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dbparser

dbparser 2.2.1

This is a major feature release focused on expanding dbparser’s capabilities into real-world pharmacovigilance and drug-drug interaction analysis. The integration engine has been formalized around a “Hub and Spoke” model, with DrugBank acting as the central hub.

NEW FEATURES

• New Parser: parseOnSIDES()
  • Parses the relational CSV files from the OnSIDES database, a modern resource for adverse drug events extracted from FDA labels.
  • Returns a dvobject containing the 7 core relational tables and an optional high_confidence summary table.
• New Parser: parseTWOSIDES()
  • Parses the TWOSIDES database, the leading resource for drug-drug interaction (DDI) adverse event signals from real-world data.
  • Returns a dvobject containing the drug_drug_interactions table.
  • The parser correctly handles known column name misspellings in the source data (e.g., drug_1_rxnorn_id).
• New Integration Function: merge_drugbank_onsides()
  • Merges a DrugBank dvobject with an OnSIDES dvobject.
  • Automatically creates an enriched integrated_data list, linking OnSIDES data to DrugBank IDs via RxNorm CUIs.
  • The function is chainable, meaning it can be used in a %>% pipeline after other merge functions.
• New Integration Function: merge_drugbank_twosides()
  • Merges a DrugBank dvobject with a TWOSIDES dvobject.
  • Performs a “double join” to enrich both drugs in an interaction pair with their DrugBank IDs and names.
  • Uses a robust “union” logic to keep interactions even if only one of the two drugs is present in the input DrugBank object.
  • The function is also chainable.
• Subset a DrugBank dvobject function: subset_drugbank_dvobject()
  • Intelligently filters a DrugBank dvobject to retain only the data associated with a specified list of drugbank_ids. It correctly handles the deep, multi-level nested structure of the entire object, including the complex relationships within the cett list.
• Subset an OnSIDES dvobject function: subset_onsides_dvobject()
  • Intelligently filters an OnSIDES dvobject by cascading filters through the relational tables, ensuring the final subset is self-consistent.
• Adding metadata to existing dvobject objects using function: add_database_info()
• Major enhancements to function show_dvobject_metadata()
  • Displays information about passed dbobject object including basic info, database metadata, and all data.frames contained within nested lists.
• Run vignette("dbparser_2_2", package = "dbparser") for more info

DOCUMENTATION

• New Vignette: “Integrated Pharmacovigilance”
  • A comprehensive new tutorial demonstrating a full, three-way integration of DrugBank, OnSIDES, and TWOSIDES.
  • Includes a complete scientific case study analyzing single-drug vs. polypharmacy risks.
  • Introduces a reproducible example workflow using a pre-computed RDS data object hosted externally to keep the package lightweight.
  • Run vignette("drugbank_nside", package = "dbparser") for more info
• Updated existing vignette and package Readme with enhanced examples

BUG FIXES & MINOR IMPROVEMENTS

• Several minor fixes are done

dbparser 2.0.3

Enhancements

• Updated unit tests with latest DrugBank DB info v 5.1.12

Bugs Fixes

• Fixed “Drug Targets has two drugbank_id columns” bug (#163)

dbparser 2.0.2

Enhancements

• Replaced “-” with “_” in tibbles column names (#111)
• Renamed “primary_key” to “drugbank_id” in parsed drugs “general_information” tibble (#111)
• Replaced “parent_key” keywords in different tibbles column names with original parent name (#111)
• Updated Vignette to use interactive canvasXpress package plots

dbparser 2.0.1

Bugs Fixes

• Fixed output references (#147)
• Updated parseDrugBanKparameters default values (#146)
• Fixed package documentation references (#144)
• Fixed CRAN error on some of linux info (#145)

dbparser 2.0.0

Breaking changes

• Deprecated saving parsed data into given database (#140)
• Deprecated saving parsed data into a csv file (#140)
• Deprecated old structure public methods (#141)
• Updated minimum R required version to 3.5 (#143)

New features

• Introduced new methods for paring DrugBank DB and returning dvobject (#141)

Major Updates

• Updated unit tests to work with new data structure (#141)

Minor Fixes

• Removed RMariaDB dependency (#129)
• Fix pkgdown configuration for reference (#136)

dbparser 1.2.0

UI Changes

• Introduce progress bar in parser functions

New Parsers

Collective Parsers

• drugs, cett and References Parsers

Elements Parsers

• attachments parsers for drugs and CETT
• drug_pharmacology parser
• Rename drugs_books parser to drugs_textbooks
• Rename drug_all parser to run_all_parsers
• Rename drug parser to drug_general_information

Documentation Update:

• Add returned parsed data structure
• Explain the returned data functionality as a whole and for each elements
• Point out to related/similar parsers

Package design

For those who thinking to contribute in dbparser, now parsers are implemented as R6 classes.

Minor Fixes

• Update database saver functions to accommodate new DrugBank data size.

dbparser 1.1.2

Major Changes

• Enhance many memory and performance issues for many parsers.
• Change the drug classification representations to extract more useful information. ### Minor Changes
• Change some drug tibbles features names ### DEFUNCT
• Size columns in drugs main table is no longer exist, will do full statistical analysis later using dvminer package.

dbparser 1.1.1

• Fix column size issue while importing into SQL Server (#91)
• Fix dbparser and upcoming CRAN release of dplyr issues (#92)
• Fix CRAN Notes (#93)
• Fix package documentation and site references

dbparser 1.1.0

Major Changes

• Functions have been splitted into 6 categories DrugBank Database Loading, Carriers, Targets, Transporters, Drug and common parsers. All function names are changed to reflect the function family. The related documentation is also updated (#66, #75).
• dbparser now can cite the package by calling citation("dbparser") (#71).
• Adding more user friendly error messages (#76, #81).
• User can now pass DBI database connection to parser functions as an argument beside SQLite and MariaDB (#87).

DEFUNCT

• open_db, open_mdb and close_db functions are no longer supported. Creating and maintaining database is completely user responsibility and the database connection can be passed to parser functions (#87).

DOCUMENTATION FIXES

• New tutorials for how to use dbparser have been created (#78, #79).
• Contribution guide has been added.
• Code of conduct has been added (#70).
• Enhance function reference documentation to include section for each type (#68).

dbparser 1.0.4

• Fix save drugs tibbles as csv several issues.
• Update SQL database tibbles saver functions.
• Update SQL database saver functions documentations.
• Support MariaDB and introduce related functionalities.

dbparser 1.0.3

• Fix CRAN errors and notes

dbparser 1.0.2

• Fix zip file location issue
• Replace Secondary and third keys columns from drug framework with other_keys column that contains any other keys that might exist in addition to the primary key
• Add average-mass, monoisotopic-mass and calculated-properties parsers.
• Support saving parsed drugs related parsed database as csv

dbparser 1.0.1

• Fix CRAN Note
• Improve documentation
• Refactor unused functions
• Remove Count features from drug data set
• Fix several typos in documentation and code
• Fix consistency issue of CLASS of tibbles Returned by dbparser
• Check if DrugBank database exist before parsing
• Add support for international_brands and salts elements
• Properly rename some features to have clear names
• Reduce datasets size by getting unique rows only
• Support reading zip file containing DrugBank xml database

dbparser 1.0.0

• Initial release that contains core functionalities

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.