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

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