In MohammedFCIS/covid19dbcand: Selected 'Drugbank' Drugs for COVID-19 Treatment Related Data in R Format

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Overview

covid19dbcand is a data package containing different tibbles that constitute the dataset parsed from DrugBank. The dataset was extracted from the DrugBank XML database via dbparser R package.

The dataset can be used for conveniently exploring and analyzing the contents of the DrugBank database. The dataset is also intended to assist in drug discovery endeavors that plan to make use of the DrugBank database.

Moreover; it also can be used to in Machine Learning in many sub-fields such as:

• Natural Language Processing (NLP)
• Web Scrapping
• Visualization

Installation

As the package size exceeds the limit set by CRAN, it will be hosted on Github only for now. Hence, it could be installed via the following command.

devtools::install_github("MohammedFCIS/covid19dbcand")

The datasets will then be available after running the following command:

library(covid19dbcand)

Then the pakages will be available to be used as regular R object

head(covid19dbcand::Articles_Drug)

head(covid19dbcand::Drugs)

head(covid19dbcand::Drugs_Pathway_Drug)

The 74 object names are listed in the next section and can be used immediately as any regular R dataframe.

Package Version

The package version will always be the same as the DrugBank database used.

Naming Convention

Each data frame is named based on its position in DrugBank's data hierarchy. For example:

• Drugs: is the master data frame at the root of the hierarchy that contains the list of all drugs in DrugBank.
• Enzymes_Drug: is the data frame containing the enzymes info pertaining to the drugs in the Drugs data frame. In other words,
• Enzymes: is a child of Drug in the hierarchy (i.e. Drug --> Enzymes).
• Enzymes_Pathway_Drug: is the data frame containing the enzymes info pertaining to the pathways that the drugs in Drugs are involved in (i.e. Drug --> Pathways --> Enzymes).

Dataset Contents

The following are the datasets in our package

DT::datatable(data(package = "covid19dbcand")[["results"]][,c(3,4)])

Dataset Hierarchy

The following illustrates how the datasets are related to each other:

library(data.tree)
library(networkD3)
# search for salts, international-brands
# Main node
build_drug_bank_tree <- function() {
  drug <- Node$new("Drugs")
  drug$AddChild("Groups")
  drug$AddChild("Pharmacology")
  references <- drug$AddChild("References")

  references$AddChild("Articles")
  references$AddChild("Books")
  references$AddChild("Links")
  references$AddChild("Attachments")

  drug$AddChild("Classification")
  drug$AddChild("Calculated Properties")
  drug$AddChild("Synonyms")
  drug$AddChild("Products")
  drug$AddChild("Mixtures")
  drug$AddChild("Packagers")
  drug$AddChild("Manufacturers")
  drug$AddChild("Prices")
  drug$AddChild("Categories")
  drug$AddChild("Affected Organisms")
  drug$AddChild("Dosages")
  drug$AddChild("ATC")
  drug$AddChild("AHFS")
  drug$AddChild("PDB Entries")
  drug$AddChild("Patents")
  drug$AddChild("PDB Entries")
  drug$AddChild("international_brands")
  drug$AddChild("salts")

  interactions <- drug$AddChild("Interactions")
  interactions$AddChild("Food")
  interactions$AddChild("Drugs")

  drug$AddChild("Sequences")
  drug$AddChild("Experimental Properties")
  drug$AddChild("External Identifiers")
  drug$AddChild("External Links")

  pathways <- drug$AddChild("Pathways")
  pathways$AddChild("Drugs")
  pathways$AddChild("Enzymes")

  reactions <- drug$AddChild("Reactions")
  reactions$AddChild("Reactions Enzymes")

  drug$AddChild("SNP Effects")
  drug$AddChild("SNP Adverse DRs")

  targets <- drug$AddChild("Targets")
  targets$AddChild("Actions")

  targets_references <- targets$AddChild("References")
  targets_references$AddChild("Articles")
  targets_references$AddChild("Books")
  targets_references$AddChild("Links")
  targets_references$AddChild("Attachments")

  targets_polypeptides <- targets$AddChild("Polypeptides")
  targets_polypeptides$AddChild("External Identifiers")
  targets_polypeptides$AddChild("GO Classifiers")
  targets_polypeptides$AddChild("PFAMS")
  targets_polypeptides$AddChild("Synonyms")

  enzymes <- drug$AddChild("Enzymes")
  enzymes$AddChild("Actions")
  enzymes_references <- enzymes$AddChild("References")
  enzymes_references$AddChild("Articles")
  enzymes_references$AddChild("Books")
  enzymes_references$AddChild("Links")
  enzymes_references$AddChild("Attachments")
  enzymes_polypeptides <- enzymes$AddChild("Polypeptides")
  enzymes_polypeptides$AddChild("External Identifiers")
  enzymes_polypeptides$AddChild("GO Classifiers")
  enzymes_polypeptides$AddChild("PFAMS")
  enzymes_polypeptides$AddChild("Synonyms")

  carriers <- drug$AddChild("Carriers")
  carriers$AddChild("Actions")
  carriers_references <- carriers$AddChild("References")
  carriers_references$AddChild("Articles")
  carriers_references$AddChild("Books")
  carriers_references$AddChild("Links")
  carriers_references$AddChild("Attachments")
  carriers_polypeptides <- carriers$AddChild("Polypeptides")
  carriers_polypeptides$AddChild("External Identifiers")
  carriers_polypeptides$AddChild("GO Classifiers")
  carriers_polypeptides$AddChild("PFAMS")
  carriers_polypeptides$AddChild("Synonyms")

  transporters <- drug$AddChild("Transporters")
  transporters$AddChild("Actions")
  transporters_references <- transporters$AddChild("References")
  transporters_references$AddChild("Articles")
  transporters_references$AddChild("Books")
  transporters_references$AddChild("Links")
  transporters_references$AddChild("Attachments")
  transporters_polypeptides <- transporters$AddChild("Polypeptides")
  transporters_polypeptides$AddChild("External Identifiers")
  transporters_polypeptides$AddChild("GO Classifiers")
  transporters_polypeptides$AddChild("PFAMS")
  transporters_polypeptides$AddChild("Synonyms")

  return(drug)
}

radialNetwork(
  ToListExplicit(build_drug_bank_tree(), unname = TRUE))

MohammedFCIS/covid19dbcand documentation built on April 14, 2024, 10:28 a.m.