Skip to contents

Query and Retrieve any Reactome knowledge-base Object

Source: R/reactome_content.R
rba_reactome_query.Rd

Using this Comprehensive function, You can Retrieve any object from Reactome knowledge-base

Usage

rba_reactome_query(
  ids,
  enhanced = FALSE,
  map = FALSE,
  attribute_name = NULL,
  ...
)

Arguments

ids

A single or Multiple database IDs (DbId), Stable IDs (StId) or a mixture of both.

enhanced

Logical: (Default = FALSE) If 'TRUE' more information on the supplied entry will be returned. (You can set this argument to 'TRUE' Only when you supply a single ID).

map

(Default = FALSE) Should the supplied IDs be mapped? This argument will only be considered when you supply multiple IDs. (e.g. when you supply previous version of stable identifiers.)

attribute_name

(Optional) Only Return an Attribute of the supplied Database Object. (You can use this argument Only when you supply a single ID)

...

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

Value

List containing your query outputs.

Corresponding API Resources

"POST https://reactome.org/ContentService/data/query/ids"
"POST https://reactome.org/ContentService/data/query/ids/map"
"GET https://reactome.org/ContentService/data/query/{id}"
"GET https://reactome.org/ContentService/data/query/enhanced/{id}"
"GET https://reactome.org/ContentService/data/query/{id}/{attributeName}"

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_query(ids = c("8953958", "11982506", "R-ALL-9649879"))
# }
# \donttest{
rba_reactome_query(ids = "R-HSA-9656256", enhanced = TRUE)
# }
# \donttest{
rba_reactome_query(ids = "8863054", attribute_name = "displayName")
# }