Participating molecules in a Reactome comprises set of 'Physical Entity' and 'Reference Entities' class objects. Use this function to retrieve all, only 'Physical Entity' or only 'Reference Entities' participants of given event.

rba_reactome_participants(
  event_id,
  only_physical_entities = FALSE,
  only_reference_entities = FALSE,
  ...
)

Arguments

event_id

Reactome event's database ID (DbId) or Stable ID (StId).

only_physical_entities

Logical: If TRUe, only participating 'Physical Entities' will be returned.

only_reference_entities

Logical: If TRUe, only participating 'Reference Entities' will be returned.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

List with the participant of your supplied Event ID. A Data frame if only physical or 'Reference Entities' was requested.

Details

A 'Physical Entity' Instance could include an individual molecule, a multi-molecular complex or a set of molecule forming a group based on some characteristics. a single molecule can have different 'Physical Entity' instances based on it's associated attributes. For example, IgK Ig kappa chain, has two 'Physical Entity' instances; one, with ID "R-HSA-197041" refers to the secreted antibody protein to the extra-cellular region; And the second one is with ID "R-HSA-2038819" and refers to the plasma-membrane-integrated form of the antibody protein.
To make it possible to link multiple 'Physical Entity' instances of a molecule, Reactome uses a data class named "'Reference Entities'" which correspond to the invariant attribute of a molecule. for example, both of the above-mentioned 'Physical Entities' see a 'Reference Entities' named "UniProt:P01834 IGKC.
See Reactome Data Model for more information about the data model and Physical Entities.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/participants/id"
"GET https://reactome.org/ContentService/data/participants/id/ participatingPhysicalEntities"
"GET https://reactome.org/ContentService/data/participants/id/ referenceEntities"

References

  • Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031. PubMed PMID: 31691815.

  • Reactome Content Services API Documentation

See also

Examples

# \donttest{
rba_reactome_participants("R-HSA-5682012")
# }
# \donttest{
rba_reactome_participants("R-HSA-5682012", only_physical_entities = TRUE)
# }
# \donttest{
rba_reactome_participants("R-HSA-5682012", only_reference_entities = TRUE)
# }