GPML Plugin for Cytoscape Thomas Kelder Maastricht University

Overview Introduction – GPML, PathVisio, WikiPathways Implementation Use case examples Summary

Introduction GPML - GenMAPP Pathway Markup Language Biological pathways – Textbooks, articles, presentations – Understanding biology – Communicating biological knowledge – Data analysis

Networks and Pathways

GPML GenMAPP format – Shapes, labels, colors – Annotated gene products GPML – 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 Use Improve GPML PathVisioWikiPathwaysGenMAPP MAPPFinder PathVisio 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

Data analysis Omics data Functional annotation Literature search Protein interaction data Usage example

Extend network

Extract relevant subnetwork – Network analysis – Clustering – Merge networks – Combine different data sources Protein interaction databases Your own data Literature GO annotations

Layout and curate

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! Summary

GenMAPP Alexander Pico Kristina Hanspers Bruce Conklin Martijn van Iersel Chris Evelo Allan Kuchinsky Thanks!

Check out the GPML plugin at: – GPML tools: – WikiPathways – PathVisio