# covid19dbcand

## 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)
    #>    ref-id pubmed-id
    #> 1    A165  17409907
    #> 2 A192825  28801849
    #> 3 A192828  27329360
    #> 4 A192831  29798953
    #> 5 A192834  30030240
    #> 6 A192837  11970755
    #>                                                                                                                                                                                                                                                                                     citation
    #> 1                                                        Velcheti V, Viswanathan A, Govindan R: The proportion of patients with metastatic non-small cell lung cancer potentially eligible for treatment with bevacizumab: a single institutional survey. J Thorac Oncol. 2006 Jun;1(5):501.
    #> 2                                                                                        Rosen LS, Jacobs IA, Burkes RL: Bevacizumab in Colorectal Cancer: Current Role in Treatment and the Potential of Biosimilars. Target Oncol. 2017 Oct;12(5):599-610. doi: 10.1007/s11523-017-0518-1.
    #> 3            Han K, Peyret T, Marchand M, Quartino A, Gosselin NH, Girish S, Allison DE, Jin J: Population pharmacokinetics of bevacizumab in cancer patients with external validation. Cancer Chemother Pharmacol. 2016 Aug;78(2):341-51. doi: 10.1007/s00280-016-3079-6. Epub 2016 Jun 21.
    #> 4 Apsangikar PD, Chaudhry SR, Naik MM, Deoghare SB, Joseph J: Comparative pharmacokinetics, efficacy, and safety of bevacizumab biosimilar to reference bevacizumab in patients with metastatic colorectal cancer. Indian J Cancer. 2017 Jul-Sep;54(3):535-538. doi: 10.4103/ijc.IJC_394_17.
    #> 5                                                                                              Karaman S, Leppanen VM, Alitalo K: Vascular endothelial growth factor signaling in development and disease. Development. 2018 Jul 20;145(14). pii: 145/14/dev151019. doi: 10.1242/dev.151019.
    #> 6                                           Verheul HM, Pinedo HM: The role of vascular endothelial growth factor (VEGF) in tumor angiogenesis and early clinical development of VEGF-receptor kinase inhibitors. Clin Breast Cancer. 2000 Sep;1 Suppl 1:S80-4. doi: 10.3816/cbc.2000.s.015.
    #>   parent_key
    #> 1    DB00112
    #> 2    DB00112
    #> 3    DB00112
    #> 4    DB00112
    #> 5    DB00112
    #> 6    DB00112

    head(covid19dbcand::Drugs)
    #>   primary_key         other_keys           type    created    updated
    #> 1     DB00112 BTD00087;BIOD00087        biotech 2005-06-13 2020-07-01
    #> 2     DB00207          APRD00397 small molecule 2005-06-13 2020-07-01
    #> 3     DB00503          APRD00312 small molecule 2005-06-13 2020-07-01
    #> 4     DB00608          APRD00468 small molecule 2005-06-13 2020-07-01
    #> 5     DB00959          APRD00342 small molecule 2005-06-13 2020-07-01
    #> 6     DB01050          APRD00372 small molecule 2005-06-13 2020-07-01
    #>                 name
    #> 1        Bevacizumab
    #> 2       Azithromycin
    #> 3          Ritonavir
    #> 4        Chloroquine
    #> 5 Methylprednisolone
    #> 6          Ibuprofen
    #>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       description
    #> 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      There is a great deal of evidence indicating that vascular endothelial growth factor (VEGF) is important for the survival and proliferation of cancer cells.[A192939,A192837,A192891,A193275] VEGF plays an important role in angiogenesis, lymphangiogenesis, and tumor growth, which are all factors that contribute to its attractiveness as a therapeutic target for anti-cancer therapies.[A192834,A192888,A192837,A192891,A192894] \r\n\r\nIn 2004, bevacizumab (Avastin) gained FDA approval for specific types of cancer, and became the first antiangiogenic agent introduced to the market.[A193272,A193275] It is a humanized monoclonal IgG antibody, and inhibits angiogenesis by binding and neutralizing VEGF-A.[A192888,A192939] Bevacizumab is generally indicated for use in combination with different chemotherapy regimens which are specific to the type, severity, and stage of cancer.[L12648] \r\n\r\nInterestingly, researchers have identified higher VEGF expression in patients with COVID-19, which may contribute to lung pathologies including acute respiratory syndrome (ARDS) and acute lung injury (ALI).[L12699] As such, bevacizumab is being investigated for the treatment of lung complications associated with severe cases of COVID-19.[L12699]
    #> 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Azithromycin is a broad-spectrum macrolide antibiotic with a long half-life and a high degree of tissue penetration [A174172]. It was initially approved by the FDA in 1991 [A174175].\r\n\r\nIt is primarily used for the treatment of respiratory, enteric and genitourinary infections and may be used instead of other macrolides for some sexually transmitted and enteric infections. It is structurally related to erythromycin [A174169].\r\n\r\nAzithromycin [9-deoxo-9a-aza-9a-methyl-9a-homoerythromycin] is a part of the _azalide_ subclass of macrolides, and contains a 15-membered ring, with a methyl-substituted nitrogen instead of a carbonyl group at the 9a position on the aglycone ring, which allows for the prevention of its metabolism. This differentiates azithromycin from other types of macrolides [A174175].\r\n\r\nIn March 2020, a small study was funded by the French government to investigate the treatment of COVID-19 with a combination of azithromycin and the anti-malaria drug [hydroxychloroquine]. The results were positive, all patients taking the combination were virologically cured within 6 days of treatment, however, larger studies are required.[A192546]
    #> 3 Ritonavir is an HIV protease inhibitor that interferes with the reproductive cycle of HIV. Although it was initially developed as an independent antiviral agent, it has been shown to possess advantageous properties in combination regimens with low-dose ritonavir and other protease inhibitors. It is now more commonly used as a booster of other protease inhibitors and is available in both liquid formulation and as capsules. \r\n\r\nWhile ritonavir is not an active antiviral agent against hepatitis C virus (HCV) infection, it is added in combination therapies indicated for treatment of HCV infections as a booster. Ritonavir is a potent CYP3A inhibitor that increases peak and trough plasma drug concentrations of other protease inhibitors such as [DB09297] and overall drug exposure. American Association for the Study of Liver Diseases (AASLD) and the Infectious Diseases Society of America (IDSA) guidelines recommend ritonavir-boosted combination therapies as a first-line therapy for HCV Genotype 1a/b and 4 treatment-na\032ve patients with or without cirrhosis. \r\n\r\nRitonavir is found in a fixed-dose combination product with [DB09296], [DB09183], and [DB09297] as the FDA-approved product Viekira Pak. First approved in December 2014, Viekira Pak is indicated for the treatment of HCV genotype 1b without cirrhosis or with compensated cirrhosis, and when combined with Ribavirin for the treatment of HCV genotype 1a without cirrhosis or with compensated cirrhosis.\r\n\r\nRitonavir is also available as a fixed-dose combination product with [DB09296] and [DB09297] as the FDA- and Health Canada-approved product Technivie. First approved in July 2015, Technivie is indicated in combination with Ribavirin for the treatment of patients with genotype 4 chronic hepatitis C virus (HCV) infection without cirrhosis or with compensated cirrhosis.\r\n\r\nIn Canada, ritonavir is also available as a fixed-dose combination product with [DB09296], [DB09183], and [DB09297] as the Health Canada-approved, commercially available product Holkira Pak. First approved in January 2015, Holkira Pak is indicated for the treatment of HCV genotype 1b with or without cirrhosis, and when combined with Ribavirin for the treatment of HCV genotype 1a with or without cirrhosis. Inclusion of ritonavir can can select for HIV-1 protease inhibitor resistance-associated substitutions. Any HCV/HIV-1 co-infected patients treated with ritonavir-containing combination therapies should also be on a suppressive antiretroviral drug regimen to reduce the risk of HIV-1 protease inhibitor drug resistance.
    #> 4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Chloroquine is an aminoquinolone derivative first developed in the 1940s for the treatment of malaria.[A191655] It was the drug of choice to treat malaria until the development of newer antimalarials such as [pyrimethamine], [artemisinin], and [mefloquine].[A191787] Chloroquine and its derivative [hydroxychloroquine] have since been repurposed for the treatment of a number of other conditions including HIV, systemic lupus erythematosus, and rheumatoid arthritis.[A192432]\r\n\r\n**The FDA emergency use authorization for [hydroxychloroquine] and chloroquine in the treatment of COVID-19 was revoked on 15 June 2020.[L14312]**\r\n\r\nChloroquine was granted FDA Approval on 31 October 1949.[L12054]
    #> 5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Methylprednisolone is a [prednisolone] derivative glucocorticoid with higher potency than [prednisone].[A188811] It was first described in the literature in the late 1950s.[A188811,A188814]\r\n\r\nMethylprednisolone was granted FDA approval on 24 October 1957.[L10785] In the outbreak of COVID-19, low dose methylprednisolone-based therapy was successful in treating COVID-19-associated pneumonia in one patient with long-term immunosuppression.[A192813] The efficacy of methylprednisolone in novel coronavirus pneumonia is being investigated further in clinical trials.[L12666]
    #> 6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Ibuprofen is a non-steroidal anti-inflammatory drug (NSAID) derived from propionic acid and it is considered the first of the propionics.[A39074] The formula of ibuprofen is 2-(4-isobutylphenyl) propionic acid and its initial development was in 1960 while researching for a safer alternative for aspirin.[A39075] Ibuprofen was finally patented in 1961 and this drug was first launched against rheumatoid arthritis in the UK in 1969 and USA in 1974. It was the first available over-the-counter NSAID.[A39076]\r\n\r\nOn the available products, ibuprofen is administered as a racemic mixture. Once administered, the R-enantiomer undergoes extensive interconversion to the S-enantiomer _in vivo_ by the activity of the alpha-methylacyl-CoA racemase. In particular, it is generally proposed that the S-enantiomer is capable of eliciting stronger pharmacological activity than the R-enantiomer.[A39194]
    #>    cas_number       unii average_mass monoisotopic_mass  state
    #> 1 216974-75-3 2S9ZZM9Q9V         <NA>              <NA> liquid
    #> 2  83905-01-5 J2KLZ20U1M     748.9845     748.508525778  solid
    #> 3 155213-67-5 O3J8G9O825      720.944     720.312760056  solid
    #> 4     54-05-7 886U3H6UFF      319.872     319.181525554  solid
    #> 5     83-43-2 X4W7ZR7023     374.4706      374.20932407  solid
    #> 6  15687-27-1 WK2XYI10QM     206.2808      206.13067982  solid
    #>                                                                                                                                                                                            synthesis_reference
    #> 1                                                                                                                                                                                                         <NA>
    #> 2                                                         William Heggie, Zita Maria De Mouro Vaz Azevedo Mendes, "Process for the preparation of azithromycin." U.S. Patent US6013778, issued November, 1994.
    #> 3                                                                                                                                                                                                         <NA>
    #> 4                                                                             Andersag, H., Breitner, S.and Jung, H.; U S . Patent 2,233,970; March 4,1941; assigned to\r\nWinthrop Chemical Company, Inc.\r\n
    #> 5 Klaus Annen, Karl Petzoldt, Henry Laurent, Rudolf Wiechert, Helmut Hofmeister, "Novel 6.alpha.-methylprednisolone derivatives, their preparation, and their use." U.S. Patent US4587236, issued March, 1973.
    #> 6                                                                                                                                                                                                         <NA>
    #>                                                                 fda_label
    #> 1 //s3-us-west-2.amazonaws.com/drugbank/fda_labels/DB00112.pdf?1265922813
    #> 2                                                                    <NA>
    #> 3 //s3-us-west-2.amazonaws.com/drugbank/fda_labels/DB00503.pdf?1497888352
    #> 4 //s3-us-west-2.amazonaws.com/drugbank/fda_labels/DB00608.pdf?1265922797
    #> 5 //s3-us-west-2.amazonaws.com/drugbank/fda_labels/DB00959.pdf?1265922799
    #> 6 //s3-us-west-2.amazonaws.com/drugbank/fda_labels/DB01050.pdf?1265922800
    #>                                                                msds
    #> 1                                                              <NA>
    #> 2 //s3-us-west-2.amazonaws.com/drugbank/msds/DB00207.pdf?1548453627
    #> 3 //s3-us-west-2.amazonaws.com/drugbank/msds/DB00503.pdf?1497888312
    #> 4 //s3-us-west-2.amazonaws.com/drugbank/msds/DB00608.pdf?1265922737
    #> 5 //s3-us-west-2.amazonaws.com/drugbank/msds/DB00959.pdf?1265922739
    #> 6 //s3-us-west-2.amazonaws.com/drugbank/msds/DB01050.pdf?1265922739

    head(covid19dbcand::Drugs_Pathway_Drug)
    #>   drugbank-id                name parent_key
    #> 1     DB00112         Bevacizumab SMP0000420
    #> 2     DB00117           Histidine SMP0000247
    #> 3     DB00131 Adenosine phosphate SMP0000247
    #> 4     DB00134          Methionine SMP0000247
    #> 5     DB00149             Leucine SMP0000247
    #> 6     DB00156           Threonine SMP0000247

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

## Dataset Hierarchy

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