This function will Return a list of all pathways with the class "TopLevelPathway" which are annotated in your supplied species.

rba_reactome_pathways_top(species, ...)

Arguments

species

Numeric or Character: 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.

...

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

Value

Data frame where each row is a Top Level Pathway and columns are pertinent information.

Details

Reactome's Events hierarchy for any specie will begin with pathways with class "TopLevelPathway" (e.g. "Immune System", "Metabolism of proteins"). further down in the event's hierarchy tree, each TopLevelPathway has has other events itself (e.g. "Adaptive immune system", "Innate immune system"). Based on the chosen pathway, the hierarchy tree would typically goes further down.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/pathways/top/species"

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

See also

Other "Reactome Content Service - Pathway Related Queries": rba_reactome_pathways_events(), rba_reactome_pathways_low()

Examples

# \donttest{
rba_reactome_pathways_top(species = 9606)
# }
# \donttest{
rba_reactome_pathways_top(species = "Saccharomyces cerevisiae")
# }