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Map Cross-Reference Identifiers to Reactome

Source: R/reactome_content.R
rba_reactome_xref.Rd

Retrieve the Reactome reference entities associated with an identifier from an external database. With expanded = TRUE, also retrieve the other external identifiers associated with each reference entity and the stable identifiers of its physical forms in Reactome.

Usage

rba_reactome_xref(
  xref_id,
  expanded = FALSE,
  db_filter = NULL,
  page_size = 100,
  page = 1,
  ...
)

Arguments

xref_id

Character or Numeric vector: One or more cross-reference identifiers from external databases. Multiple identifiers can only be supplied when expanded = TRUE.

expanded

Logical: (default = FALSE) Should other external identifiers and associated Reactome physical forms also be retrieved?

db_filter

Character: (optional) When expanded = TRUE, restrict the returned cross-references to this external database name as used by Reactome, e.g. "ENSEMBL".

page_size

Numeric: (default = 100) For an expanded query with multiple identifiers, the number of supplied identifiers to process per page.

page

Numeric: (default = 1) For an expanded query with multiple identifiers, the one-based page to retrieve.

...

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

Value

An R object containing the corresponding Reactome reference entities. Expanded results also contain associated cross-references and stable identifiers of physical entities. Expanded queries with multiple identifiers additionally contain pagination information.

Details

Multiple identifiers can be supplied for an expanded query. Reactome processes these identifiers in pages, while a standard query accepts one identifier. See rba_reactome_participants for more information about how Reactome represents molecules.

Corresponding API Resources

"GET https://reactome.org/ContentService/references/mapping/{identifier}"
"POST https://reactome.org/ContentService/references/mapping/xrefs"

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. (2020). ReactomeGSA—Efficient Multi-Omics Comparative Pathway Analysis. Molecular & Cellular Proteomics, 19(12), 2115–2125. doi: 10.1074/mcp.TIR120.002155

  • Reactome Content Services API Documentation

  • Citations note on Reactome website

See also

rba_pages

Examples

# \donttest{
rba_reactome_xref("CD40")
# }
# \donttest{
rba_reactome_xref("ENSP00000361350")
# }
# \donttest{
rba_reactome_xref("P36897", expanded = TRUE, db_filter = "ENSEMBL")
# }
# \donttest{
rba_reactome_xref(
  c("P36897", "Q5S007"),
  expanded = TRUE,
  db_filter = "ENSEMBL",
  page_size = 2,
  page = 1
)
# }