drug_general_information: Drugs General Information parser

Description

A description of the hierarchical chemical classification of the drug; imported from ClassyFire.

Usage

drug_general_information(
  save_table = FALSE,
  save_csv = FALSE,
  csv_path = ".",
  override_csv = FALSE,
  database_connection = NULL
)

Value

a tibble with 15 variables:

primary_key: Drugbank id
other_keys: Other identifiers that may be associated with the drug
type: Either small molecule, or biotech. Biotech is used for any drug that is derived from living systems or organisms, usually composed of high molecular weight mixtures of protein, while small molecule describes a low molecular weight organic compound.
name
created: Date that this drug was first added to DrugBank.
updated: Denotes when this drug was last updated in DrugBank.
description: Descriptions of drug chemical properties, history and regulatory status.
cas_number: The Chemical Abstracts Service (CAS) registry number assigned to the drug.
unii: Unique Ingredient Identifier (UNII) of this drug.
average_mass: The weighted average of the isotopic masses of the drug
state: One of solid, liquid, or gas
monoisotopic_mass: The mass of the most abundant isotope of the drug
synthesis_reference: Citation for synthesis of the drug molecule.
fda_label: Contains a URL for accessing the uploaded United States Food and Drug Administration (FDA) Monograph for this drug.
msds: Contains a URL for accessing the Material Safety Data Sheet (MSDS) for this drug.

Arguments

save_table: boolean, save table in database if true.
save_csv: boolean, save csv version of parsed tibble if true
csv_path: location to save csv files into it, default is current location, save_csv must be true
override_csv: override existing csv, if any, in case it is true in the new parse operation
database_connection: DBI connection object that holds a connection to user defined database. If save_table is enabled without providing value for this function an error will be thrown.

read_drugbank_xml_db

read_drugbank_xml_db function must be called first before any parser.

If read_drugbank_xml_db is called before for any reason, so no need to call it again before calling this function.

Examples

Run this code

if (FALSE) {
# the same parameters and usage will be applied for any parser
# return only the parsed tibble
run_all_parsers()

# will throw an error, as database_connection is NULL
run_all_parsers(save_table = TRUE)

# save in database in SQLite in memory database and return parsed tibble
sqlite_con <- DBI::dbConnect(RSQLite::SQLite())
run_all_parsers(save_table = TRUE, database_connection = sqlite_con)

# save parsed tibble as csv if it does not exist in current location,
# and return parsed tibble.
# if the csv exist before read it and return its data.
run_all_parsers(save_csv = TRUE)

# save in database, save parsed tibble as csv,
# if it does not exist in current location and return parsed tibble.
# if the csv exist before read it and return its data.
run_all_parsers(save_table = TRUE, save_csv = TRUE,
database_connection = sqlite_con)

# save parsed tibble as csv if it does not exist in given location,
# and return parsed tibble.
# if the csv exist before read it and return its data.
run_all_parsers(save_csv = TRUE, csv_path = TRUE)

# save parsed tibble as csv if it does not exist in current location and
# return parsed tibble.
# if the csv exist override it and return it.
run_all_parsers(save_csv = TRUE, csv_path = TRUE, override = TRUE)
}