README.md
In OmnipathR: OmniPath web service client

OmnipathR

Utility functions to work with OmniPath in R.

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:

Interactions: protein-protein interactions from different datasets.
Enzyme-substrate: enzyme-PTM (post-translational modification) relationships.
Complexes: comprehensive database of more than 22000 protein complexes.
Annotations: large variety of data about proteins and complexes features.
Intercell: information on the roles in inter-cellular signaling.

For a more detailed information, we recommend you to visit the following sites:

https://omnipathdb.org/

https://omnipathdb.org/info

https://github.com/saezlab/pypath/blob/master/webservice.rst

https://saezlab.github.io/OmnipathR/articles/OmnipathMainVignette.html

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 R console:

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:

https://saezlab.github.io/OmnipathR/articles/OmnipathMainVignette.html

You can also check the manual:

https://saezlab.github.io/OmnipathR/reference/index.html

In addition, we provide here some examples for a quick start:

library(OmnipathR)

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 (igraph objects)

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[[1]],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:

https://github.com/saezlab/OmnipathR/issues

Many thanks for using OmnipathR!