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Get Full Event Hierarchy of a Species

Source: R/reactome_content.R
rba_reactome_event_hierarchy.Rd

This function will retrieve the full Events hierarchy of your supplied species. Directly under each species, each child element is a "top Level Pathway". You can traverse the events tree down by following the "children" element.

Usage

rba_reactome_event_hierarchy(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

List which is a representation of the species's events hierarchy described in the "Details section".

Details

By Reactome's definition, Events are the building blocks of biological processes and could be of two main classes: "Pathway" or "Reaction-like events". The events are organized in a hierarchical structure; and each event could be child or parent to another event; The hierarchy will always begin with a "Top level pathway" event. Also note that a given event could be part of more that one hierarchies.

Corresponding API Resources

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

References

  • Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

  • Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

  • 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) {
#very large response!
rba_reactome_event_hierarchy("Homo sapiens")
}
if (FALSE) {
#very large response!
rba_reactome_event_hierarchy(9606)
}