1. GPML Plugin for Cytoscape Thomas Kelder Maastricht University thomas.kelder@bigcat.unimaas.nl

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

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

4. Networks and Pathways

5. 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

6. Improving and using pathways Tools that work with GPML: Improving pathway content – PathVisio – WikiPathways Using pathways for data analysis – PathVisio – GenMAPP/MAPPFinder

7. Goals Build a framework of tools around GPML Include Cytoscape in this framework Use Improve GPML PathVisioWikiPathwaysGenMAPP MAPPFinder PathVisio Cytoscape

8. GPML plugin Import/export GPML files Copy/paste between WikiPathways, PathVisio and Cytoscape

9. How does it work? Network elements (nodes, edges) – Structured – Dynamic Annotations – Not part of the network – Help ‘reading’ the pathway manually – No computational use

10. 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

12. Converted pathway

13. Network only

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

15. Extend network

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

17. Layout and curate

19. 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

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

21. Check out the GPML plugin at: – http://www.pathvisio.org/Cytoscape_plugin GPML tools: – WikiPathways http://wikipathways.org – PathVisio http://pathvisio.org