rbioapi (version 0.8.1)

rba_reactome_mapping: Map External ID to Reactome Pathways/Reactions

Description

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

Usage

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

Value

Data frame where each row is a pathway/reaction and columns are pertinent information.

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.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/mapping/{resource}/ {identifier}/pathways"
"GET https://reactome.org/ContentService/data/mapping/{resource}/ {identifier}/reactions"

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_mapping(id = "PTEN", resource =  "UniProt",
    map_to = "reactions", species = 9606)
# }