drug_general_information: Drugs General Information parser

Description Usage Arguments Value read_drugbank_xml_db See Also Examples

View source: R/drug_main_node_parser.R

Description

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

Usage

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

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.

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.

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.

See Also

Other drugs: drug_affected_organisms(), drug_ahfs_codes(), drug_atc_codes(), drug_calc_prop(), drug_categories(), drug_classification(), drug_dosages(), drug_ex_identity(), drug_exp_prop(), drug_external_links(), drug_food_interactions(), drug_groups(), drug_interactions(), drug_intern_brand(), drug_manufacturers(), drug_mixtures(), drug_packagers(), drug_patents(), drug_pdb_entries(), drug_pharmacology(), drug_prices(), drug_products(), drug_reactions_enzymes(), drug_reactions(), drug_salts(), drug_sequences(), drug_snp_adverse_reactions(), drug_snp_effects(), drug_syn()

Examples

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## Not run: 
# 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)

## End(Not run)

dbparser documentation built on Aug. 26, 2020, 5:10 p.m.