Package 'dbparser'

Title: Drugs Databases Parser
Description: This tool is for parsing public drug databases such as 'DrugBank' XML database <https://go.drugbank.com/>. The parsed data are then returned in a proper 'R' object called 'dvobject'.
Authors: Mohammed Ali [aut, cre], Ali Ezzat [aut], Hao Zhu [rev], Emma Mendelsohn [rev]
Maintainer: Mohammed Ali <[email protected]>
License: MIT + file LICENSE
Version: 2.0.3
Built: 2024-08-17 05:27:53 UTC
Source: https://github.com/ropensci/dbparser

Help Index

returns carriers, enzymes,targets and transporters node valid options.

Description

returns carriers, enzymes,targets and transporters node valid options.

Usage

cett_nodes_options()

Value

list of CETT valid options

See Also

Other parsers: drug_node_options(), parseDrugBank(), references_node_options()

returns drug node valid options.

Description

returns drug node valid options.

Usage

drug_node_options()

Value

list of drug valid options

See Also

Other parsers: cett_nodes_options(), parseDrugBank(), references_node_options()

parseDrugBank

Description

parses given DrugBank XML database into a dvobject. dvobject is a list of data.frames in which each data.frame represents a part of parsed data (i.e drugs, prices, carriers, ...)

Usage

parseDrugBank(
  db_path,
  drug_options = NULL,
  parse_salts = FALSE,
  parse_products = FALSE,
  references_options = NULL,
  cett_options = NULL
)

Arguments

db_path

string, full path for the DrugBank xml or zip file.
drug_options

character vector, list of sub drug related nodes names options to parse (default = NULL). Check drug_node_options() for all available options. If its value is 'NULL' ONLY 'drug_general_information' will be placed in the returned dvobject.
parse_salts

boolean, parse salts info (default = FALSE)
parse_products

boolean, parse products info (default = FALSE)
references_options

character vector, list of sub references related nodes names options to parse (default = NULL). Check references_node_options() for all available options.
cett_options

character vector, list of sub cett related nodes names options to parse (default = NULL). Check cett_nodes_options() for all available options.

Value

dvobject

See Also

Other parsers: cett_nodes_options(), drug_node_options(), references_node_options()

returns references node valid options.

Description

returns references node valid options.

Usage

references_node_options()

Value

list of references valid options

See Also

Other parsers: cett_nodes_options(), drug_node_options(), parseDrugBank()

init_dvobject Returns data.frame with two columns (key, value) of dvobject attributes

Description

init_dvobject Returns data.frame with two columns (key, value) of dvobject attributes

Usage

show_dvobject_metadata(dvobject)

Arguments

dvobject

- dvobject list to show related metadata

Value

data.frame