dbparser v1.2.0

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'DrugBank' Database XML Parser

This tool is for parsing the 'DrugBank' XML database <https://www.drugbank.ca/>. The parsed data are then returned in a proper 'R' dataframe with the ability to save them in a given database.

Readme

dbparser

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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 5.1.6 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

Functions in dbparser

Name Description
cett_poly_pfms_doc Carriers/ Enzymes/ Targets/ Transporters Polypeptide PFAMS parsers
cett_doc Carriers/ Enzymes/ Targets/ Transporters parsers
cett Run all CETT related parsers
cett_ex_identity_doc Carriers/ Enzymes/ Targets/ Transporters Polypeptide External Identifiers parsers
cett_actions_doc Carriers/ Enzymes/ Targets/ Transporters Actions parsers
cett_go_doc Carriers/ Enzymes/ Targets/ Transporters Polypeptide GO Classifier parsers
cett_poly_doc Carriers/ Enzymes/ Targets/ Transporters Polypeptide parsers
books Drugs/ Carriers/ Enzymes/ Targets/ Transporters books element parser
attachments Drugs/ Carriers/ Enzymes/ Targets/ Transporters attachments element parser
articles Drugs/ Carriers/ Enzymes/ Targets/ Transporters articles element parser
drug_dosages Drug Dosages parser
drug_atc_codes Drug ATC Codes element parser
drug_calc_prop Drug Calculated Properties parser
drug_affected_organisms Drug Affected Organism parser
dbparser dbparser: A package for reading and parsing DrugBank xml database.
cett_poly_syn_doc Carriers/ Enzymes/ Targets/ Transporters Polypeptide Synonyms parsers
drug_manufacturers Drug Manufacturers parser
drug_intern_brand Drug International Brands parser
drug_categories Drug Categories parser
drug_general_information Drugs General Information parser
drug_classification Drug Classification parser
drug_food_interactions Drug Groups parser
drug_exp_prop Drug Experimental Properties parser
drug_external_links Drug External Links parser
drug_ahfs_codes Drug ahfs-codes parser
drug_element extracts the given drug elements and return data as list of tibbles.
drug_mixtures Drug Mixtures parser
drug_packagers Drug Packagers parser
drug_groups Drug Groups parser
drug_interactions Drug Interactions parser
drug_element_options returns drug_element valid options.
drug_pathway_drugs Drug Pathway Drugs parser
drug_pdb_entries Drug pdb-entries parser
drugs Run all drug related parsers
drug_syn Drug Synonyms parser
get_drugbank_version Return uploaded drugbank database version
links Drugs/ Carriers/ Enzymes/ Targets/ Transporters links element parser
drug_patents Drug Patents parser A property right issued by the United States Patent and Trademark Office (USPTO) to an inventor for a limited time, in exchange for public disclosure of the invention when the patent is granted. Drugs may be issued multiple patents.
drug_snp_effects Drug SNP Effects parser
drug_snp_adverse_reactions Drug SNP Adverse Drug Reactions parser
drug_pharmacology Drug Pharmacology parser
get_drugbank_metadata Return uploaded drugbank database metadata
read_drugbank_xml_db Reads DrugBank xml database and load it into memory.
get_drugbank_exported_date Return uploaded drugbank database exported date
drug_prices Drug Prices Parsers
drug_ex_identity Drug External Identifiers parser
drug_products Drug Products parser
drug_pathway_enzyme Drug Pathway Enzymes parser
drug_reactions Drug Reactions Parsers
drug_reactions_enzymes Drug Reactions Enzymes Parsers
drug_pathway Drug Pathway parser
drug_sequences Drug Sequences parser
drug_salts Drug Salts parser
run_all_parsers extracts the all drug elements and return data as list of tibbles.
references Drugs/ Carriers/ Enzymes/ Targets/ Transporters references element parser
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Vignettes of dbparser

Name
Database_Saving.Rmd
dbparser.Rmd
fig1.png
fig2.png
fig3.png
maria_tables.png
new_database.png
new_database_2.png
sql_connection.png
sql_tables.png
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