Compound property lookup via pubchem — pubchem_property

Uses the PubChem API to search for CID based onthe input annotation column and returns property information.

Usage

pubchem_property_lookup(
  query_column,
  search_by,
  suffix = "_pubchem",
  property = "InChIKey",
  ...
)

Arguments

query_column: (character) The column name to use as the reference for searching the database e.g. "HMBD_ID".
search_by: (character) The PubChem domain to search for matches to the annotation_column.
suffix: (character) A suffix appended to all column names in the returned result. The default is "_pubchem".
property: (character) A comma separated list of properties to return from the pubchem database. (see https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest#section=Compound-Property-Tables for details). Keyword ".all" will return all properties. The default is "InChIKey".
...: Additional slots and values passed to struct_class.

Value

A pubchem_property_lookup object with the following output slots:

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

Inheritance

A pubchem_property_lookup object inherits the following struct classes:

[pubchem_property_lookup] -> [pubchem_compound_lookup] -> [rest_api] -> [model] -> [struct_class]

Examples

M <- pubchem_property_lookup(
        search_by = "cid",
        property = "InChIKey",
        output = "cids",
        records = "best",
        base_url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound",
        url_template = "<base_url>/<search_by>/<query_column>/property/<property>/JSON",
        query_column = character(0),
        cache = NULL,
        status_codes = list(),
        delay = 0.5,
        suffix = "_rest_api")