into another element of truth (if A exists and B exits, then A AND B exists) in order to apply influences.
+\SBGNERLone{} provides three \glyph{logical operators}, \glyph{and}, \glyph{or}, and \glyph{not}.
+%\SBGNERLone{} provides four \glyph{logical operators}, \glyph{and}, \glyph{or}, \glyph{not} and \glyph{delay}.
\input{sources/and.tex}
\input{sources/or.tex}
\input{sources/not.tex}
-%\input{sources/delay.tex}
+\input{sources/delay.tex}
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Modified: EntityRelationship/trunk/sources/acknowledgments.tex
===================================================================
--- EntityRelationship/trunk/sources/acknowledgments.tex 2015-04-22 12:33:50 UTC (rev 910)
+++ EntityRelationship/trunk/sources/acknowledgments.tex 2015-04-22 12:38:45 UTC (rev 911)
@@ -1,3 +1,4 @@
+% !TEX root = ../sbgn_ER-level1.tex
\chapter{Acknowledgments}\label{sec:acknowledgments}
SBGN specifications are developed by many people, and with the support of many organisations.
@@ -4,7 +5,7 @@
\section{Main contributors}
-In addition to the SBGN editors, the specification of SBGN ER benefited enormously from the contribution of many people. In particular, the specification of \SBGNERLone benefited much from deep discussions with Mirit Aladjem, Kurt Kohn, Emek Demir, Augustin Luna, Sohyoung Kim, Yukiko Matsuoka and Hiroaki Kitano.
+In addition to the SBGN editors, the specification of SBGN ER benefited enormously from the contribution of many people. In particular, the specification of \SBGNERLone benefited much from deep discussions with Mirit Aladjem, Kurt Kohn, Emek Demir, Sohyoung Kim, Yukiko Matsuoka and Hiroaki Kitano.
\section{Comprehensive list of contributors}
Modified: EntityRelationship/trunk/sources/er-overview.tex
===================================================================
--- EntityRelationship/trunk/sources/er-overview.tex 2015-04-22 12:33:50 UTC (rev 910)
+++ EntityRelationship/trunk/sources/er-overview.tex 2015-04-22 12:38:45 UTC (rev 911)
@@ -1,3 +1,4 @@
+% !TEX root = ../sbgn_ER-level1.tex
% =============================================================================
% overview
% =============================================================================
@@ -14,7 +15,7 @@
\label{fig:eg1}
\end{figure}
-The essence of the \ERs is to depict the influences of entities upon the behaviour of others. The entities are classes of things that can exist, either on their own, or when statements (interactions and assignments) become true, so existence is the key concept in \ERs. For entity to participate in relationship at least one instance of it should exist otherwise entity will be non-existent. Instances of different entities can interact (such as ``entity A'' and ``entity B'' in \fig{eg1}), or a value can be assigned to a property of some instance of an entity (such as ``value 1'' to property ``var'' of ``entity A'' in \fig{eg1}). The influences can therefore be understood as logical consequences of existence of its instances. The stimulation of the interaction between ``entity A'' and ``entity B'' in \fig{eg1} takes place if ``value 1'' is really assigned to property ``var'' of some instance of the ``entity A''. The existence of the assignment (set of instances where value is really assigned to the property) is represented by the black dot (called \glyph{outcome}). On the contrary to the \PDl, where the different processes affect each other in a way that the behaviour of the depicted system can only be understood taking into account the whole system, the relationships are essentially independent. One can imagine that each of the relationships represents a specific conclusion of a scientific experiment reported in an article. Their addition on a map represents the knowledge we have of the effects of the entities represented upon each other. In \fig{eg1}, we have three statements:
+The essence of the \ERs is to depict the influences of entities upon the behaviour of others. The entities are classes of things that can exist, either on their own, or when statements (interactions and assignments) become true, so existence is the key concept in \ERs. For entity to participate in relationship at least one of it's instance should exist. Instances of different entities can interact (such as ``entity A'' and ``entity B'' in \fig{eg1}), or a value can be assigned to a property of some instance of an entity (such as ``value 1'' to property ``var'' of ``entity A'' in \fig{eg1}). The entities can modify the interactions between other entities, for example, stimulation of the interaction between ``entity A'' and ``entity B'' in \fig{eg1} takes place if ``value 1'' is really assigned to property ``var'' of some instance of the ``entity A''. The existence of the assignment (set of instances where value is really assigned to the property) is represented by the black dot (called \glyph{outcome}). The influences can therefore be understood as logical consequences of existence of participating instances. On the contrary to the \PDl, where the different processes affect each other in a way that the behaviour of the depicted system can only be understood taking into account the whole system, the relationships are essentially independent. One can imagine that each of the relationships represents a specific conclusion of a scientific experiment reported in an article. Their addition on a map represents the knowledge we have of the effects of the entities represented upon each other. In \fig{eg1}, we have three statements:
\begin{itemize}
\item ``entity A'' can interact with ``entity B''.
Modified: EntityRelationship/trunk/sources/front-page.tex
===================================================================
--- EntityRelationship/trunk/sources/front-page.tex 2015-04-22 12:33:50 UTC (rev 910)
+++ EntityRelationship/trunk/sources/front-page.tex 2015-04-22 12:38:45 UTC (rev 911)
@@ -1,3 +1,4 @@
+% !TEX root = ../sbgn_ER-level1.tex
% =============================================================================
% front-page
% =============================================================================
@@ -31,14 +32,13 @@
\begin{tabular}{l>{\hspace*{15pt}}r}
Anatoly Sorokin & \emph{Institute of Cell Biophysics RAS, RU}\\
Nicolas \lenov & \emph{Babraham Institute, UK}\\
+Augustin Luna & \emph{Memorial Sloan-Kettering Institute, USA}\\
+Tobias Czauderna & \emph{Monash University, Australia}\\
+Emek Demir & \emph{Memorial Sloan-Kettering Institute, USA}\\
+Huaiyu Mi & \emph{University of Southern California, USA}\\
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}
+Alice Vill\'{e}ger & \emph{Freelance IT Consultant, UK}
\end{tabular}
\vfill
Modified: EntityRelationship/trunk/sources/introduction.tex
===================================================================
--- EntityRelationship/trunk/sources/introduction.tex 2015-04-22 12:33:50 UTC (rev 910)
+++ EntityRelationship/trunk/sources/introduction.tex 2015-04-22 12:38:45 UTC (rev 911)
@@ -1,3 +1,4 @@
+% !TEX root = ../sbgn_ER-level1.tex
% =============================================================================
% introduction
% =============================================================================
Modified: EntityRelationship/trunk/sources/outcome.tex
===================================================================
--- EntityRelationship/trunk/sources/outcome.tex 2015-04-22 12:33:50 UTC (rev 910)
+++ EntityRelationship/trunk/sources/outcome.tex 2015-04-22 12:38:45 UTC (rev 911)
@@ -1,4 +1,4 @@
-
+% !TEX root = ../sbgn_ER-level1.tex
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% Outcome
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Modified: EntityRelationship/trunk/sources/revision_history.tex
===================================================================
--- EntityRelationship/trunk/sources/revision_history.tex 2015-04-22 12:33:50 UTC (rev 910)
+++ EntityRelationship/trunk/sources/revision_history.tex 2015-04-22 12:38:45 UTC (rev 911)
@@ -1,6 +1,7 @@
+% !TEX root = ../sbgn_ER-level1.tex
\chapter{Revision History}
-\section{Version 1 to Version 2}
+\section{Version 1.2 to Version 2}
Below are the changes incorporated into Version 2 of the \SBGNERLone specification. The Tracker IDs correspond to the sourceforge tracker ``SBGN ER L1'' (\url{http://sourceforge.net/p/sbgn/sbgn-er-l1/}). The message IDs correspond to the ``sbgn-discuss'' mailing list (https://utils.its.caltech.edu/pipermail/sbgn-discuss/).
@@ -18,6 +19,15 @@
\hline}
\tablelasttail{\hline}
\begin{supertabular}{|p{0.75\textwidth}|p{0.25\textwidth}|}\hline
+Definition of outcome as a subset of instances & \\\hline
+User manual (RTK example with extended description) is added & \\\hline
+Synchronous events & \\\hline
+Nested entities & \\\hline
+Clarification of entity definition & \\\hline
+Clarification of outcome definition & \\hline
+Add interaction outcome in the ER spec. & track: 25 \\\hline
+Definition of outcome with rel to nested entities & track: 22 \\\hline
+Error in SBGN-ER Specifications & track: 27 \\\hline
& track: \\\hline
\end{supertabular}
\end{center}
Modified: EntityRelationship/trunk/sources/semantics.tex
===================================================================
--- EntityRelationship/trunk/sources/semantics.tex 2015-04-22 12:33:50 UTC (rev 910)
+++ EntityRelationship/trunk/sources/semantics.tex 2015-04-22 12:38:45 UTC (rev 911)
@@ -1,3 +1,4 @@
+% !TEX root = ../sbgn_ER-level1.tex
%\color{red}
\section{Semantic description of \ERs}
@@ -5,7 +6,7 @@
\subsection{Entities and states}
-An \glyph{entity} (\sect{entity}) represents a set of individual instances of some kind (molecules, agents etc). The difference from \SBGNPDLone \glyph{entity pool node} is that \glyph{entity} instances are independent, while \glyph{entity pool node} form one nonseparable object acting as a whole. A set of \glyph{state variables} (\sect{stateVariable}) and their \glyph{values} (\sect{variableValue}) describe a part of the \glyph{entity} instances state space. The \glyph{entity}, or interaction \glyph{outcome} (\sect{outcome}) acquire the true state if the set of entity instances compatible with the \glyph{entity} state, or actualisation of interaction is non-empty.
+An \glyph{entity} (\sect{entity}) represents a set of individual instances of some kind (molecules, agents etc). The difference from \SBGNPDLone \glyph{entity pool node} is that \glyph{entity} instances are independent, while \glyph{entity pool node} form one inseparable object acting as a whole. A set of \glyph{state variables} (\sect{stateVariable}) and their \glyph{values} (\sect{variableValue}) describe a part of the \glyph{entity} instances state space. The \glyph{entity}, or interaction \glyph{outcome} (\sect{outcome}) acquire the true state if the set of entity instances compatible with the \glyph{entity} state, or actualisation of interaction is non-empty.
\subsection{Statements}
@@ -110,6 +111,8 @@
\label{fig:nesting-existence}
\end{figure}
+Outcome of an interaction that involves contained entities is defined along the same line as in \sect{outcome}: the outcome represents set of all possible instances of topmost containing entity has domains represented by contained entity involved in interaction.
+
\subsection{(In)Validation of ER maps}
Based on the definitions above, it should be possible to use the toolkit of formal logic to analyse \ERs{}. In particular, one can envision to build truth tables describing the consequences of the existences of the various entities. Those tables should point to inconsistencies leading to contradictory predicates.
Modified: EntityRelationship/trunk/sources/working.tex
===================================================================
--- EntityRelationship/trunk/sources/working.tex 2015-04-22 12:33:50 UTC (rev 910)
+++ EntityRelationship/trunk/sources/working.tex 2015-04-22 12:38:45 UTC (rev 911)
@@ -1,3 +1,4 @@
+% !TEX root = ../sbgn_ER-level1.tex
\chapter{Issues postponed to future levels}\label{sec:postponed}
\section{Generics and instances}\label{sec:instances}
@@ -2,6 +3,21 @@
-In \SBGNERLone, an entity is represented only once. One cannot explicitely represent different instances of the ``same'' entity. Several instances can be infered from relationships acting in \glyph{trans}. However, one cannot generally express the fact that several relationships involving the same entity actually involve the same, or different, instances of this entity. This problem is tied to the problem of generics. Indeed, if one discriminate between classes of instances, how can one represent, in the same map, the generic entity?
+In \SBGNERLone, an entity is represented only once. One cannot explicitly represent different instances of the ``same'' entity. Several instances can be inferred from relationships acting in \glyph{trans}. However, one cannot generally express the fact that several relationships involving the same entity actually involve the same, or different, instances of this entity. This problem is tied to the problem of generics. Indeed, if one discriminate between classes of instances, how can one represent, in the same map, the generic entity?
-\section{Synchronous events}\label{sec:syncEvents}
-In \SBGNERLone, each influence arc started from its own outcome and so asynchronous . There is a need to represent that two events happened simultaneously or caused by one outcome, for example to represent chemical reaction we need to show that destruction of substrates and creation of products happened simultaneously.
\ No newline at end of file
+\section{Groups}\label{sec:groups}
+
+The \SBGNERLone needs a mechanism to "tag" an SBGN glyph as belonging to one or several groups. Those groups would correspond for instance to "pathways" or "metabolic network", glyphs associated with a disease or biological function. A group does not affect the syntax of the map, but is merely a multi-glyph annotation.
+
+Groups would be a way for instance to organise nodes together in a certain subpart of the plan, or highligtht them in some way. Software would have to conserve groups, and it could thus be a way to lightly constrain the layout, without going all the way to specify position and size of the nodes. A group would not be "linked" to any node using edges, but would "contain" EPN/PN in PD, EN in ER, AN in AF (i.e. in PD and AF, a group could span several compartment). Groups could be named and could be annotated with "floating" annotations, similarly to the default compartment.
+
+\section{Submap}\label{sec:submap}
+
+The \SBGNPDLone has a \glyph{Submap} as placeholder for another process and is used when one wishes to hide the detail of this process from the Process Description map, but make it available to the reader as a separate related map. The similar concept could be implemented in \SBGNERLone.
+
+\section{Spatial organisation}\label{sec:spacial}
+
+Introduction of \glyph{Nested entities} makes representation of domains possible. The additional feature required by some users is to be able to show relation between domains. For example, promoter, coding region and terminator would be domains of the plasmid entity and it would be important to show that promoter is located before coding region.
+
+%\section{Synchronous events}\label{sec:syncEvents}
+
+%In \SBGNERLone, each influence arc started from its own outcome and so asynchronous . There is a need to represent that two events happened simultaneously or caused by one outcome, for example to represent chemical reaction we need to show that destruction of substrates and creation of products happened simultaneously.
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ca...@us...> - 2015-04-22 12:33:53
|
Revision: 910
http://sourceforge.net/p/sbgn/code/910
Author: cannin
Date: 2015-04-22 12:33:50 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Edited the Appendix A of ER spec
Modified Paths:
--------------
EntityRelationship/trunk/sources/examples.tex
EntityRelationship/trunk/sources/usermanual.tex
Modified: EntityRelationship/trunk/sources/examples.tex
===================================================================
--- EntityRelationship/trunk/sources/examples.tex 2015-04-22 08:57:03 UTC (rev 909)
+++ EntityRelationship/trunk/sources/examples.tex 2015-04-22 12:33:50 UTC (rev 910)
@@ -1,11 +1,11 @@
\chapter{Complete examples of \SBGNERLone maps}
-The following maps present complete examples of SBGN \ERs representing biological processes. They by no mean exhaust the possibilities of \SBGNERLone.\\
+The following are complete examples of SBGN \ERs maps.\\
\input{sources/usermanual.tex}
-\section{More realistic examples}
-\fig{PCR} presents the different relations between the four entities involved in a Polymerase Chain Reaction (PCR). This examplifies the use of the \glyph{entity}, the logical operator \glyph{or}, the \glyph{state variable} ``existence'', the \glyph{unit of information}, as well as the relationships \glyph{interaction}, \glyph{assignment}, \glyph{necessary stimulation} and \glyph{absolute inhibition}.
+\section{Additional examples}
+\fig{PCR} presents the different relations between the four entities involved in a Polymerase Chain Reaction (PCR). This example shows the usage of the \glyph{entity}, the logical operator \glyph{or}, the \glyph{state variable} ``existence'', the \glyph{unit of information}, as well as the relationships \glyph{interaction}, \glyph{assignment}, \glyph{necessary stimulation} and \glyph{absolute inhibition}.
\begin{figure}[htb]
\begin{center}
@@ -14,7 +14,7 @@
\end{center}
\end{figure}
-\fig{CaMKII} depicts the effect of a depolarisation (dV) on the intracellular calcium, that binds to calmodulin, that itself binds to the calcium/calmoduline kinase II (CaMKII). The binding of calmodulin inhibits the folding of CaMKII monomer on itself, thus relieving the inhibition on the kinase activity. The phosphorylation of the glutamate receptors finally leads to the Long Term Potentiation (LTP) of the synapses. In addition, the map shows the effect of trans-phosphorylation on threonine 286, that makes the enzyme constitutively active, and on threonine 306, that renders the kinase insensitive to calmodulin, as well as the dimerisation of the kinase.
+\fig{CaMKII} depicts the effect of depolarisation (dV) on the intracellular calcium, that binds to calmodulin, that itself binds to the calcium/calmoduline kinase II (CaMKII). In this diagram, the binding of calmodulin inhibits the folding of CaMKII monomer on itself, thus relieving the inhibition on the kinase activity. The phosphorylation of the glutamate receptors finally leads to the Long Term Potentiation (LTP) of the synapses. In addition, the map shows the effect of trans-phosphorylation on threonine 286, that makes the enzyme constitutively active, and on threonine 306, that renders the kinase insensitive to calmodulin, as well as the dimerisation of the kinase.
\begin{figure}[H]
\centering
Modified: EntityRelationship/trunk/sources/usermanual.tex
===================================================================
--- EntityRelationship/trunk/sources/usermanual.tex 2015-04-22 08:57:03 UTC (rev 909)
+++ EntityRelationship/trunk/sources/usermanual.tex 2015-04-22 12:33:50 UTC (rev 910)
@@ -1,27 +1,27 @@
\section{Activation of RTK}
-The \SBGNERLone language is designed with so called ``open world assumption'' in mind. This means that all entities, state variables and interactions assumed to be independent, unless explicitly specified with influence arc. That approach helps to avoid combinatorial explosion and makes drawing of the diagram much easier compared to \SBGNPDLone, but it makes reading and analysis of the diagram more difficult and laborious.
+The \SBGNERLone language is designed under the ``open world'' assumption. Under this assumption, all entities, state variables and interactions are assumed to be independent, unless explicitly specified with influence arc. This approach helps to avoid a combinatorial explosion of the states represented in the map and makes drawing diagrams much easier compared to \SBGNPDLone, but it makes reading and analysis of the diagram more difficult.
To illustrate creation and analysis of \SBGNERLone diagram we will create the diagram of receptor tyrosine kinase (RTK) activation pathway in a step by step manner. Wikipedia (\url{https://en.wikipedia.org/wiki/Receptor_tyrosine_kinase}) describes the process of RTK activation as follows:
\begin{quote}
``When a growth factor binds to the extracellular domain of an RTK, its dimerization is triggered with other adjacent RTKs. Dimerization leads to a rapid activation of the protein's cytoplasmic kinase domains, the first substrate for these domains being the receptor itself. The activated receptor as a result then becomes autophosphorylated on multiple specific intracellular tyrosine residues.''
\end{quote}
-Drawing \SBGNERLone the diagram is simple, we will follow the textual description of the pathway and add required elements. Let's start with identification of key players of the pathway. In a text we can figure out that two main entities are ``RTK'' and ``growth factor''. We will draw them as ``receptor'' and ``ligand'' entities (\sect{entity}) respectively. We could also notice that RTK has two domains: the ``extracellular domain'' (``receptor'') and the ``kinase domain'', they will also be shown in \fig{rtk-entities}. The pathway description also mentions ``multiple specific intracellular tyrosine residues'', so we've added two state variables (\sect{stateVariable}) ``Y1'' and ``Y2''' to the receptor entity to be able to show events related to modification of tyrosine residues.
+Drawing \SBGNERLone diagrams is simple, we will follow the textual description of the pathway and add required elements. Let's start with identification of key players of the pathway. From the text, we can determine that the two main entities are ``RTK'' and ``growth factor''. We will draw them as ``receptor'' and ``ligand'' entities (\sect{entity}), respectively. We also notice that RTK has two domains: the ``extracellular domain'' (``receptor'') and the ``kinase domain'', they will also be shown in \fig{rtk-entities}. The pathway description also mentions ``multiple specific intracellular tyrosine residues'', so we have added two state variables (\sect{stateVariable}) ``Y1'' and ``Y2''' to the receptor entity to be able to show events related to modification of the tyrosine residues.
\begin{figure}[H]
\centering
\vspace*{-0.75em}
\includegraphics[scale=0.75]{examples/rtk-entities.png}
- \caption{Receptor tyrosine kinase activation: entities definition.}
+ \caption{Receptor tyrosine kinase activation: definition of entities.}
\label{fig:rtk-entities}
\end{figure}
-By creation of entities we have populated our system with instances of two kinds: a ``receptor'' and a ``ligand''. We show also the internal structure of a receptor by depicting its two domains as nested entities (\sect{domain}). Receptor and its ``kinase'' domain carry out the ``state variable'' (\sect{stateVariable}) to define the basis of the entity state space.
+Through this entity creation process, we have populated our system with instances of two kinds: a ``receptor'' and a ``ligand''. We also show the internal structure of the receptor by depicting its two domains as nested entities (\sect{domain}). The receptor and its ``kinase'' domain have ``state variables'' (\sect{stateVariable}) that define the basis for the entity state space.
-The next step is to describe the part of entities state space we are going to be interested in. Two assignment arcs (\sect{assignment}) pointing to the ``Y1'' and ``Y2'' receptor state variables on figure \fig{rtk-states} demonstrate that we are going to analyse phosphorylation of tyrosine residues. We need also to take into account that according to the description ``Dimerization leads to a rapid activation of the protein's cytoplasmic kinase domains'', that means that the ``active'' state variable of ``kinase'' domain could become ``true'' after some perturbations in the system. So we've added an appropriate variable value (\sect{variableValue}) node and an assignment arc.
+We will now describe the entity state space for each entity that we are interested in. The two assignment arcs (\sect{assignment}) pointing to the ``Y1'' and ``Y2'' receptor state variables on \fig{rtk-states} demonstrate that we are going to analyse phosphorylation of tyrosine residues. From the statement: ``Dimerization leads to a rapid activation of the protein's cytoplasmic kinase domains'', we need to take into account that the ``active'' state variable of ``kinase'' domain could become ``true'' after some perturbations in the system. Therefore, we have added an appropriate variable value (\sect{variableValue}) node and an assignment arc.
-\SBGNERLone is a so called ``open world'' language, which means that as diagram developers we are not obliged to describe the whole system, we can leave unknown parts unaddressed and focus on the most important parts of the system. That's why we included only ``P'' state value for those residues. To describe the whole system we ought include ``unphosphorylate'' or some other ``default'' value as well (see \sect{assignment} to check how to do it properly), but in our case it is not important so we'll use ``open world'' assumption and omit it. \SBGNERLone assumes that all interactions are internally reversible, so even if we describe only the switch from default to phosphorylated state explicitly, that description implies that there is a mechanism to put ``Y1'' and ``Y2'' variables back to their default state. For the same reason we haven't added ``false'' value to the ``active'' state of the kinase domain.
+Given that the \SBGNERLone follows the ``open world'' assumption, diagram authors are not obliged to describe the entire system, and we can focus on the most important parts of the system. For this reason, we include only the ``P'' state value for the residues. For a more accurate description of the system, we need to include a default value, such as the ``unphosphorylated'' state (see \sect{assignment} to check how to do it properly), but in our case it is not important so we will rely on the ``open world'' assumption and omit this detail. \SBGNERLone assumes that all interactions are internally reversible, so if we only describe the switch from default to phosphorylated state explicitly, that description implies that there is a mechanism to put ``Y1'' and ``Y2'' variables back to their default state. For the same reason, we have not added ``false'' value to the ``active'' state of the kinase domain.
\begin{figure}[H]
\centering
@@ -31,7 +31,7 @@
\label{fig:rtk-states}
\end{figure}
-By now we have prepared all elements that are taking part in the process description, and we are ready to draw the pathway itself. The first sentence of the pathway description starts with ``When a growth factor \textbf{binds} to the extracellular domain of an RTK'', so the first event we are going to draw is a receptor ligand binding (\fig{rtk-binding}). We will use an interaction arc (\sect{interaction}) to show that the ligand can bind the receptor.
+We have now prepared all elements that are taking part in the process, and we are ready to draw the pathway itself. The first sentence of the pathway description states ``When a growth factor \textbf{binds} to the extracellular domain of an RTK'', so the first event we are going to draw is a receptor ligand binding (\fig{rtk-binding}). We will use an interaction arc (\sect{interaction}) to show that the ligand can bind the receptor.
\begin{figure}[H]
\centering
@@ -41,9 +41,9 @@
\label{fig:rtk-binding}
\end{figure}
-The binding happens between the ligand entity and the receptor domain of the receptor entity. The interaction event is reversible in a same way as assignment. That means that even if two instances of ligand and receptor are bound at some time that bond will not last forever, it will dissociate with some probability.
+The binding happens between the ligand entity and the receptor domain of the RTK entity. The interaction event is reversible in a same way as assignment. That means that even if two instances of ligand and receptor are bound at some time that bond will not last forever, it will dissociate with some probability.
-Next step in the pathway is ``When a growth factor binds to the extracellular domain of an RTK, its \textbf{dimerization} is triggered with other adjacent RTKs''. The dimerisation event is added in \fig{rtk-dimerisation}. The interaction arc in that figure connects the entity with itself, so we need to distinguish two possibilities: receptor molecule binds another molecule of the same kind (what we need according to the pathway description) or it undergoes some intramolecular interaction. In the former case we add \glyph{unit of information} ``trans'' to the arc to emphasise that the interaction is intermolecular, the latter case would require \glyph{unit of information} ``cis'' (see \sect{unitInformation}, \sect{miscellaneous-cv} and \sect{cis-trans-semantics}). Definition of ``cis'' or ``trans'' interaction is meaningful only for events involving instances of the same entity, directly or via chain of events. If you do not specify cis/trans type of interaction it will be undefined, because of the ``open world'' nature of \SBGNERLone, which is absolutely legitimate and sometimes unavoidable choice, but the diagram is much more understandable if an \glyph{unit of information} of appropriate type is added to the interaction arc according to biological knowledge.
+The next statement in the description is ``When a growth factor binds to the extracellular domain of an RTK, its \textbf{dimerisation} is triggered with other adjacent RTKs''. The dimerisation event is added in \fig{rtk-dimerisation}. The interaction arc connects the entity with itself, so we need to distinguish two possibilities: 1) the receptor molecule binds another molecule of the same kind (what we need according to the pathway description) or 2) that RTK undergoes an intramolecular interaction. In the first case, we add a \glyph{unit of information} ``trans'' to the arc to emphasise that the interaction is intermolecular. The second case would require \glyph{unit of information} ``cis'' (see \sect{unitInformation}, \sect{miscellaneous-cv} and \sect{cis-trans-semantics}). Definition of ``cis'' or ``trans'' interaction is meaningful only for events involving instances of the same entity occurring directly or via chain of events. If you do not specify cis/trans type of interaction, this information will be undefined, because of the ``open world'' nature of \SBGNERLone. This is correct and sometimes unavoidable, but the diagram is more understandable when the appropriate \glyph{unit of information} is added to the interaction arc in accordance with biological knowledge.
\begin{figure}[H]
\centering
@@ -53,7 +53,7 @@
\label{fig:rtk-dimerisation}
\end{figure}
-Now we have to emphasise that the dimerisation depends upon the ligand-receptor binding. There are two key elements of \SBGNERLone we are going to use in this step (see \fig{rtk-dimer-control}): outcome (\sect{outcome}) and influence arc (\sect{influences}). This is the first time we came across the need to use a result of interaction. In our case the result of interaction is a complex containing instances of receptor and ligand, but not limited to the binary complex, as we will see soon. To show the result of an interaction on the diagram the black dot is drawn on the interaction arc and this dot is the origin of our influence arc (\sect{influences}). Influence arcs are designed to depict the way one part of the system controls the behaviour of the other. The word ``triggered'' in a pathway description means that the interaction between receptor and ligand is necessary for the dimerisation process, so we've used necessary stimulation (\sect{necessaryStimulation}), which assumes that without the stimulator entity the target interaction would not take place. And we have placed ``cis'' \glyph{unit of information} on the influence arc to emphasise that the control happens within the same molecular complex. That means that the receptor-ligand complex is not the catalyst that forms a dimer from some other instances of receptor entity, instead the complex is always involves instance of a receptor that bound the ligand.
+Now, we have to emphasise that the dimerisation depends upon the ligand-receptor binding. There are two key elements of \SBGNERLone we will use in this step (see \fig{rtk-dimer-control}): outcome (\sect{outcome}) and influence arc (\sect{influences}). In our case the result of interaction is a complex containing instances of receptor and ligand, but this is not limited to the binary complex, as we will see soon. To show the results of an interaction on the diagram an outcome node is placed on the on the interaction arc, as a black dot. This outcome dot is the origin of our influence arc (\sect{influences}). Influence arcs are designed to depict the way one part of the system controls the behaviour of the other. The word ``triggered'' in a pathway description implies that the interaction between receptor and ligand is necessary for the dimerisation process, so we have used necessary stimulation (\sect{necessaryStimulation}), which indicates that without the stimulator entity the target interaction cannot take place. Furthermore, we have placed ``cis'' \glyph{unit of information} on the influence arc to emphasise that the control happens within the same molecular complex. That means that the receptor-ligand complex is a member of the formed dimer.
\begin{figure}[H]
\centering
@@ -63,7 +63,7 @@
\label{fig:rtk-dimer-control}
\end{figure}
-Following the next sentence in the pathway description, which says ``Dimerization leads to a rapid activation of the protein's cytoplasmic kinase domains,'' we are going to add another influence arc (see \fig{rtk-kinase-activation}), but this time the arc is a stimulation (\sect{stimulation}), which means that the kinase domain may be active to some extent even in monomeric form of a receptor. Again we have the outcome dot to represent the dimer, but in this case the outcome represents any kind of complex where two receptor molecules bound together.
+The next sentence in the description states: ``Dimerization leads to a rapid activation of the protein's cytoplasmic kinase domains,''. In \fig{rtk-kinase-activation}, we will add another influence arc, stimulation (\sect{stimulation}) that means the kinase domain may be active to some extent even in monomeric form of a receptor. On the dimerisation interaction, we again have an outcome dot to represent the dimer, as the source of the influence arc, but in this case the outcome represents any kind of complex where two receptor molecules bound together.
\begin{figure}[H]
\centering
@@ -73,7 +73,7 @@
\label{fig:rtk-kinase-activation}
\end{figure}
-The last and most important part of our pathway is the ``autophosphorylation of multiple specific intracellular tyrosine residues'' by activated kinase domain. The complete pathway is shown in \fig{rtk-full}. All interactions and influences in \SBGNERLone are independent, so for each stimulation arc representing autophosphorylation of the tyrosine residue we created their own outcome. Those outcomes represent independent sets of instances where kinase is active.
+The last part of our pathway is the ``autophosphorylation of multiple specific intracellular tyrosine residues'' by activated kinase domain. The complete pathway is shown in \fig{rtk-full}. All interactions and influences in \SBGNERLone are independent, so each stimulation arc representing autophosphorylation of the tyrosine residue has its own outcome, and these outcomes represent independent sets of instances where kinase is active.
\begin{figure}[H]
\centering
@@ -83,7 +83,7 @@
\label{fig:rtk-full}
\end{figure}
-Now, when our diagram is ready let's analyse it to get a better understanding of rules of the language and meaning of the diagram elements. The diagram consists of two types of entities, three types of outcomes, two interaction arcs, three assignment arcs, and four influence arcs. If we take into account independence and reversibility of all interactions we can count the total number of complexes that could be created in the system. It will be 153 complex types in total: 8 monomeric receptors, 8 monomeric receptor-ligand complexes, 36 receptor dimers, 64 receptor dimers with one ligand, 36 receptor dimers with two ligands and free ligand. Those numbers come from simple combinatorics, taking into account the number of state variables and assuming that each of them can have two values: ``undefined'' and specified by assignment arc. \fig{rtk-complexes} shows three of the 144 complexes compatible with the definition of outcome on the active kinase state assignment.
+Now that our diagram is ready let's analyse it to get a better understanding of rules of the language and meaning of the diagram elements. The diagram consists of two types of entities, three types of outcomes, two interaction arcs, three assignment arcs, and four influence arcs. If we take into account independence and reversibility of all interactions we can count the total number of complexes that could be created in the system. It will be 153 complex types in total: 8 monomeric receptors, 8 monomeric receptor-ligand complexes, 36 receptor dimers, 64 receptor dimers with one ligand, 36 receptor dimers with two ligands and free ligand. Those numbers come from simple combinatorics, taking into account the number of state variables and assuming that each of them can have two values: ``undefined'' or specified by assignment arc. \fig{rtk-complexes} shows three of the 144 complexes compatible with the defined outcome.
\begin{figure}[H]
\centering
@@ -93,4 +93,4 @@
\label{fig:rtk-complexes}
\end{figure}
-That big number of possible complexes should not be scared of, because influence arcs in our model control the set of reachable states quite firmly. For example, blocking any phosphorylation sites reduces the number of reachable complexes to 45, and blocking kinase activation reduces the total set of possible complexes types to just 6. It could be easily seen from the diagram: in the former case we switch off one receptor state variable, in the later we effectively block all three: blocking activation assignment we render all its outcomes to false state. That means that activation will never happen and so tyrosine residues will never be phosporylated. Our diagram is quite simple, it does not contain any complex feed-backs, so results of analysis are rather trivial. The next sections show more complex and meaningful diagrams.
+The large number possible complexes is defined by the influence arcs, which dictate the number of available states. For example, blocking any single phosphorylation site reduces the number of reachable complexes to 45, and blocking the kinase activation reduces the total set of possible complexes types to just 6. This can easily be seen from the diagram. In the first case, we switch off one receptor state variable, and in the second case, we effectively block all three; blocking activation assignment we render all its outcomes to false state. This means that activation will never happen and that the tyrosine residues will never be phosporylated. In the next section, we will present more complex examples.
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