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
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 | |
| No Results! | ||
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 | ||
| No Results! | ||
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