| Type: | Package |
| Title: | Selected 'Drugbank' Drugs for COVID-19 Treatment Related Data in R Format |
| Version: | 0.1.1 |
| Depends: | R (≥ 3.1) |
| Maintainer: | Mohammed Ali <moh_fcis@yahoo.com> |
| Description: | Provides different datasets parsed from 'Drugbank' https://www.drugbank.ca/covid-19 database using 'dbparser' package. It is a smaller version from 'dbdataset' package. It contains only information about COVID-19 possible treatment. |
| License: | CC0 |
| Encoding: | UTF-8 |
| LazyData: | true |
| URL: | https://github.com/MohammedFCIS/covid19dbcand |
| BugReports: | https://github.com/MohammedFCIS/covid19dbcand/issues |
| Suggests: | knitr, rmarkdown, data.tree, DT, networkD3 |
| VignetteBuilder: | knitr |
| RoxygenNote: | 7.1.0 |
| NeedsCompilation: | no |
| Packaged: | 2020-08-25 16:11:33 UTC; Mohammed |
| Author: | Mohammed Ali [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2020-08-26 12:30:02 UTC |
The American Hospital Formulary Service (AHFS) identifier for Drugs
Description
A list of the American Hospital Formulary Service (AHFS) identifier for drugs
Usage
AHFS_Codes_Drug
Format
a tibble with 2 variables:
- text
ahfs code
- parent_id
drugbank id
Source
Drug related ATC Codes
Description
The Anatomical Therapeutic Classification (ATC) code for the drug assigned by the World Health Organization Anatomical Chemical Classification System.
Usage
ATC_Codes_Drug
Format
a tibble with 4 variables:
- atc_code
drug related atc code
- level_n
atc-code related level_n
- code_n
atc-code and level_n related code_n
- drugbank-id
drugbank id
Details
Each drug may have one or more atc-code.
Each atc-code has one or more level.
The atc-code and level elements each have a code which specifies the code assigned by World Health Organization Anatomical Chemical Classification System.
Source
Drug related Affected Organisms
Description
A list of organisms in which the drug may display activity; activity may depend on local susceptibility patterns and resistance.
Usage
Affected_Organisms_Drug
Format
a tibble with 2 variables:
- text
affected organism description
- parent_id
drugbank id
Source
Drug Calculated Properties
Description
Drug properties that have been predicted by ChemAxon or ALOGPS based on the imputed chemical structure. Associated links below will redirect to descriptions of the specific term.
Usage
Calculated_Properties_Drug
Format
a tibble with 3 variables:
- kind
Name of the property
- value
Predicted physicochemical properties; obtained by the use of prediction software such as ALGOPS and ChemAxon
- source
Name of the software used to calculate this property, either ChemAxon or ALOGPS
- parent_key
drugbank id
Details
Each drug may have one or more calculated property.
The following calculated properties are provided:
| Property | Description |
| logP | The predicted partition coefficient (LogP) based on the ratio of solubility of the molecule in 1-octanol compared to water; predicted by ALOGPS |
| logS | The predicted solubility (LogS) of the molecule; predicted by ALOGPS. |
| IUPAC Name | The predicted International Union of Pure and Applied Chemistry (IUPAC) nomenclature for the structure; predicted by ChemAxon |
| Traditional IUPAC Name | The non-systematic (or common) name for the molecule, which is not recognized by any formal nomenclature system; imported from ChemAxon. |
| Molecular Weight | The predicted ratio of the average mass of one molecule of an element or compound to one twelfth of the mass of an atom of carbon-12; calculated by ChemAxon. |
| Monoisotopic Weight | The predicted mass of the most abundant isotope of the drug; calculated by ChemAxon. |
| SMILES | The simplified molecular-input line-entry system (SMILES) is a line notation used for describing the structure of chemical species using short ASCII strings; calculated by ChemAxon. |
| InChI | A prediction of the IUPAC International Chemical Identifier (InChI); imported by ChemAxon. |
| InChIKey | The condensed digital representation of the IUPAC International Chemical Identifier (InChI); imported by ChemAxon. |
| Polar Surface Area (PSA) | A descriptor, based on the polarized atoms of the molecule, that allows estimation of transport properties and of the passive molecular transport through membranes of the drug; predicted by ChemAxon. |
| Refractivity | The predicted molar refractivity of the molecule, which is strongly related to the volume of the molecules and to London dispersive forces that play crucial part in drug-receptor interactions; predicted by ChemAxon. |
| Polarizability | The predicted relative tendency of the electron cloud (charge distribution) of the molecule to be distorted by an external electric field; polarizability values predicted by ChemAxon. |
| Rotatable Bond Count | The predicted number of rotatable bonds in the molecule; predicted by ChemAxon. Unsaturated bonds, and single bonds connected to hydrogens or terminal atoms, single bonds of amides, sulphonamides and those connecting two hindered aromatic rings (having at least three ortho substituents) are considered non-rotatable. |
| H Bond Acceptor Count | A calculation of the sum of the hydrogen bond acceptor atoms. An acceptor atom always has a lone electron pair/lone electron pairs that is capable of establishing a H bond. Predicted by ChemAxon. |
| H Bond Donor Count | A calculation of the sum of the atoms in the molecule which have hydrogen bond donor property. Predicted by ChemAxon. |
| pKa (strongest acidic) | The strongest acidic pka value of the molecule; predicted by ChemAxon. |
| pKa (strongest basic) | The strongest basic pka value of the molecule; predicted by ChemAxon. |
| Physiological Charge | Charge of the molecule at physiological pH; predicted by ChemAxon. |
| Number of Rings | A calculation of the number of rings in the molecule; predicted by ChemAxon. |
| Bioavailability | Fraction of administered dose that is predicted to reach the systemic circulation; predicted by ChemAxon. |
| Rule of Five | A reflection of the absorption or permeation of a molecule; considered “yes” when the molecular weight is under 500 g/mol, the value of logP is lower than 5, and the molecule has utmost 5 H-donor and 10 H-acceptor atoms; predicted by ChemAxon. |
| Ghose Filter | A filter that defines drug-likeness constraints as follows: calculated log P is between -0.4 and 5.6, molecular weight is between 160 and 480, molar refractivity is between 40 and 130, and the total number of atoms is between 20 and 70. Imported from ChemAxon. |
| MDDR-Like Rule | Indicates compliance of drug-like characteristics based on number of rings, rigid bonds and rotatable bonds; calculated by ChemAxon. |
Source
Drug Categories General categorizations of the drug
Description
Each drug may have one or more category.
Usage
Categories_Drug
Format
a tibble with 3 variables:
- category
Category name
- mesh-id
The Medical Subjects Headings (MeSH) identifier for the category.
- parent_id
drugbank id
Source
Drug Classification
Description
A description of the hierarchical chemical classification of the drug; imported from ClassyFire.
Usage
Classifications_Drug
Format
a tibble with 9 variables:
- description
- direct_parent
- kingdom
- superclass
- class
- subclass
- alternative_parents
One or more alternative parents
- substituents
One or more substituents
- drugbank_id
drugbank id
Source
Drug Dosages A list of the commercially available dosages of the drug.
Description
Each drug may have one or more dosage.
Usage
Dosages_Drug
Format
a tibble with 4 variables:
- form
The pharmaceutical formulation by which the drug is introduced into the body.
- route
The path by which the drug or product is taken into the body
- strength
The amount of active drug ingredient provided in the dosage
- parent_id
drugbank id
Source
Drugs
Description
Substance other than water and food that when administered by any route can cause a physiological or biological change in the body.
Usage
Drugs
Format
An object of class tbl_df (inherits from tbl, data.frame) with 33 rows and 15 columns.
Value
a tibble with 15 variables:
- primary_key
Drugbank id
- other_keys
Other identifiers that may be associated with the drug
- type
Either small molecule, or biotech. Biotech is used for any drug that is derived from living systems or organisms, usually composed of high molecular weight mixtures of protein, while small molecule describes a low molecular weight organic compound.
- name
- created
Date that this drug was first added to DrugBank.
- updated
Denotes when this drug was last updated in DrugBank.
- description
Descriptions of drug chemical properties, history and regulatory status.
- cas_number
The Chemical Abstracts Service (CAS) registry number assigned to the drug.
- unii
Unique Ingredient Identifier (UNII) of this drug.
- average_mass
The weighted average of the isotopic masses of the drug
- state
One of solid, liquid, or gas
- monoisotopic_mass
The mass of the most abundant isotope of the drug
- synthesis_reference
Citation for synthesis of the drug molecule.
- fda_label
Contains a URL for accessing the uploaded United States Food and Drug Administration (FDA) Monograph for this drug.
- msds
Contains a URL for accessing the Material Safety Data Sheet (MSDS) for this drug.
Source
Pathway Drugs Pathway Drugs Each drug may have one or more pathway and vise versa
Description
Pathway Drugs Pathway Drugs Each drug may have one or more pathway and vise versa
Usage
Drugs_Pathway_Drug
Format
a tibble with 3 variables:
- drugbank-id
- name
drug name
- parent_id
pathway id
Source
Pathway Enzymes Enzymes involved in this pathway.
Description
Each drug may have one or more pathway
Usage
Enzymes_Pathway_Drug
Format
a tibble with 2 variables:
- text
uniprot id
- parent_id
pathway id
Source
Drug Reactions Enzymes Enzymes involved in metabolizing this drug.
Description
Drug Reactions Enzymes Enzymes involved in metabolizing this drug.
Usage
Enzymes_Reactions_Drug
Format
a tibble with 3 variables:
- drugbank-id
- name
- uniprot-id
uniprot id
Source
Drug Experimental Properties
Description
Drug properties that have been experimentally proven. Each drug may have one or more experimental property.
Usage
Experimental_Properties_Drug
Format
a tibble with 4 variables:
- kind
Name of the property
- value
Drug properties that have been experimentally proven
- source
Reference to the source of this experimental data
- parent_key
drugbank key
Details
The following experimental properties are provided:
| Property | Description |
| Water Solubility | The experimentally determined aqueous solubility of the molecule |
| Molecular Formula | Protein formula of Biotech drugs |
| Molecular Weight | Protein weight of Biotech drugs |
| Melting Point | The experimentally determined temperature at which the drug molecule changes from solid to liquid at atmospheric temperature. |
| Boiling Point | The experimentally determined temperature at which the drug molecule changes from liquid to gas at atmospheric temperature |
| Hydrophobicity | The ability of a molecule to repel water rather than absorb or dissolve water |
| Isoelectric Point | The pH value at which the net electric charge of a molecule is zero |
| caco2 Permeability | A continuous line of heterogeneous human epithelial colorectal adenocarcinoma cells, CAC02 cells are employed as a model of human intestinal absorption of various drugs and compounds. CAC02 cell permeability is ultimately an assay to measure drug absorption |
| pKa | The experimentally determined pka value of the molecule. |
| logP | The experimentally determined partition coefficient (LogP) based on the ratio of solubility of the molecule in 1-octanol compared to water |
| logS | The intrinsic solubility of a given compound is the concentration in equilibrium with its solid phase that dissolves into solution, given as the natural logarithm (LogS) of the concentration. |
| Radioactivity | The property to spontaneously emit particles (alpha, beta, neutron) or radiation (gamma, K capture), or both at the same time, from the decay of certain nuclides |
Source
Drugs External Links.
Description
Each drug may have one or more link.
Usage
External_Links_Drug
Format
a tibble with 3 variables:
- resource
Name of the source website.
- identifier
Identifier for this drug in the given resource
- parent_id
drugbank id
Details
Links may be provided for the following resources:
Source
Drug Food Interactions
Description
Description of interactions this drug has with food.
Usage
Food_Interactions_Drug
Format
a tibble 2 variables:
- interaction
descripts of interactions this drug has with food.
- parent_key
drugbank key
Details
Each drug may have one or more food interaction.
Source
Drug Groups
Description
Groups that this drug belongs to.
Usage
Groups_Drug
Format
a tibble with 2 variables:
- group
one of the above values
- drugbank-id
drugbank id
Details
Each drug may have one or more category.
Groups include:
approved
vet_approved
nutraceutical
illicit
withdrawn
investigational
experimental
Source
#' Drug Interactions
Description
Describe interactions between the drug being described by the parent drug, and other drugs.
Usage
Interactions_Drug
Format
a tibble with 4 variables:
- drugbank-id
Drugbank ID of the interacting drug
- name
Name of the interacting drug
- description
Textual description of the physiological consequences of the drug interaction
- parent_key
parent drugbank id
Details
Drug-drug interactions detailing drugs that, when administered concomitantly with the drug of interest, will affect its activity or result in adverse effects. These interactions may be synergistic or antagonistic depending on the physiological effects and mechanism of action of each drug.
Each drug may have one or more drug interaction.
Source
Drug International Brands
Description
The proprietary names used by the manufacturers for commercially available forms of the drug, focusing on brand names for products that are available in countries other than Canada and the Unites States.
Usage
International_Brands_Drug
Format
a tibble with 3 variables:
- name
The proprietary, well-known name for given to this drug by a manufacturer.
- company
The company or manufacturer that uses this name.
- parent_key
drugbank id
Details
Each drug may have one or more international brand.
Source
Drug Manufacturers
Description
A list of companies that are manufacturing the commercially available forms of this drug that are available in Canada and the Unites States.
Usage
Manufacturers_Drug
Format
a tibble with 3 variables:
- text
the name or description of the manufacturer
- parent_key
drugbank id
Details
Each drug may have one or more Manufacturer.
Source
Drug Mixture
Description
All commercially available products in which this drug is available in combination with other drug molecules.
Usage
Mixtures_Drug
Format
a tibble with 3 variables:
- name
The proprietary name provided by the manufacturer for this combination product.
- ingredients
A list of ingredients, separated by addition symbols.
- parent_key
drugbank id
Details
Each drug may have one or more mixture.
Source
Drug PDB Entries
Description
Protein Data Bank (PDB) identifiers for this drug
Usage
PDB_Entries_Drug
Format
a tibble with 2 variables:
- text
PDB identifier
- parent_key
drugbank id
Details
Each drug may have one or more PDB Entry
Source
Drug Packagers
Description
A list of companies that are packaging the drug for re-distribution.
Usage
Packagers_Drug
Format
a tibble with 3 variables:
- name
- url
A link to any companies that are packaging the drug for re-distribution
- parent_key
drugbank id
Details
Each drug may have one or more Packagers.
Source
Drug Patent
Description
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.
Usage
Patents_Drug
Format
a tibble with 6 variables:
- number
The patent number(s) associated with the drug
- country
The country that issued the patent rights
- approved
The date that the patent request was filed
- expires
The date that the patent rights expire
- pediatric-extension
Indicates whether or not a pediatric extension has been approved for the patent. Granted pediatric extensions provide an additional 6 months of market protection
- parent_key
drugbank id
Details
Each drug may have one or more patent.
Source
Drug Pathways
Description
Metabolic, disease, and biological pathways that the drug is involved in, as identified by the Small Molecule Protein Database (SMPDB).
Usage
Pathways_Drug
Format
a tibble with 4 variables:
- smpdb_id
Small Molecule Protein Database (SMPDB) identifier for this pathway.
- name
Pathway name
- category
Pathway category
- parent_key
drugbank id
Details
Each drug may have one or more pathway.
Source
Drug Pharmacology
Description
Describes the use, mechanism of action, pharmacokinetics, pharmacodynamics, and physiological or biochemical effects in the body.
Usage
Pharmacology
Format
An object of class tbl_df (inherits from tbl, data.frame) with 33 rows and 12 columns.
Value
a tibble with the following variables:
- indication
The approved conditions, diseases, or states for which a drug can safely and effectively be used. An indication is considered to be FDA-approved when it has any of the following designations: NDA, ANDA, BLA, or OTC. May also include indications in other countries, such as Canada (through Health Canada) or in Europe (through the European Medicines Agency).
- pharmacodynamics
A description of how the drug modifies or affects the organism it is being used in. May include effects in the body that are desired (enzyme or protein targets for example) and undesired (also known as “side effects”). This is in contrast to pharmacokinetics, which describes how the body modifies the drug being used.
- mechanism_of_action
A component of pharmacodynamics that describes the biochemical interaction through which a drug produces its intended effect. May include the exact molecular protein or enzyme targets and/or a description of the physiological effects produced.
- toxicity
Any adverse reaction, or side effect, that may or may not occur with use of the drug. May be attributed to a number of effects including: an enhanced therapeutic effect, rare anaphylactic reactions, interactions with other medications, or unanticipated binding of the molecule at different sites within the body.
- metabolism
A description of the chemical degradation of the drug molecule within the body; most commonly by enzymes from the Cytochrome P450 (CYP) system in the liver.
- absorption
A description of the movement of the drug from the site of administration into the bloodstream or target tissue. Common pharmacokinetic metrics used to evaluate absorption include Area Under the Curve (AUC), bioavailability (F), maximum concentration (Cmax), and time to maximum concentration (Tmax).
- half-life
The period of time it takes for the amount of drug in the body to be reduced by one half. Provides a description of how quickly the drug is being eliminated and how much is available in the bloodstream.
- protein-binding
A description of the drug’s affinity for plama proteins and the proportion of the drug that is bound to them when in circulation within the body.
- route_of_elimination
A description of the pathway that is used to excrete the drug from the body. Common pharmacokinetic parameters used to evaluate excretion include elemination half life, renal clearance, and tracking of radiolabelled compounds through the renal and GI system.
- volume_of_distribution
The Vd of a drug represents the degree to which it is distributed into body tissue compared to the plasma.
- clearance
A pharmacokinetic measurement of the rate of removal of the drug from plasma, expressed as mL/min; reflects the rate of elimination of the drug.
- drugbank_id
drugbank id
Source
Drug Prices
Description
Unit drug prices
Usage
Prices_Drug
Format
a tibble with 5 variables:
- description
- cost
Drug price per unit
- unit
- currency
Currency of price, example: USD
- parent_key
drugbank id
Details
Each drug may have one or more price
Source
Drug Products
Description
A list of commercially available products in Canada and the United States that contain the drug.
Usage
Products_Drug
Format
a tibble with 19 variables:
- name
The proprietary name(s) provided by the manufacturer for any commercially available products containing this drug.
- labeller
The corporation responsible for labelling this product.
- ndc-id
The National Drug Code (NDC) identifier of the drug.
- ndc-product-code
The National Drug Code (NDC) product code from the FDA National Drug Code directory.
- dpd-id
Drug Product Database (DPD) identification number (a.k.a. DIN) from the Canadian Drug Product Database. Only present for drugs that are marketed in Canada.
- ema-product-code
EMA product code from the European Medicines Agency Database. Only present for products that are authorised by central procedure for marketing in the European Union.
- ema-ma-number
EMA marketing authorisation number from the European Medicines Agency Database. Only present for products that are authorised by central procedure for marketing in the European Union.
- started-marketing-on
The starting date for market approval.
- ended-marketing-on
The ending date for market approval.
- dosage-form
The pharmaceutical formulation by which the drug is introduced into the body.
- strength
The amount of active drug ingredient provided in the dosage.
- route
The path by which the drug or product is taken into the body.
- fda-application-number
The New Drug Application [NDA] number assigned to this drug by the FDA.
- over-the-counter
A list of Over The Counter (OTC) forms of the drug
- generic
Whether this product is a generic drug
- approved
Indicates whether this drug has been approved by the regulating government.
- country
The country where this commercially available drug has been approved.
- source
Source of this product information. For example, a value of DPD indicates this information was retrieved from the Canadian Drug Product Database.
- parent_key
drugbank id
Details
Each drug may have one or more product.
Source
Drug Reactions
Description
A sequential representation of the metabolic reactions that this drug molecule is involved in. Depending on available information, this may include metabolizing enzymes, reaction type, substrates, products, pharmacological activity of metabolites, and a structural representation of the biochemical reactions.
Usage
Reactions_Drug
Format
a tibble with 6 variables:
- sequence
Reactions are displayed within a numerical sequence.
- left_drugbank_id
The substrate of the reaction. May be a drug or a metabolite.
- left_drugbank_name
- right_drugbank_id
The product of the reaction. May be a drug or a metabolite.
- right_drugbank_name
- parent_key
drugbank id
Details
Each drug may have one or more reaction.
Source
SNP Adverse Drug Reactions
Description
The adverse drug reactions that may occur as a result of the listed single nucleotide polymorphisms (SNPs).
Usage
SNP_Adverse_Drug_Reactions_Drug
Format
a tibble with 9 variables:
- protein-name
Proteins involved in this SNP.
- gene-symbol
Genes involved in this SNP.
- uniprot-id
Universal Protein Resource (UniProt) identifiers for proteins involved in this pathway.
- rs-id
The SNP Database identifier for this single nucleotide polymorphism.
- allele
The alleles associated with the identified SNP.
- adverse-reaction
- description
- pubmed-id
Reference to PubMed article.
- parent_key
Details
Each drug may have one or more SNP Adverse.
Source
Drug SNP Effects
Description
A list of single nucleotide polymorphisms (SNPs) relevant to drug activity or metabolism, and the effects these may have on pharmacological activity. SNP effects in the patient may require close monitoring, an increase or decrease in dose, or a change in therapy.
Usage
SNP_Effects_Drug
Format
a tibble with 9 variables:
- protein-name
Proteins involved in this SNP.
- gene-symbol
Genes involved in this SNP.
- uniprot-id
Universal Protein Resource (UniProt) identifiers for proteins involved in this pathway.
- rs-id
The SNP Database identifier for this single nucleotide polymorphism.
- allele
The alleles associated with the identified SNP.
- defining-change
A written description of the SNP effects.
- pubmed-id
Reference to PubMed article
- description
A written description of the SNP effects
- parent_key
drugbank id
Details
Each drug may have one or more SNP Effect.
Source
Drug Salts
Description
Available salt forms of the drug. Ions such as hydrochloride, sodium, and sulfate are often added to the drug molecule to increase solubility, dissolution, or absorption.
Usage
Salts_Drug
Format
a tibble with 8 variables:
- drugbank-id
DrugBank identifiers of the available salt form(s)
- name
Name of the available salt form(s)
- unii
Unique Ingredient Identifier (UNII) of the available salt form(s).
- cas-number
Chemical Abstracts Service (CAS) registry number assigned to the salt form(s) of the drug.
- inchikey
IUPAC International Chemical Identifier (InChi) key identifier for the available salt form(s)
- average-mass
Average molecular mass: the weighted average of the isotopic masses of the salt.
- monoisotopic-mass
The mass of the most abundant isotope of the salt
- parent_key
drugbank id
Details
Each drug may have one or more salt.
Source
Drug Sequences
Description
The amino acid sequence; provided if the drug is a peptide.
Usage
Sequences_Drug
Format
a tibble with 3 variables:
- sequence
- format
- parent_key
drugbank id
Details
Each drug may have one or more sequence.
Describes peptide sequences of biotech drugs. The sequence variable contains a textual representation of the sequence, in the format described by the format variable. Currently, only the FASTA format is used.
Source
Drugs Synonyms
Description
Other names or identifiers that are associated with the associated Drug
Usage
Synonyms_Drug
Format
a tibble with 4 variables:
- synonym
alternative name
- language
Names of the drug in languages other than English.
- coder
Organisation or source providing the synonym. For example, INN indicates the synonym is an International Nonproprietary Name, while IUPAC indicates the synonym is the nomenclature designated by the International Union of Pure and Applied Chemistry.
- drugbank-id
drugbank id
Details
Each element may have one or more synonyms.
Source
Drug Carriers/ Enzymes/ Targets/ Transporters related Actions
Description
A collection of actions related to drugs carriers
Usage
Actions_Carrier_Drug
Actions_Enzyme_Drug
Actions_Target_Drug
Actions_Transporter_Drug
Format
a tibble with 2 variables:
- text
describe related action
- parent_id
drug/ carrier/ target/ enzyme/ transporter id
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 15 rows and 2 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 90 rows and 2 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 136 rows and 2 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 55 rows and 2 columns.
Source
Drugs/ Carriers/ Enzymes/ Targets/ Transporters related Articles
Description
A list of articles that were used as references for drugs carriers
Usage
Articles_Carrier_Drug
Articles_Drug
Articles_Enzyme_Drug
Articles_Target_Drug
Articles_Transporter_Drug
Format
a tibble with 4 variables:
- ref-id
Identifier for the article being referenced. This is unique across all reference types (books, links, article).
- pubmed-id
The PubMed identifier for the article.
- citation
Article citation in a standard format.
- parent_id
drug/carrier/target/enzyme/transporter id
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 410 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 238 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 4003 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 1404 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 1312 rows and 4 columns.
Source
Drugs/ Carriers/ Enzymes/ Targets/ Transporters Attachments
Description
Return a list of attachment that were used as references for drugs or CETT
Usage
Attachments
Attachments_Enzymes
Attachments_Carriers
Attachments_Targets
Attachments_Transporters
Format
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 3 rows and 4 columns.
An object of class tbl_df (inherits from tbl, data.frame) with 388 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 6 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 11 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 37 rows and 4 columns.
Value
a tibble with 4 variables:
- ref-id
Identifier for the article being referenced. This is unique across all reference types (books, links, article, attachments).
- title
The title of the attachment.
- url
The url to download the attachment from.
- parent_id
drug/carrier/target/enzyme/transporter id
Source
Drugs/ Carriers/ Enzymes/ Targets/ Transporters related Books
Description
A list of text books that were used as references for drugs
Usage
Books_Drug
Textbooks_Carrier_Drug
Textbooks_Enzyme_Drug
Textbooks_Target_Drug
Textbooks_Transporter_Drug
Format
a tibble with 4 variables:
- ref-id
Identifier for the article being referenced. This is unique across all reference types (books, links, article).
- isbn
ISBN identifying the textbook.
- citation
A Textbook citation in a standard format.
- parent_id
drug/ carrier/ target/ enzyme/ transporter id
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 1 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 8 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 62 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 11 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 4 rows and 4 columns.
Source
Carriers/ Enzymes/ Targets/ Transporters
Description
Protein targets of drug action, enzymes that are inhibited/induced or involved in metabolism, and carrier or transporter proteins involved in movement of the drug across biological membranes.
Usage
Carriers_Drug
Enzymes_Drug
Targets_Drug
Transporters_Drug
Format
a tibble with 6 variables:
- id
Identifier for the record
- name
related name
- organism
Organism that the protein comes from.
- known_action
Whether the pharmacological action of the drug is due to this target interaction.
- position
related position
- parent_id
drugbank id
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 15 rows and 6 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 90 rows and 8 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 59 rows and 6 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 49 rows and 6 columns.
Details
Each of targets, enzymes, carriers and transporters contain one or more child elements tibbles
Source
covid19dbcand: A data package that contains different datasets extracted from DrugBank xml database.
Description
The datasets in 'covid19dbcand' is related to [DrugBank](https://www.drugbank.ca/covid-19#drugs) selected drugs for covid-19
Details
The package is a smaller version from [dbdataset package](https://github.com/MohammedFCIS/dbdataset).
It is extracted using [dbparser](https://docs.ropensci.org/dbparser/)
For more information kindly check the reference/index (https://mohammedfcis.github.io/covid19dbcand/reference/index.html)
External Identifiers for Drugs/ Carriers/ Enzymes/ Targets/ Transporters
Description
Identifiers used in other websites or databases providing information about this drug.
Usage
External_Identifiers_Drug
External_Identifiers_Polypeptide_Carrier_Drug
External_Identifiers_Polypeptide_Enzyme_Drug
External_Identifiers_Polypeptide_Target_Drug
External_Identifiers_Transporter_Drug
Format
a tibble with following features:
- resource
Name of the source database
- identifier
Identifier for this drug in the given resource
- parent_key
drugbank key
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 232 rows and 3 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
Details
Each drug may have one or more external identifier.
Drug identifiers may be provided for the following resources
ChemSpider
PharmGKB
ZINC
Source
Carriers/ Enzymes/ Targets/ Transporters related Gene Ontology (GO)
Description
The Gene Ontology (GO) Consortium identifier
Usage
GO_Classifiers_Polypeptide_Carrier_Drug
GO_Classifiers_Polypeptides_Enzyme_Drug
GO_Classifiers_Polypeptide_Target_Drug
GO_Classifiers_Polypeptide_Transporter_Drug
Format
a tibble with 3 variables:
- category
- description
- polypeptide_id
polypeptide id
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
Details
Each Carriers/ Enzymes/ Targets/ may have zero or more GO.
Source
Drugs/ Carriers/ Enzymes/ Targets/ Transporters related Links
Description
A list of websites that were used as references for Drugs/ Carriers/ Enzymes/ Targets/ Transporters
Usage
Links_Drug
Links_Carrier_Drug
Links_Enzyme_Drug
Links_Target_Drug
Links_Transporter_Drug
Format
a tibble with 3 variables:
- ref-id
Name of the source website
- title
Identifier for this drug in the given resource
- url
The url of the website
- parent_id
drug/ carrier/ target/ enzyme/ transporter id
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 94 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 88 rows and 4 columns.
An object of class tbl_df (inherits from tbl, data.frame) with 645 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 60 rows and 4 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 168 rows and 4 columns.
Details
Each drug/ carrier/ target/ enzyme/ transporter may have one or more link.
Source
PFAMs
Description
The protein family (pfam) identifier
Usage
PFAMS_Polypeptide_Carrier_Drug
PFAMS_Polypeptides_Enzyme_Drug
PFAMS_Polypeptide_Target_Drug
PFAMS_Polypeptid_Transporter_Drug
Format
a tibble with 3 variables:
- identifier
- name
- polypeptide_id
polypeptide id
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 3 columns.
Details
Each Polypeptid may have one or more PFAM.
Source
Polypeptide Synonyms
Description
Alternate names or identifiers that may be associated with this polypeptide
Usage
Synonyms_Polypeptide_Carrier_Drug
Synonyms_Polypeptides_Enzyme_Drug
Synonyms_Polypeptide_Target_Drug
Synonyms_Polypeptide_Transporter_Drug
Format
a tibble with 2 variables:
- syn
alternative name
- polypeptide_id
polypeptide id
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 2 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 2 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 2 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 0 rows and 2 columns.
Details
Each element may have one or more synonyms.
Source
Polypeptide
Description
Descriptions of identified polypeptide targets, enzymes, carriers, or transporters.
Usage
Polypeptides_Carrier_Drug
Polypeptides_Enzyme_Drug
Polypeptide_Target_Drug
Polypeptides_Transporter_Drug
Format
a tibble with 20 variables:
- id
- source
Specifies whether the identified polypeptide ID is associated with any of the following UniProt knowledge bases: Swiss-Prot, which is manually annotated and reviewed, or TrEMBL, which is automatically annotated and not reviewed.
- name
- general_function
General summary of the physiological function of the polypeptide
- specific_function
A more specific description of the polypeptide’s physiological function within the cell.
- gene_name
The short name commonly associated with the associated gene. Eg. PTGS1.
- locus
The specific chromosomal location or position of the gene’s sequence on a chromosome.
- cellular_location
The cellular location of the polypeptide.
- transmembrane_regions
Areas of the polypeptide sequence that span a biological membrane.
- signal_regions
Location of any signal peptides within the polypeptide sequence.
- theoretical_pi
Theoretical isoelectric point.
- molecular_weight
The molecular weight of the polypeptide.
- chromosome_location
The chromosomal location of the polypeptide gene
- organism
The organism in which this polypeptide functions.
- organism_ncbi_taxonomy_id
- amino_acid_sequence
The amino acid sequence of the polypeptide
- amino_acid_format
- gene_sequence
The sequence of the associated gene.
- gene_format
- parent_key
drugbank id
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 3 rows and 20 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 35 rows and 20 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 50 rows and 20 columns.
An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 17 rows and 20 columns.
Details
Each target, enzyme, carrier and transporter elements may include one or more polypeptide.