UniProt Protein Protein Network

Created: 2015-12-04 12:05:21

This workflow uses the Europe PMC Web Services searchPublications and getDatabaseLinks to reconstruct a protein-protein network based on co-occurence in the scientific literature, arbitrary filtered by a PubMed query, e.g. the word "complex" appearing in the title or abstract. The workflow also looks up the second degree connections, i.e. proteins co-occuring with proteins co-occuring with the protein given as input, but not with this protein itself. The output is a (1) Pajek graph file, a GML graph file, and a visualization of the network by the igraph package, captured by Taverna as a PNG and also saved as vector graphics in PDF. The Pajek or GML files may be further analyzed in software such as Cytoscape (GML only), Pajek or VOSviewer.

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