NCBI E-utils query — eutils_lookup • MetMashR

Submit a query to one of the NCBI E-utils databases. See https://www.ncbi.nlm.nih.gov/books/NBK25501/ for details.

Usage

eutils_lookup(query_column, database, term, result_fields = "idlist", ...)

Arguments

query_column: (character) The column name to use as the reference for searching the database e.g. "HMBD_ID".
database: (character) The name of the E-utils database to search. See https://www.ncbi.nlm.nih.gov/books/NBK25501/ for details.
term: (character) A correctly formated search term to use with E-utils. See https://www.ncbi.nlm.nih.gov/books/NBK25501/ for details. When used with the provided url template will automatically include the value from the query_column at the beginning of the term.
result_fields: (character) The name of the search result field to return. For E-utils this is often "idlist". The default is "idlist".
...: Additional slots and values passed to struct_class.

Value

A eutils_lookup object with the following output slots:

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

Inheritance

A eutils_lookup object inherits the following struct classes:

[eutils_lookup] -> [rest_api] -> [model] -> [struct_class]

Examples

M <- eutils_lookup(
        database = "gene",
        term = "[pdat]",
        result_fields = "idlist",
        base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils",
        url_template = "<base_url>/esearch.fcgi?db=<database>&term=<query_column><term>&retmode=json",
        query_column = character(0),
        cache = NULL,
        status_codes = list(),
        delay = 0.5,
        suffix = "_rest_api")