Imports the database from https://omnipathdb.org/interactions, which contains only interactions supported by literature references. This part of the interaction database compiled a similar way as it has been presented in the first paper describing OmniPath (Turei et al. 2016).

## Usage

import_omnipath_interactions(
resources = NULL,
organism = 9606,
datasets = "omnipath",
fields = NULL,
default_fields = TRUE,
references_by_resource = TRUE,
exclude = NULL,
...
)

## Arguments

resources

interactions not reported in these databases are removed. See get_interaction_resources for more information.

organism

Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse

datasets

Names of the interaction datasts to download: omnipath (by default). Other possiblites are: pathwayextra, kinaseextra, ligrecextra, dorothea,tf_target, mirnatarget, tf_mirna, lncrna_mrna. The user can select multiple datasets as for example: c('omnipath', 'pathwayextra', 'kinaseextra')

fields

The user can define here the fields to be added. If used, set the next argument, default_fields, to FALSE.

default_fields

whether to include the default fields (columns) for the query type. If FALSE, only the fields defined by the user in the fields argument will be added.

references_by_resource

if FALSE, removes the resource name prefixes from the references (PubMed IDs); this way the information which reference comes from which resource will be lost and the PubMed IDs will be unique.

exclude

Character: datasets or resources to exclude.

...

## Value

A dataframe of protein-protein interactions

• get_interaction_resources

• import_all_interactions

• interaction_graph

• print_interactions

## Examples

interactions = import_omnipath_interactions(