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dbparser (development version)

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