Uses the PubChem API to search for CID based on the input annotation column.
Usage
pubchem_compound_lookup(
query_column,
search_by,
suffix = "_pubchem",
output = "cids",
records = "best",
...
)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".- output
(character) The value returned from the pubchem database. The default is
"cids".- records
(character) Returned record(s). Allowed values are limited to the following:
"": Sometimes there are multiple matches to the PubChem, database especially when searhcing by name."best": Return only the best matching record."all": Return all matching records.
The default is
"best".- ...
Additional slots and values passed to
struct_class.
Value
A pubchem_compound_lookup object with the following
output slots:
updated | (annotation_source) The annotation_source after adding data returned by the API. |
Inheritance
A pubchem_compound_lookup object inherits the following struct
classes: [pubchem_compound_lookup] -> [rest_api] -> [model] ->
[struct_class]
Examples
M = pubchem_compound_lookup( search_by = "cid", output = "cids",
records = "best", base_url =
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound", url_template =
"<base_url>/<search_by>/<query_column>/<output>/JSON", query_column =
character(0), cache = NULL, status_codes = list(), delay = 0.5,
suffix = "_rest_api")