Utility functions to work with OmniPath in
OmnipathR is an
R package built to provide easy access to the data stored in the OmniPath webservice:
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.
The package also provides some utility functions to filter, analyse and visualize the data.
We provide here a brief summary about the data available through OmnipathR. OmnipathR provides access to 5 types of queries:
For a more detailed information, we recommend you to visit the following sites:
First of all, you need a current version of
R (https://r-project.org). OmnipathR is a freely available package deposited on Bioconductor and Github: (https://bioconductor.org/, https://github.com/saezlab/OmnipathR).
You can install it by running the following commands on a
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") ## Last release in Bioconductor BiocManager::install("OmnipathR") ## Development version with the lastest updates BiocManager::install(version='devel')
To get started, we strongly recommend to read our main vignette in order to deal with the different types of queries and handle the data they return:
You can also check the manual:
In addition, we provide here some examples for a quick start:
Download human protein-protein interactions from the specified resources:
interactions <- import_omnipath_interactions(resources=c("SignaLink3","PhosphoSite", "SIGNOR"))
Download human enzyme-PTM relationships from the specified resources:
enzsub <- import_omnipath_enzsub(resources=c("PhosphoSite", "SIGNOR"))
Convert both data frames into networks (
ptms_g = ptms_graph(ptms = enzsub) OPI_g = interaction_graph(interactions = interactions)
Print some interactions in a nice format:
print_interactions(head(interactions)) source interaction target n_resources n_references 4 SRC (P12931) ==( + )==> TRPV1 (Q8NER1) 9 6 2 PRKG1 (Q13976) ==( - )==> TRPC6 (Q9Y210) 7 5 1 PRKG1 (Q13976) ==( - )==> TRPC3 (Q13507) 9 2 5 LYN (P07948) ==( + )==> TRPV4 (Q9HBA0) 9 2 6 PTPN1 (P18031) ==( - )==> TRPV6 (Q9H1D0) 3 2 3 PRKACA (P17612) ==( + )==> TRPV1 (Q8NER1) 6 1
Find interactions between a specific kinase and a specific substrate:
print_interactions(dplyr::filter(enzsub,enzyme_genesymbol=="MAP2K1", substrate_genesymbol=="MAPK3")) enzyme interaction substrate modification n_resources 1 MAP2K1 (Q02750) ====> MAPK3_Y204 (P27361) phosphorylation 8 2 MAP2K1 (Q02750) ====> MAPK3_T202 (P27361) phosphorylation 8 3 MAP2K1 (Q02750) ====> MAPK3_Y210 (P27361) phosphorylation 2 4 MAP2K1 (Q02750) ====> MAPK3_T207 (P27361) phosphorylation 2
Find shortest paths on the directed network between proteins:
print_path_es(shortest_paths(OPI_g,from = "TYRO3",to = "STAT3", output = 'epath')$epath[],OPI_g) source interaction target n_resources n_references 1 TYRO3 (Q06418) ==( ? )==> AKT1 (P31749) 2 0 2 AKT1 (P31749) ==( - )==> DAB2IP (Q5VWQ8) 3 1 3 DAB2IP (Q5VWQ8) ==( - )==> STAT3 (P40763) 1 1
Find all shortest paths between proteins:
print_path_vs(all_shortest_paths(OPI_g,from = "DYRK2",to = "MAPKAPK2")$res,OPI_g) Pathway 1: DYRK2 -> TBK1 -> NFKB1 -> MAP3K8 -> MAPK3 -> MAPKAPK2 Pathway 2: DYRK2 -> TBK1 -> AKT3 -> MAP3K8 -> MAPK3 -> MAPKAPK2 Pathway 3: DYRK2 -> TBK1 -> AKT2 -> MAP3K8 -> MAPK3 -> MAPKAPK2 Pathway 4: DYRK2 -> TBK1 -> AKT1 -> MAP3K8 -> MAPK3 -> MAPKAPK2 Pathway 5: DYRK2 -> TBK1 -> AKT3 -> PEA15 -> MAPK3 -> MAPKAPK2 Pathway 6: DYRK2 -> TBK1 -> AKT2 -> PEA15 -> MAPK3 -> MAPKAPK2 .....
Feedbacks and bugreports are always very welcomed!
Please use the Github issue page to report bugs or for questions:
Many thanks for using OmnipathR!