PathVisio 3 has been refactored using the OSGi framework, allowing it to be more modular and extensible through plugins. The new plugin system includes a plugin repository and manager that allows users to easily install plugins to add additional functionality. PathVisio's core functionality includes creating and editing pathways, visualizing experimental data on pathways, performing pathway analysis, and exporting results. It is open source and compatible with databases like Wikipathways, making it a flexible tool for pathway analysis.

1. PathVisio 3 NBIC Conference 2013 1

2. PathVisio www.pathvisio.org
PathVisio 3 NBIC Conference 2013 2

3. New Structure
Refactored using the OSGi framework for a better, modular
system that can be easily extended with plugins.
Plugins
• Extensions of the core application that provide features
relevant for a specific task.
• This allows users to build an application with all the
necessary modules relevant for their work.
• Plugins are available through the new plugin repository
and they can be installed through the plugin manager
from within the application.
PathVisio 3 NBIC Conference 2013 3

4. Plugin repository & manager
The new plugin manager displays available plugins in the
repository to the users and provides easy and fast installation.
PathVisio 3 NBIC Conference 2013 4

5. Core Software + Plugins
PATHVISIO WORKFLOW
PathVisio 3 NBIC Conference 2013 5

6. • Create Pathways / Get Pathways
• Visualize Data
• Perform pathway analysis
• Export Results
PathVisio 3 NBIC Conference 2013 6

7. But unlike any other drawing program, usingas you would in any other
In PathVisio you can draw pathways, PathVisio you can annotate
your genes, proteins, program, like PowerPoint orusing database identifiers.
drawing metabolites and interactions Photoshop.
PathVisio 3 NBIC Conference 2013 7

8. Drawing with standards
SBGN Plugin
MIM Plugin
http://www.sbgn.org/
http://discover.nci.nih.gov/mim/
Luna A.et al, PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs),
Bioinformatics Applications Note, doi:10.1093/bioinformatics/btr336
PathVisio 3 NBIC Conference 2013 8

9. Pathway Validator
This plugin ensures the correct usage of the MIM notation in pathway diagrams.
Chandan K. et al, PathVisio-Validator: a rule-based validation plugin for graphical
pathway notations, Bioinformatics Applications Note, doi:10.1093/bioinformatics/btr694
PathVisio 3 NBIC Conference 2013 9

10. www.wikipathways.org
Wikipathways
Share, curate & discuss!
• Wiki for biological pathways
• Free and open source resource
• Reactome pathways also available
• Fully compatible with PathVisio
PathVisio 3 NBIC Conference 2013 10

11. Download pathways
PathVisio 3 NBIC Conference 2013 11

12. Standard Workflow using PathVisio
• Create Pathways / Get Pathways
• Visualize Data
• Perform pathway analysis
• Export Results
PathVisio 3 NBIC Conference 2013 12

13. Data Import http://www.pathvisio.org/wiki/DatabasesMapps
Data : quantitative information about the different elements of
The system code is used to identify which
a pathway, obtained experimentally or by modeling
database a particular identifier belongs to.
PathVisio accepts delimited text files
PathVisio 3 NBIC Conference 2013 13

14. Database identifier mapping
BridgeDB
HMDB HMDB00122
HMDB00122
Kegg
HMDB01401 Compound
C00092
HMDB00124
??
PubChem 69507
Data annotated
with HMDB IDs Pathway metabolites
annotated with
different IDs
PathVisio 3 NBIC Conference 2013 14

15. BridgeDb www.bridgedb.org
• Id mapping framework for bioinformatics
applications
• Translates identifiers from one system to
another
• Links out to online information for an identifier
Create your own BridgeDb derby database!
http://www.bridgedb.org/wiki/BridgeDbCreator
PathVisio 3 NBIC Conference 2013 15

16. Gene Database
http://www.pathvisio.org/downloads/download-bridgedbs/
• 32 species supported
• Annotation database
for metabolites
• Annotation database
for interactions
(in development)
PathVisio 3 NBIC Conference 2013 16

17. Data mapped
PathVisio 3 NBIC Conference 2013 17

18. PathVisio core application includes the visualization plugin to
visualize data on datanodes(genes, proteins, metabolites).
The EdgeVisualization plugin in PathVisio enables visualizing
data on the reactions and interactions of the pathways.
PathVisio 3 NBIC Conference 2013 18

19. Data Visualized
Legend:
Metabolites visualized
0 5
with a color gradient
Positive fluxes
Negative fluxes
Thickness of the arrows
correspond to the amount of
flux
Example case :Flux & metabolite data visualized together
This gives a global view of flux distribution over
the entire biological pathway
PathVisio 3 NBIC Conference 2013 19

20. Standard Workflow using PathVisio
• Create Pathways / Get Pathways
• Visualize Data
• Perform pathway analysis
• Export Results
PathVisio 3 NBIC Conference 2013 20

21. Over Representation Analysis
The Z-score can be used as a measure for how
much a subset of genes is different from the rest
R
(rn )
zscore
= N
R R n1
n(1 )(
1 )
N N N1
• r = changed genes in Pathway
• n = total genes in Pathway
• R = changed genes
• N = total genes Other enrichment calculation methods
Ackermann M et al., A general modular framework for gene
set enrichment analysis, BMC bioinformatics, 2009
PathVisio 3 NBIC Conference 2013 21

22. Z-score Calculation
PathVisio 3 NBIC Conference 2013 22

23. Gene Ontology Plugin
Create Gene Ontology (GO) pathways in PathVisio
1. Browse GO Tree
2. Create GO pathway
PathVisio 3 NBIC Conference 2013 23

24. Gene Set Enrichment Analysis plugin
PathVisio 3 NBIC Conference 2013 24

25. Plugin for categorizing pathways based on GO terms
(in development)
Notch signalling pathway
http://wikipathways.org/index.php/Pathway:WP268
PathVisio 3 NBIC Conference 2013 25

26. Standard Workflow using PathVisio
• Create Pathways / Get Pathways
• Visualize Data
• Perform pathway analysis
• Export Results
PathVisio 3 NBIC Conference 2013 26

27. Export pathway images and analysis
results
• Export to image formats
• Png
PNG
• Svg
• Tiff
• Export as pdf
• Html Export Plugin : export pathway images, statistics results
and backpages as html pages
• Biopax3GPML : import biopax (.owl) files as GPML for use in
PathVisio and export Wikipathways pathways as .owl files
• GPML plugin : Cytoscape plugin which allows a pathway to be
opened as a cytoscape network
PathVisio 3 NBIC Conference 2013 27

28. Incorporation into workflows
PathVisioRPC
PathVisio 3 NBIC Conference 2013 28

29. Summary
• Completely free and open source
• Fully compatible with Wikipathways
• Modular architecture, easily extendable
• Easy incorporation into pipelines
• Very active mailing list
PathVisio 3 NBIC Conference 2013 29

30. PathVisio 3 NBIC Conference 2013 30

31. Acknowledgements
Max Planck Instt.,
TNO, Zeist, NL
Gladstone Institutes, SF, USA Berlin,Germany
Funding
General Bioinformatics,
Reading,UK
Maastricht University, NL
and many contributors around the
PathVisio 3 NBIC Conference 2013 31

32. Thank you for your time and attention!
wikipathways-discuss@googlegroups.com
anwesha.dutta@maastrichtuniversity.nl
PathVisio 3 NBIC Conference 2013 32