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

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

Arguments

id

Molecule's external Identifier

resource

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

map_to

Either "pathways" or "reactions".

species

Numeric or Character: 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

  • Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031. PubMed PMID: 31691815.

  • Reactome Content Services API Documentation

Examples

# \donttest{
rba_reactome_mapping(id = "PTEN", resource =  "UniProt",
    map_to = "reactions", species = 9606)
# }