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Search the Reactome Knowledgebase

Source: R/reactome_content.R
rba_reactome_search.Rd

Search Reactome for entries that match a text query. The search can be limited by species, result type, cellular compartment, and keyword.

Usage

rba_reactome_search(
  query,
  species = NULL,
  types = NULL,
  compartments = NULL,
  keywords = NULL,
  cluster = TRUE,
  page_size = 10,
  page = 1,
  scope = "PHYSICAL_ENTITY",
  force_filters = FALSE,
  ...
)

Arguments

query

Character: Text to search for in the Reactome knowledgebase.

species

Character vector: (optional) Scientific species name(s) used to filter the results, e.g. "Homo sapiens". See rba_reactome_species for species available in Reactome.

types

Character vector: (optional) Result type(s) used to filter the search, e.g. "Protein", "Pathway", or "Reaction".

compartments

Character vector: (optional) Cellular compartment name(s) used to filter the results.

keywords

Character vector: (optional) Reactome search keyword(s) used to filter the results.

cluster

Logical: (default = TRUE) Should matches be separated into groups according to their result type? If FALSE, matches are returned in one ranked group.

page_size

Numeric: (default = 10) Maximum number of matches to return from each result group on a page. If cluster = FALSE, this is the maximum number returned from the single combined group.

page

Numeric: (default = 1) One-based results page to retrieve.

scope

Character: (default = "PHYSICAL_ENTITY") Which form of matching entities should be returned? Can be one of:

  • "PHYSICAL_ENTITY": Return specific physical forms annotated in Reactome.

  • "REFERENCE_ENTITY": Group applicable physical forms by their underlying reference molecule; entries without a reference molecule are retained as physical entities.

  • "BOTH": Return both representations.

force_filters

Logical: (default = FALSE) Should Reactome keep all supplied filters when they produce no matches? If FALSE, Reactome may remove the filters and return results from a broader search.

...

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

Value

A list with the following elements:

results

A data frame with one row per returned result group. The entries column contains data frames of matching Reactome entries; their fields vary according to result type.

rowCount

Number of matching entries returned on the requested page.

numberOfGroups

Number of matching result groups reported by Reactome.

numberOfMatches

Total number of matches reported by Reactome.

Details

By default, matches are separated into groups such as proteins, pathways, and reactions. In this case, page_size is applied separately to each group. If cluster = FALSE, matches are returned in one group and page_size applies to that group.

Reactome normally removes supplied filters when they produce no matches. Set force_filters = TRUE to require all supplied filters, so that a search with no filtered matches is reported instead of being broadened. Reactome also marks matching text in some returned names and descriptions; rbioapi leaves these highlighting markers unchanged.

Corresponding API Resources

"GET https://reactome.org/ContentService/search/query"

References

  • Ragueneau, E., Gong, C., Sinquin, P., Sevilla, C., Beavers, D., Grentner, A., ... D’Eustachio, P. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Res., 54(D1), D673–D681. doi: 10.1093/nar/gkaf1223

  • Griss, J., Viteri, G., Sidiropoulos, K., Nguyen, V., Fabregat, A., & Hermjakob, H. (2020). ReactomeGSA—Efficient Multi-Omics Comparative Pathway Analysis. Molecular & Cellular Proteomics, 19(12), 2115–2125. doi: 10.1074/mcp.TIR120.002155

  • Reactome Content Services API Documentation

  • Citations note on Reactome website

See also

rba_reactome_query rba_reactome_species rba_pages

Examples

# \donttest{
rba_reactome_search(
  query = "TP53",
  species = "Homo sapiens",
  types = c("Protein", "Pathway")
)
# }
# \donttest{
rba_reactome_search(
  query = "apoptosis",
  cluster = FALSE,
  page_size = 20
)
# }