rbioapi: rba_reactome_participants – R documentation

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rba_reactome_participants

Get Participants of a Reactome Event

Description

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.

Usage

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). Refer to `rba_options`'s arguments documentation for more information on available options.

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' refer to a 'Reference Entities' named "UniProt:P01834 IGKC.
See Reactome Data Model for more information about the data model and Physical Entities.

Value

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

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

Examples

rba_reactome_participants("R-HSA-5682012")


rba_reactome_participants("R-HSA-5682012", only_physical_entities = TRUE)


rba_reactome_participants("R-HSA-5682012", only_reference_entities = TRUE)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release