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Map Cross References IDs to Reactome ReferenceEntity

Source: R/reactome_content.R
rba_reactome_xref.Rd

Use this function To retrieve a list of Reactome ReferenceEntity associated to your supplied Cross Reference (i.e. External) ID.

Usage

rba_reactome_xref(xref_id, ...)

Arguments

xref_id

molecule's cross-reference (external) identifier.

...

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

Value

List containing the ReferenceEntity corresponding to your supplied cross-reference (external) ID.

Details

Reactome cross-references external database's identifiers to it's database Entries named ReferenceEntity, which resembles the invariant aspect of a molecule. Thus there is a one-to-many relationship between Reactome's ReferenceEntity object and the molecule's ID in external databases, which in Reactome's terms is called Cross Reference.
See rba_reactome_participants's "Details section" to learn more about how Reactome classifies molecules.

Corresponding API Resources

"GET https://reactome.org/ContentService/references/mapping/{identifier}"

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

Examples

# \donttest{
rba_reactome_xref("CD40")
# }
# \donttest{
rba_reactome_xref("ENSP00000361350")
# }