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
Character or Numeric: Reactome event's database ID (DbId) or Stable ID (StId).
- only_physical_entities
Logical: (default =
FALSE) If TRUE, only participating 'Physical Entities' will be returned.- only_reference_entities
Logical: (default =
FALSE) 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
Ragueneau, E., Gong, C., Sinquin, P., Sevilla, C., Beavers, D., Grentner, A., ... D’Eustachio, P. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Res., 54(D1), D673–D681. doi: 10.1093/nar/gkaf1223
Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.