OmnipathR is an R package built to provide easy access to the data stored in the OmniPath webservice (Türei, Korcsmáros, and Saez-Rodriguez 2016):
The webservice implements a very simple REST style API. This package make requests by the HTTP protocol to retreive the data. Hence, fast Internet access is required for a proper use of OmnipathR.
OmnipathR can retrieve five different types of data:
Post-translational modifications (PTMs): It provides enzyme-substrate reactions in a very similar way to the aforementioned interactions. Some of the biological databases related to PTMs integrated in OmniPath are Phospho.ELM (Dinkel et al. 2010) and PhosphoSitePlus [Hornbeck et al. (2014)}.
Complexes: it provides access to a comprehensive database of more than 22000 protein complexes. This data comes from different resources such as: CORUM (Giurgiu et al. 2018) or Hu.map (Drew et al. 2017).
Annotations: it provides a large variety of data regarding different annotations about proteins and complexes. These data come from dozens of databases covering different topics such as: The Topology Data Bank of Transmembrane Proteins (TOPDB) (Dobson et al. 2014) or ExoCarta (Keerthikumar et al. 2016), a database collecting the proteins that were identified in exosomes in multiple organisms.
Intercell: it provides information on the roles in inter-cellular signaling. For instance. if a protein is a ligand, a receptor, an extracellular matrix (ECM) component, etc. The data does not come from original sources but combined from several databases by us. The source databases, such as CellPhoneDB (Vento-Tormo et al. 2018) or Receptome (Ben-Shlomo et al. 2003), are also referred for each reacord.
Figure 1 shows an overview of the resources featured in OmniPath. For more detailed information about the original data sources integrated in Omnipath, please visit: