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Retrieve Reactome Knowledgebase Objects

Source: R/reactome_content.R
rba_reactome_query.Rd

Retrieve one or more Reactome objects by database or stable identifier. A single object can be returned with additional related information or reduced to one of its attributes. Multiple identifiers can optionally be mapped to the corresponding current Reactome objects.

Usage

rba_reactome_query(
  ids,
  enhanced = FALSE,
  map = FALSE,
  attribute_name = NULL,
  fetch_incoming_relationships = TRUE,
  summarize_reference_entity = FALSE,
  include_disease = TRUE,
  ...
)

Arguments

ids

Character or Numeric vector: One or more database identifiers (DbIds), stable identifiers (StIds), or a mixture of both. At most 20 identifiers can be supplied.

enhanced

Logical: (default = FALSE) Should additional related information be retrieved? This can only be used with one identifier.

map

Logical: (default = FALSE) When multiple identifiers are supplied, should each input identifier be mapped to its current Reactome object? This is useful for previous versions of stable identifiers.

attribute_name

Character: (optional) Return only this attribute of a single Reactome object. This cannot be combined with enhanced = TRUE.

fetch_incoming_relationships

Logical: (default = TRUE) When enhanced = TRUE, should incoming relationships be included where they are relevant to the queried object?

summarize_reference_entity

Logical: (default = FALSE) When enhanced = TRUE and the queried object is a ReferenceEntity, should its physical forms be represented by a summary?

include_disease

Logical: (default = TRUE) When enhanced = TRUE, should disease-specific information be included?

...

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

Value

An R object containing the requested Reactome object or objects. The returned fields depend on the type of each object. Mapped multiple-ID queries return a named list, and attribute queries return character values.

Details

With enhanced = TRUE, Reactome also retrieves second-level relationships involving regulations and catalysts. The enhanced query can include incoming relationships and disease-specific information. When the queried object is a ReferenceEntity, its physical forms can instead be represented by a summary.

Corresponding API Resources

"POST https://reactome.org/ContentService/data/query/ids"
"POST https://reactome.org/ContentService/data/query/ids/map"
"GET https://reactome.org/ContentService/data/query/{id}"
"GET https://reactome.org/ContentService/data/query/enhanced/v2/{id}"
"GET https://reactome.org/ContentService/data/query/{id}/{attributeName}"

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

Examples

# \donttest{
rba_reactome_query(ids = c("8953958", "11982506", "R-ALL-9649879"))
# }
# \donttest{
rba_reactome_query(ids = "R-HSA-9656256", enhanced = TRUE)
# }
# \donttest{
rba_reactome_query(
  ids = 66247,
  enhanced = TRUE,
  summarize_reference_entity = TRUE
)
# }
# \donttest{
rba_reactome_query(ids = "8863054", attribute_name = "displayName")
# }