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This function will export a supplied Reactome Event (Pathway or Reaction) to a SBGN (Systems Biology Graphical Notation) or SBML (Systems Biology Markup Language)

Usage

rba_reactome_exporter_event(event_id, output_format, save_to = NULL, ...)

Arguments

event_id

Reactome event's database IDs (DbId) or Stable IDs (StId).

output_format

Either "sbgn" or "sbml".

save_to

NULL or Character:

  • NULL: Save the file to an automatically-generated path.

  • Character string: A valid file path to save the file to.

...

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

Value

NULL, According to the inputs, a SBGN or SBML file will be saved to disk.

Corresponding API Resources

"GET https://reactome.org/ContentService//exporter/event/ identifier.sbgn" "GET https://reactome.org/ContentService//exporter/event/ identifier.sbml"

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 - Format Exporter": rba_reactome_exporter_diagram(), rba_reactome_exporter_overview(), rba_reactome_exporter_reaction()

Examples

if (FALSE) {
rba_reactome_exporter_event(event_id = "R-HSA-177929",
    output_format = "sbgn",
    save_to = "R-HSA-177929.sbgn")
}
if (FALSE) {
rba_reactome_exporter_event(event_id = "R-HSA-177929",
    output_format = "sbgn")
}