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
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).
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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