Changes in version 2.2.1.9000 Changes in version 2.2.1 (2026-01-08) 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 Changes in version 2.0.3 (2024-04-20) 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) Changes in version 2.0.2 (2024-02-16) 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 Changes in version 2.0.1 (2023-03-27) 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) Changes in version 2.0.0 (2023-03-17) 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) Changes in version 1.2.0 (2020-08-26) 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. Changes in version 1.1.2 (2020-06-08) 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. Changes in version 1.1.1 (2020-05-10) - 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 Changes in version 1.1.0 (2020-02-21) 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). Changes in version 1.0.4 (2019-08-28) - 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. Changes in version 1.0.3 (2019-07-11) - Fix CRAN errors and notes Changes in version 1.0.2 (2019-07-08) - 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 Changes in version 1.0.1 (2019-04-16) - 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 Changes in version 1.0.0 (2018-12-17) - Initial release that contains core functionalities