OmnipathR

OmnipathR provides access to five main types of queries via the OmniPath web service:

1. Interactions: Protein-protein interactions from various datasets.
2. Enzyme-substrate: Enzyme-PTM (post-translational modification) relationships.
3. Complexes: A database of over 22,000 protein complexes.
4. Annotations: Data regarding protein and complex features.
5. Intercell: Information on intercellular signaling roles.

If you need the most recent features that are not yet available in the Bioconductor release, you can install the package directly from GitHub using devtools.

require(devtools)
install_github('saezlab/OmnipathR')

You can install the stable version of OmnipathR using BiocManager. Ensure you have a current version of R installed.

To install the last official release from Bioconductor:

if (!requireNamespace('BiocManager', quietly = TRUE))
    install.packages('BiocManager')

BiocManager::install('OmnipathR', version = '3.12')

To install the development version with the latest updates:

BiocManager::install('OmnipathR', version = 'devel')

Once you have an igraph object (e.g., created via interaction_graph), you can find shortest paths between proteins.

Single shortest path:

# Find the shortest path between TYRO3 and STAT3
print_path_es(shortest_paths(OPI_g, from = 'TYRO3', to = 'STAT3', output = 'epath')$epath[[1]], OPI_g)

All shortest paths:

# Find all shortest paths between DYRK2 and MAPKAPK2
print_path_vs(all_shortest_paths(OPI_g, from = 'DYRK2', to = 'MAPKAPK2')$res, OPI_g)

Use the enzyme_substrate() function to retrieve enzyme-PTM (post-translational modification) relationships.

library(OmnipathR)

# Download human enzyme-PTM relationships from specified resources
enzsub <- enzyme_substrate(resources = c('PhosphoSite', 'SIGNOR'))

You can convert data frames returned by omnipath() or enzyme_substrate() into igraph network objects using interaction_graph() and ptms_graph().

# Convert enzyme-PTM data to a graph
ptms_g = ptms_graph(ptms = enzsub)

# Convert protein-protein interaction data to a graph
OPI_g = interaction_graph(interactions = interactions)

Use the omnipath() function to retrieve protein-protein interactions from specific datasets (resources).

library(OmnipathR)

# Download human protein-protein interactions from specified resources
interactions <- omnipath(
    resources = c('SignaLink3', 'PhosphoSite', 'SIGNOR')
)