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Map External ID to Reactome Pathways/Reactions

Source: R/reactome_content.R
rba_reactome_mapping.Rd

By providing an external identifier from a given resource, you can retrieve a list of pathways/reactions that include your supplied ID.

Usage

rba_reactome_mapping(id, resource, map_to, species = "Homo sapiens", ...)

Arguments

id

Character or Numeric: Molecule's external Identifier

resource

Character: What is the resource of your supplied ID? see: Reactome External Identifiers

map_to

Character: Either "pathways" or "reactions".

species

Character or Numeric: (default = "Homo sapiens") NCBI Taxonomy identifier (Human is 9606), species name (e.g. "Homo sapiens") or Reactome DbId (e.g Homo sapiens is 48887). See rba_reactome_species or Reactome Data Schema: Entries: Species.

...

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

Value

Data frame where each row is a pathway/reaction and columns are pertinent information.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/mapping/{resource}/ {identifier}/pathways"
"GET https://reactome.org/ContentService/data/mapping/{resource}/ {identifier}/reactions"

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_mapping(id = "PTEN", resource =  "UniProt",
    map_to = "reactions", species = 9606)
# }