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README.md

OmnipathR

Utility functions to work with Omnipath in R.

Description

OmnipathR is an R package built to provide easy access to the data stored in the Omnipath webservice:

http://omnipathdb.org/

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.

Query types

We provide here a brief summary about the data available through OmnipathR. OmnipathR provides access to 5 types of queries:

  1. Interactions: protein-protein interactions from different datasets.
  2. Post-translational modifications (PTMs): enzyme-substrate interactions.
  3. Complexes: comprehensive database of more than 22000 protein complexes.
  4. Annotations: large variety of data about proteins and complexes features.
  5. Intercell: information on the roles in inter-cellular signaling.

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

http://omnipathdb.org/

http://omnipathdb.org/info

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

https://bioconductor.org/packages/release/bioc/vignettes/OmnipathR/inst/doc/OmnipathR.pdf

Installation

First of all, you need a current version of R (http://www.r-project.org). OmnipathR is a freely available package deposited on Bioconductor and Github: (http://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")

BiocManager::install("OmnipathR")

Getting started and some usage examples

To get started, we strongly recommend to read our vignette in order to deal with the different types of queries and handle the data they return:

https://bioconductor.org/packages/release/bioc/vignettes/OmnipathR/inst/doc/OmnipathR.pdf

You can also check the manual:

https://bioconductor.org/packages/release/bioc/manuals/OmnipathR/man/OmnipathR.pdf

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

library(OmnipathR)

Download human protein-protein interactions for some source databases:

interactions <- 
  import_Omnipath_Interactions(filter_databases=c("SignaLink3","PhosphoSite", 
  "Signor"))

Download human post-translational modifications for some source databases:

ptms <- import_Omnipath_PTMS(filter_databases=c("PhosphoSite", "Signor"))

Convert both data frames into networks (igraph objects)

ptms_g = ptms_graph(ptms = ptms )
OPI_g = interaction_graph(interactions = interactions )

Print some interactions in a nice format:

print_interactions(head(interactions))

            source interaction           target nsources nrefs
1     UBC (P0CG48)  ==( ? )==>   IKBKG (Q9Y6K9)        5    41
2   IKBKG (Q9Y6K9)  ==( ? )==>     UBC (P0CG48)        5    41
4   PINK1 (Q9BXM7)  ==( + )==>     UBC (P0CG48)        5    19
3     UBC (P0CG48)  ==( + )==>    PRKN (O60260)        3    16
5     UBC (P0CG48)  ==( ? )==> TNFAIP3 (P21580)        5    14
6 TNFAIP3 (P21580)  ==( ? )==>     UBC (P0CG48)        5    14

Find interactions between a specific kinase and a specific substrate:

print_interactions(dplyr::filter(ptms,enzyme_genesymbol=="MAP2K1",
  substrate_genesymbol=="MAPK3"))

           enzyme interaction           substrate    modification nsources
4 MAP2K1 (Q02750)       ====> MAPK3_Y204 (P27361) phosphorylation        6
3 MAP2K1 (Q02750)       ====> MAPK3_T202 (P27361) phosphorylation        6
1 MAP2K1 (Q02750)       ====> MAPK3_Y210 (P27361) phosphorylation        1
2 MAP2K1 (Q02750)       ====> MAPK3_T207 (P27361) phosphorylation        1
           

Find shortest paths on the directed network between proteins:

printPath_es(shortest_paths(OPI_g,from = "TYRO3",to = "STAT3", 
    output = 'epath')$epath[[1]],OPI_g)

          source interaction         target nsources nrefs
1 TYRO3 (Q06418)  ==( + )==>  GRB2 (P62993)        1     1
2  GRB2 (P62993)  ==( + )==>  EGFR (P00533)       11    63
3  EGFR (P00533)  ==( + )==> STAT3 (P40763)       10    21

Find all shortest paths between proteins:

printPath_vs(all_shortest_paths(OPI_g,from = "DYRK2",to = "MAPKAPK2")$res,OPI_g)
[1] "pathway 1: DYRK2 -> TP53 -> MAPK3 -> MAPKAPK2"
          source interaction            target nsources nrefs
1 DYRK2 (Q92630)  ==( + )==>     TP53 (P04637)        7   100
2  TP53 (P04637)  ==( - )==>    MAPK3 (P27361)        5     3
3 MAPK3 (P27361)  ==( + )==> MAPKAPK2 (P49137)        4     4
[1] "pathway 2: DYRK2 -> TP53 -> MAPK14 -> MAPKAPK2"
           source interaction            target nsources nrefs
1  DYRK2 (Q92630)  ==( + )==>     TP53 (P04637)        7   100
2   TP53 (P04637)  ==( ? )==>   MAPK14 (Q16539)        5     7
3 MAPK14 (Q16539)  ==( + )==> MAPKAPK2 (P49137)       21    27
[1] "pathway 3: DYRK2 -> TP53 -> MAPK1 -> MAPKAPK2"
          source interaction            target nsources nrefs
1 DYRK2 (Q92630)  ==( + )==>     TP53 (P04637)        7   100
2  TP53 (P04637)  ==( ? )==>    MAPK1 (P28482)        7     8
3 MAPK1 (P28482)  ==( + )==> MAPKAPK2 (P49137)       10     9

Feedbacks, bug reports, features

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!

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