In Dainanahan/dbdataset: DrugBank parsed datasets in R data format

knitr::opts_chunk$set(
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Overview

dbdataset is a data package containing dvobject R object. dvobjectcontains lists of different dataframes of the parsed DrugBank database. dvobject has been built using dbparser R package.

dvobject can be used for conveniently exploring and analyzing the contents of the DrugBank database. dvobject 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

Although dvobject is much smaller that the unparsed DrugBank database size, it still exceeds the limit set by CRAN. So, it will be hosted on Github only for now. Hence, it could be installed via the following command.

devtools::install_github("interstellar-Consultation-Services/dbdataset")

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

library(dbdataset)

Then a dvobject called drugbank will be available to be used as regular R object

dvobject Structure

dvobject introduces a unified and compressed format of drugs data. It is an R list object that contains one or more of the following sub-lists:

names(dbdataset::drugbank)

The following is the definition for each sub-list:

drugs

A list of data.frames that contain drugs information (i.e. synonyms, classifications, …) and it is the only mandatory list

names(dbdataset::drugbank[["drugs"]])

drugs

A data.frame contains drugs salts information

head(dbdataset::drugbank[["salts"]], 5)

products

A data.frame of commercially available drugs products in the world

head(dbdataset::drugbank[["products"]], 5)

references

A list of data.frames of articles, links and textbooks about drugs or CETT data

names(dbdataset::drugbank[["references"]])

cett

A list of data.frames contain targets, enzymes, carriers and transporters information

names(dbdataset::drugbank[["cett"]])

Package Version

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

Dainanahan/dbdataset documentation built on April 23, 2024, 2:24 a.m.