Transcript GPML Plugin for Cytoscape - BiGCaT - Data Server

GPML Plugin for Cytoscape
Thomas Kelder
Maastricht University
[email protected]
Overview
• Introduction
– GPML, PathVisio, WikiPathways
• Implementation
• Use case examples
• Summary
Introduction
• GPML - GenMAPP Pathway Markup Language
• Biological pathways
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Textbooks, articles, presentations
Understanding biology
Communicating biological knowledge
Data analysis
Networks and Pathways
GPML
• GenMAPP format
– Shapes, labels, colors
– Annotated gene products
• GPML
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XML schema definition
Link elements
Grouping
Refer to BioPAX elements
Bridge between visually oriented and
data oriented format
Improving and using pathways
Tools that work with GPML:
• Improving pathway content
– PathVisio
– WikiPathways
• Using pathways for data analysis
– PathVisio
– GenMAPP/MAPPFinder
Goals
• Build a framework of tools around GPML
• Include Cytoscape in this framework
GPML
Use
Improve
GenMAPP
MAPPFinder
PathVisio
Cytoscape
PathVisio
WikiPathways
Cytoscape
GPML plugin
• Import/export GPML files
• Copy/paste between WikiPathways, PathVisio
and Cytoscape
How does it work?
• Network elements (nodes, edges)
– Structured
– Dynamic
• Annotations
– Not part of the network
– Help ‘reading’ the pathway manually
– No computational use
How does it work?
• node for elements with clearly defined semantic meaning:
– DataNode
• annotation node for other elements
– Draws on foreground canvas
• edge for each line,
– If both endpoints connect to a node
Converted pathway
Network only
Usage example
Data analysis
•Omics data
•Functional annotation
•Literature search
•Protein interaction data
Extend network
Extract relevant subnetwork
– Network analysis
– Clustering
– Merge networks
– Combine different data sources
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Protein interaction databases
Your own data
Literature
GO annotations
Layout and curate
Summary
• PathVisio/WikiPathways for curated pathways
• Cytoscape as tool in workflow for improving these
pathways
Combine different tools and data sources to
improve your data analysis!
Thanks!
Allan Kuchinsky
GenMAPP
Alexander Pico
Kristina Hanspers
Bruce Conklin
Martijn van Iersel
Chris Evelo
• Check out the GPML plugin at:
– http://www.pathvisio.org/Cytoscape_plugin
• GPML tools:
– WikiPathways
• http://wikipathways.org
– PathVisio
• http://pathvisio.org