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Download GPML Plugin for Cytoscape - BiGCaT - Data Server
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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 – – – – 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 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 • • • • 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
