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CyEVEX: Literature-Scale Network Integration and Visualization Through Cytoscape

Kai Hakala, Sofie van Landeghem, Suwisa Kaewphan, Tapio Salakoski, Yves van de Peer, Filip Ginter, CyEVEX: Literature-Scale Network Integration and Visualization Through Cytoscape. In: Sophia Ananiadou, Sampo Pyysalo, Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Tapio Salakoski (Eds.), Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine, 91–96, ACM Press, 2012.

Abstract:

EVEX is a literature-scale event extraction resource, publicly available via a web application and as a relational database. In this paper we present CyEVEX, a plug-in which integrates EVEX with the widely used Cytoscape network analysis platform, making the text mining data readily available for integration with experimental data sources and subsequent biological analysis. CyEVEX can populate existing networks with edges corresponding to EVEX events, as well as add new nodes to the network, revealing novel interesting genes and proteins and their relationships within the existing network.

BibTeX entry:

@INPROCEEDINGS{inpHaVaKaSaVaGi12a,
  title = {CyEVEX: Literature-Scale Network Integration and Visualization Through Cytoscape},
  booktitle = {Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine},
  author = {Hakala, Kai and Landeghem, Sofie van and Kaewphan, Suwisa and Salakoski, Tapio and Peer, Yves van de and Ginter, Filip},
  editor = {Ananiadou, Sophia and Pyysalo, Sampo and Rebholz-Schuhmann, Dietrich and Rinaldi, Fabio and Salakoski, Tapio},
  publisher = { ACM Press},
  pages = {91–96},
  year = {2012},
}

Belongs to TUCS Research Unit(s): Turku BioNLP Group

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