SBGN-ED for Editing, Validating, and Translating of
SBGN Maps and Application Examples
Tobias Czauderna1, Falk Schreiber1,2
1
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Germany
2 Martin Luther University Halle-Wittenberg, Germany
COMBINE 2010
Edinburgh, UK, 06/10/2010
Outline
 SBGN-ED
 LibSBGN support
 Application examples
 RIMAS (Regulatory Interaction Maps of Arabidopsis Seed Development)
 MetaCrop (metabolic pathways in crop plants)
 The key steps in the development of diabetic retinopathy
 Layouting SBGN maps
SBGN-ED
 Editing, Validating and Translating of SBGN maps
 Add-on for VANTED
 Supports all three SBGN languages
 Syntactic and semantic validation
 Utilising information from pathway databases (MetaCrop and KEGG)
http://vanted.ipk-gatersleben.de
http:// vanted.ipk-gatersleben.de/addons/sbgn-ed/
Czauderna, T., Klukas, C., Schreiber, F.: Editing, Validating, and Translating of SBGN Maps. Bioinformatics, 26(18):2340-2341, 2010
Editing SBGN maps – Process Description
Validating SBGN maps
Translating from MetaCrop to SBGN
Translating from MetaCrop to SBGN
LibSBGN support in SBGN-ED
 Reference implementation of SBGN: diagram exchange format and library
handling import/export and validation (http://sourceforge.net/projects/libsbgn)
 SBGN-ED supports all features of Milestone 1 except:
 state variables in the form value@variable
 stoichiometry
 arcs with quadratic and cubic splines
 label positioning (especially for compartments)
 Features still to be implemented in SBGN-ML (planned for future Milestones):
 font style
 colour
 line style including arrow style
Examples – Glycolysis
original
SBGN-ML
Examples – Insulin-like Growth Factor (IGF) signaling
original
SBGN-ML
Examples – Neuronal / Muscle signalling
original
SBGN-ML
Examples – MetaCrop - Central Metabolism in Plants
T. Czauderna, E. Grafahrend-Belau, A. Junker, A. Hartmann, C. Klukas, F. Schreiber
Examples – MetaCrop - Central Metabolism in Plants
T. Czauderna, E. Grafahrend-Belau, A. Junker, A. Hartmann, C. Klukas, F. Schreiber
Examples – File size
GraphML
GML
SBGN-ML
Glycolysis
80 kB
43 kB
14 kB
Activated STAT1alpha
induction of the IRF1 gene
34 kB
17 kB
6 kB
Insulin-like Growth Factor
(IGF) signaling
73 kB
40 kB
13 kB
MAPK cascade
54 kB
29 kB
10 kB
Neuronal / Muscle
signalling
82 kB
45 kB
15 kB
MetaCrop - Central
Metabolism in Plants
3 MB
2.2 MB
450 kB
Examples – File load/save performance
GraphML
GML
SBGN-ML
load
MetaCrop - Central
Metabolism in Plants
~5 s
~4 s
~5 s
save
MetaCrop - Central
Metabolism in Plants
< 1s
< 1s
2-3 s
(Java Runtime 1.6.0_21, Windows 7 64 bit, Intel Core i7 2.67 GHz)
RIMAS - Regulatory Interaction Maps of Arabidopsis Seed Development
A. Junker, A. Hartmann, H. Bäumlein, F. Schreiber
http://rimas.ipk-gatersleben.de, A. Junker et. al. TIPS, 15(6):303-307, 2010
MetaCrop (metabolic pathways in crop plants)
MetaCrop - Central Metabolism in Plants
T. Czauderna, E. Grafahrend-Belau, A. Junker, A. Hartmann, C. Klukas, F. Schreiber
MetaCrop - Central Metabolism in Plants
T. Czauderna, E. Grafahrend-Belau, A. Junker, A. Hartmann, C. Klukas, F. Schreiber
The key steps in the development of diabetic retinopathy
B. de Bono (EBI Hinxton, UK), P. Grenon (EBI Hinxton, UK), T. Czauderna, F. Schreiber, M. Fenech (University of East Anglia,
Norfolk and Norwich University Hospital, UK), P. Luthert (University College London, UK), A. Foss (University of Nottingham, UK)
The key steps in the development of diabetic retinopathy
B. de Bono (EBI Hinxton, UK), P. Grenon (EBI Hinxton, UK), T. Czauderna, F. Schreiber, M. Fenech (University of East Anglia,
Norfolk and Norwich University Hospital, UK), P. Luthert (University College London, UK), A. Foss (University of Nottingham, UK)
The key steps in the development of diabetic retinopathy
B. de Bono (EBI Hinxton, UK), P. Grenon (EBI Hinxton, UK), T. Czauderna, F. Schreiber, M. Fenech (University of East Anglia,
Norfolk and Norwich University Hospital, UK), P. Luthert (University College London, UK), A. Foss (University of Nottingham, UK)
Layouting SBGN maps
Layouting SBGN maps
Layouting SBGN maps
Layouting SBGN maps
 Adaption of constraint based layout algorithms
 Development of sets of constraints
Thank you
Falk’s Group
 Eva Grafahrend-Belau
 Anja Hartmann
 Astrid Junker
 Matthias Klapperstück
 Hendrik Mehlhorn
 Hendrik Rohn
IPK Gatersleben
 Christian Klukas
 Helmut Bäumlein
Collaboration partners
 Kim Marriott, Michael Wybrow
(Monash University, Melbourne)
 Tim Dwyer (Microsoft)
 Bernard de Bono (EBI, Hinxton)
Examples – MAPK cascade
original
SBGN-ML
Examples – Activated STAT1alpha induction of the IRF1 gene
original
SBGN-ML