Skip to contents

Query ClassyFire database

Source: R/classyfire_lookup_class.R
classyfire_lookup.Rd

Queries the ClassyFire database by inchikey to obtain chemical ontology information.

Usage

classyfire_lookup(
  query_column,
  output_items = "kingdom",
  output_fields = "name",
  suffix = "_cf",
  ...
)

Arguments

query_column

(character) The name of a column in the annotation table containing values to search in the api call.

output_items

(character) The names of the items to return from the results of the search. Can include any number of "kingdom", "superclass", "class", "subclass", "direct_parent", "intermediate_nodes", "substituents", "smiles", "molecular_framework", "description", "ancestors", "predicted_chebi_terms". Keyword ".all" may be used to return all items. The default is "kingdom".

output_fields

(character) The names of fields to return for each output_item. Can include any of "name", "description", "chemont_id" and "url". Keyword ".all" may be used to return all fields. Some items do not have fields, so output_category is ignored. The default is "name".

suffix

(character) A suffix appended to all column names in the returned result. The default is "_cf".

...

Additional slots and values passed to struct_class.

Value

A classyfire_lookup object with the following output slots:

updated(annotation_source) The annotation_source after adding data returned by the API.

Details

This object makes use of functionality from the following packages:

  • dplyr

  • httr

Inheritance

A classyfire_lookup object inherits the following struct classes:

classyfire_lookup() ⭢ rest_api() ⭢ model() ⭢ struct_class()

References

Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.3, https://CRAN.R-project.org/package=dplyr.

Wickham H (2023). httr: Tools for Working with URLs and HTTP. R package version 1.4.7, https://CRAN.R-project.org/package=httr.

See also

Other REST API's: kegg_lookup, lipidmaps_lookup, mwb_compound_lookup, rest_api

Examples

M = classyfire_lookup(
      output_items = "kingdom",
      output_fields = "name",
      base_url = "http://classyfire.wishartlab.com/entities",
      url_template = "<base_url>/<query_column>.json",
      query_column = character(0),
      cache = NULL,
      status_codes = list(),
      delay = 0.5,
      suffix = "_rest_api")