WikiPathways and Cytoscape: bridging the gap between interaction networks and graphically annotated pathways

Thomas Kelder, BiGCaT Bioinformatics, Maastricht University

Pathway diagrams can be used to provide a visually annotated, human interpretable and often simplified representation of a biological network. The GPML plugin for Cytoscape makes it possible to convert between GPML pathways and cytoscape networks. The GPML format stores the visual representation of a pathway, as well as information on the underlying model structure, such as node-edge relationships. It is therefore possible to view such a pathway as an interaction network. The community curated pathway resource WikiPathways [1] uses GPML as data format and provides a resource for curated pathway information. Combining pathways with large scale interaction networks may be used to improve analysis of experimental biological data. In this demo I will show how to load GPML pathways in Cytoscape. After this step, the pathway can be treated like any other network and analyzed using the various plugins available in Cytoscape. Additionally, I will show how to use GPML to visually annotate part of a network that can be useful for publishing as annotated image or directly on WikiPathways to present the results to the community. Finally, I will present a workflow for curating and extending pathways using Cytoscape, in combination with community curation using WikiPathways.

1. Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, et al. (2008) WikiPathways: Pathway Editing for the People. PLoS Biol 6(7):e184

Data keywords: community curation, pathway analysis, visual annotation

Cytoscape keywords: Network and Attribute I/O, Functional Enrichment