v2.2.1

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)

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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

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dbparser 2.0.1

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)

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 v1.2.0

• 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 v1.1.2

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 v1.1.1

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 1.0.4

Fix save drugs dataframes as csv several issues
Update sql database dataframes saver functions
Update sql database saver functions documentations.
Support MariaDB and introduce related functionalities.

v1.0.2

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

v1.0.1

dbparser 1.0.1

• Fix CRAN Note
• Improve documentation
• Refactor unused functions
• Remove Count features from drug data set
• Fix serveral typoes in documentation and code
• Fix consistency issue of CLASS of Data Frames 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