Compound ID lookup via OPSIN — opsin

Uses the OPSIN API to search for identifers based on the input annotation column.

Usage

opsin_lookup(query_column, suffix = "_opsin", output = "cids", ...)

Arguments

query_column: (character) The column name to use as the reference for searching the database e.g. "compound_name". OPSIN expect molecule names as input.
suffix: (character) A suffix appended to all column names in the returned result. The default is "_opsin".
output: (character) The value returned from the pubchem database. The default is "cids".
...: Additional slots and values passed to struct_class.

Value

A opsin_lookup object with the following output slots:

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

Inheritance

A opsin_lookup object inherits the following struct classes:

[opsin_lookup] -> [rest_api] -> [model] -> [struct_class]

References

Lowe, M. D, Corbett, T. P, Murray-Rust, Peter, Glen, C. R (2011). "Chemical Name to Structure: OPSIN, an Open ", "Source Solution." Journal of Chemical Information and Modeling, 51(3), 793-753. doi:10.1021/ci100384d https://doi.org/10.1021/ci100384d.

Examples

M <- opsin_lookup(
        output = "stdinchikey",
        base_url = "https://opsin.ch.cam.ac.uk/opsin",
        url_template = "<base_url>/<query_column>.<output>",
        query_column = character(0),
        cache = NULL,
        status_codes = list(),
        delay = 0.5,
        suffix = "_rest_api")