Compound ID lookup via pubchem — hmdb

Requests HMBD records based on HMDB identifiers.

Usage

hmdb_lookup(query_column, suffix = "_hmdb", output = "inchikey", ...)

Arguments

query_column: (character) The name of a column in the annotation table containing values to search in the api call.
suffix: (character) A suffix appended to all column names in the returned result. The default is "_hmdb".
output: (character) The value returned from the HMDB xml. The default is "inchikey".
...: Additional slots and values passed to struct_class.

Value

A hmdb_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:

XML

Inheritance

A hmdb_lookup object inherits the following struct classes:

hmdb_lookup() ⭢ rest_api() ⭢ model() ⭢ struct_class()

References

Temple Lang D (2023). XML: Tools for Parsing and Generating XML Within R and S-Plus. R package version 3.99-0.16, https://CRAN.R-project.org/package=XML.

Examples

M = hmdb_lookup(
      output = "inchikey",
      base_url = "http://www.hmdb.ca/metabolites",
      url_template = "<base_url>/<query_column>.xml",
      query_column = character(0),
      cache = NULL,
      status_codes = list(),
      delay = 0.5,
      suffix = "_rest_api")