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dbparser

Introduction

DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets. As both a bioinformatics and a cheminformatics resource, DrugBank combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. More information about DrugBank can be found here.

In its raw form, the DrugBank database is a single XML file. Users must create an account with DrugBank and request permission to download the database. Note that this may take a couple of days.

The dbparser package parses the DrugBank XML database into R tibbles that can be explored and analyzed by the user, check this tutorial for more details.

Also, the package offers the option to save these tibbles in databases including SQL Server DB and Maria DB just by enabling save_table option, check this tutorial for more details.

If you are waiting for access to the DrugBank database, or do not intend to do a deep dive with the data, you may wish to use the dbdataset package, which contains the DrugBank database already parsed into R tibbles. Note that this is a large package that exceeds the limit set by CRAN. It is only available on GitHub.

dbparser is tested against DrugBank versions 5.1.0 through 5.1.4 successfully. If you find errors with these versions or any other version please submit an issue here.

Installation

You can install the released version of dbparser from CRAN with:

install.packages("dbparser")

or you can install the latest updates directly from the repo

library(devtools)
devtools::install_github("ropensci/dbparser")

Code of Conduct

Please note that the ‘dbparser’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Contributing Guide

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Version

Install

install.packages('dbparser')

Monthly Downloads

735

Version

1.1.1

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/ropensci/dbparser

Homepage

https://docs.ropensci.org/dbparser

Maintainer

Mohammed Ali

Last Published

February 16th, 2024

Functions in dbparser (1.1.1)

Extracts the drug carriers element and return data as tibble.

carriers_polypeptides_syn

Extracts the drug carriers polypeptides syn element and return data as tibble.

drug_pathway_enzyme

Extracts the drug pathway enzyme element and return data as tibble.

drug_ahfs_codes

Extracts the drug ahfs codes element and return data as tibble.

extracts the given drug elements and return data as list of tibbles.

drug_element_options

returns drug_element valid options.

drug_pdb_entries

Extracts the drug pdb entries element and return data as tibble.

dbparser: A package for reading and parsing DrugBank xml database.

carriers_textbooks

Extracts the drug carriers textbooks element and return data as tibble.

Extracts the main drug elements and return data as tibble.

carriers_actions

Extracts the drug carriers actions element and return data as tibble.

drug_classification

Extracts the drug classifications element and return data as tibble.

Extracts the drug dosages element and return data as tibble.

drug_reactions_enzymes

Extracts the drug reactions enzymes element and return data as tibble.

Extracts the drug reactions element and return data as tibble.

drug_pathway_drugs

Extracts the drug pathway drugs element and return data as tibble.

extracts the all drug elements and return data as list of tibbles.

Extracts the drug pathway element and return data as tibble.

enzymes_textbooks

Extracts the drug enzymes textbooks element and return data as tibble.

Extracts the drug calculated properties element and return data as tibble.

Extracts the drug articles element and return data as tibble.

drug_categories

Extracts the drug categories element and return data as tibble.

get_drugbank_exported_date

Return uploaded drugbank database exported date

targets_actions

Extracts the drug targ actions element and return data as tibble.

Extracts the drug prices element and return data as tibble.

transporters_articles

Extracts the drug transporters articles element and return data as tibble.

transporters_actions

Extracts the drug transporters actions element and return data as tibble.

targets_articles

Extracts the drug targ articles element and return data as tibble.

Extracts the drug products element and return data as tibble.

drug_food_interactions

Extracts the drug food interactions element and return data as tibble.

drug_ex_identity

Extracts the drug external identifiers element and return data as tibble.

drug_external_links

Extracts the drug external links element and return data as tibble.

Extracts the drug experimental properties element and return data as tibble.

drug_intern_brand

Extracts the drug international brands and return data as tibble.

drug_interactions

Extracts the drug interactions element and return data as tibble.

Extracts the drug packagers element and return data as tibble.

Extracts the drug groups element and return data as tibble.

drug_manufacturers

Extracts the drug manufacturers element and return data as tibble.

enzymes_actions

Extracts the drug enzymes actions element and return data as tibble.

Extracts the drug links element and return data as tibble.

enzymes_articles

Extracts the drug enzymes articles element and return data as tibble.

targets_polypeptide_ext_ident

Extracts the drug targ polypeptides external identifiers element and return data as tibble.

targets_polypeptide_pfams

Extracts the drug targ polypeptides pfams element and return data as tibble.

targets_polypeptide_go

Extracts the drug targ polypeptides go classifiers element and return data as tibble.

Extracts the drug patents element and return data as tibble.

targets_polypeptide_syn

Extracts the drug targ polypeptides syn element and return data as tibble.

enzymes_polypeptide_ext_ident

Extracts the drug enzymes polypeptides external identifiers element and return data as tibble.

drug_snp_effects

Extracts the drug snp effects element and return data as tibble.

drug_snp_adverse_reactions

Extracts the drug snp adverse drug reactions element and return data as tibble.

enzymes_polypeptide_go

Extracts the drug groups element and return data as tibble.

Extracts the drug syn element and return data as tibble.

read_drugbank_xml_db

Reads DrugBank xml database and load it into memory.

Extracts the drug enzymes element and return data as tibble.

enzymes_polypeptide_syn

Extracts the drug enzymes polypeptides syn element and return data as tibble.

enzymes_polypeptide_pfams

Extracts the drug enzymes polypeptides pfams element and return data as tibble.

Extracts the drug targ element and return data as tibble.

targets_textbooks

Extracts the drug targ textbooks element and return data as tibble.

Extracts the drug targ links element and return data as tibble.

targets_polypeptide

Extracts the drug targ polypeptides element and return data as tibble.

Extracts the drug mixtures element and return data as tibble.

Extracts the drug transporters element and return data as tibble.

transporters_polypeptide

Extracts the drug transporters polypeptides element and return data as tibble.

Extracts the drug salts and return data as tibble.

get_drugbank_metadata

Return uploaded drugbank database metadata

Extracts the drug enzymes links element and return data as tibble.

Extracts the drug sequences element and return data as tibble.

transporters_textbooks

Extracts the drug transporters textbooks element and return data as tibble.

enzymes_polypeptide

Extracts the drug enzymes polypeptides element and return data as tibble.

get_drugbank_version

Return uploaded drugbank database version

transporters_links

Extracts the drug transporters links element and return data as tibble.

transporters_polypep_ex_ident

Extracts the drug transporters polypeptides external identifiers element and return data as tibble.

transporters_polypeptide_pfams

Extracts the drug transporters polypeptides pfams element and return data as tibble.

transporters_polypeptide_go

Extracts the drug transporters polypeptides go classifiers element and return data as tibble.

transporters_polypeptide_syn

Extracts the drug transporters polypeptides syn element and return data as tibble.

Extracts the drug carriers links element and return data as tibble.

carriers_polypeptide_ext_id

Extracts the drug carriers polypeptides external identifiers element and return data as tibble.

carriers_polypeptides_pfams

Extracts the drug carriers polypeptides pfams element and return data as tibble.

carriers_polypeptide

Extracts the drug carriers polypeptides element and return data as tibble.

carriers_polypeptides_go

Extracts the drug carriers polypeptides go classifiers element and return data as tibble.

carriers_articles

Extracts the drug carriers articles element and return data as tibble.

drug_affected_organisms

Extracts the drug affected organisms element and return data as tibble.

Extracts the drug atc codes element and return data as tibble.

Extracts the drug books element and return data as tibble.