Interactions from the small molecule-protein dataset of OmniPathSource:
Imports the dataset from: https://omnipathdb.org/interactions?datasets=small_molecule, which contains small molecule-protein interactions. Small molecules can be metabolites, intrinsic ligands or drug compounds.
import_small_molecule_protein_interactions( resources = NULL, organism = 9606, fields = NULL, default_fields = TRUE, references_by_resource = TRUE, exclude = NULL, strict_evidences = FALSE, ... )
interactions not reported in these databases are removed. See
get_interaction_resourcesfor more information.
Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse.
Optional fields to be added.
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.
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.
Character: datasets or resources to exclude.
Logical: restrict the evidences to the queried datasets and resources. If set to FALSE, the directions and effect signs and references might be based on other datasets and resources.
optional additional arguments
# What are the targets of aspirin? interactions <- import_small_molecule_protein_interactions( sources = 'ASPIRIN' ) # The prostaglandin synthases: interactions #> # A tibble: 0 × 14 #> # ℹ 14 variables: source <chr>, target <chr>, source_genesymbol <chr>, #> # target_genesymbol <chr>, is_directed <chr>, is_stimulation <chr>, #> # is_inhibition <chr>, consensus_direction <chr>, #> # consensus_stimulation <chr>, consensus_inhibition <chr>, sources <chr>, #> # references <chr>, curation_effort <chr>, n_references <lgl>