OmnipathR: one package to access more than 100 signaling databases
Denes Turei,Alberto Valdeolivas,Attila Gabor,Julio Saez-Rodriguez Institute for Computational Biomedicine, Heidelberg University; European Molecular Biology Laboratory
OmniPath is a database of molecular signaling knowledge, combining data from more than 100 resources. It contains protein-protein and gene regulatory interactions, enzyme-PTM relationships, protein complexes, annotations about protein function, structure, localization and intercellular communication. OmniPath focuses on networks with directed interactions and effect signs (activation or inhibition) which are suitable inputs for many modeling techniques. OmniPath also features a large collection of proteins’ intercellular communication roles and interactions. OmniPath is distributed by a web service at https://omnipathdb.org/. The Bioconductor package OmnipathR is an R client with full support for all features of the OmniPath web server. Apart from OmniPath, it provides direct access to more than 15 further signaling databases (such as BioPlex, InBioMap, EVEX, Harmonizome, etc) and contains a number of convenience methods, such as igraph integration, and a close integration with the NicheNet pipeline for ligand activity prediction from transcriptomics data. In this demo we show the diverse data in OmniPath and the versatile and convenient ways to access this data by OmnipathR.
Keywords: signaling,network,database,protein-protein interaction,prior knowledge,post-translational modification,intercellular communication