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Retrieve the Reactome Event Hierarchy of a Species

Source: R/reactome_content.R
rba_reactome_event_hierarchy.Rd

Retrieve the full hierarchy of pathways and reaction-like events for a species, or restrict the hierarchy to pathways. The hierarchy begins with top-level pathways and can be traversed through the children field. Because an event can participate in more than one biological process, it may occur in more than one place in the hierarchy.

Usage

rba_reactome_event_hierarchy(
  species,
  pathways_only = FALSE,
  token = NULL,
  resource = "TOTAL",
  interactors = FALSE,
  importable_only = FALSE,
  ...
)

Arguments

species

Character or Numeric: NCBI Taxonomy identifier (Human Taxonomy ID is 9606.) or species name (e.g. "Homo sapiens"). See rba_reactome_species or Reactome Data Schema: Entries: Species.

pathways_only

Logical: (default = FALSE) Should reaction-like events be omitted from the hierarchy?

token

Character: (optional) Reactome analysis token whose results should be added to the hierarchy. See rba_reactome_analysis.

resource

Character: (default = "TOTAL") Analysis resource to add when a token is supplied. Available choices are: "TOTAL", "UNIPROT", "ENSEMBL", "CHEBI", "IUPHAR", "MIRBASE", "NCBI_PROTEIN", "EMBL", "COMPOUND", or "PUBCHEM_COMPOUND".

interactors

Logical: (default = FALSE) When a token is supplied, should interactor results be included?

importable_only

Logical: (default = FALSE) When a token is supplied, should the analysis results be restricted to importable resources?

...

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

Value

A nested list representing the species's event hierarchy. When an analysis token is supplied, the corresponding analysis information is included with the pathway entries.

Details

An analysis token can be supplied to add the corresponding analysis results to the hierarchy. The analysis resource can then be selected, and interactors or only importable resources can optionally be included.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/eventsHierarchy/{species}"

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

Other "Reactome Content Service - Queries Related to Events": rba_reactome_event_ancestors()

Examples

if (FALSE) { # \dontrun{
# Very large response
rba_reactome_event_hierarchy("Homo sapiens")
} # }
if (FALSE) { # \dontrun{
# Restrict the hierarchy to pathways
rba_reactome_event_hierarchy(9606, pathways_only = TRUE)
} # }