R Observatory: Metrics for dbparser version 2.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dbparser

2.2.1Package record

Drugs Databases Parser

0packages depend

8.8Kdownloads / year

97.3%test coverage

13/13flavors OK

Overview

About

Maintained by Mohammed AliCRAN page ↗GitHub ↗Website ↗Issues ↗

This tool is for parsing public drug databases such as 'DrugBank' XML database https://go.drugbank.com/. The parsed data are then returned in a proper 'R' object called 'dvobject'.

Changes in 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.

Show all changes in 2.2.1Hide the rest of the changes in 2.2.1

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

---

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("dbparser", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ropensci/dbparser")

Development version from ropensci/dbparser. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-dbparser

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-dbparser

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-dbparser

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.1

READMEYes · 758 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 2.2.1Citation fileYes · computed when R runs itWebsiteYes · pkgdown

Help pages: 66 (54 internal)includes a package overview page
Examples that run: 0%3 never run
Exported functions with examples: 25%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

8.8K

CRAN downloads in the past year

Rank #5,604 · ~24/day · ~730/mo

Releases R versions

Daily download trend is not available in this view yet.

59430 days

1.5K90 days

8.8K1 year

Compare downloads with other packages →

Also on130 r2u9 autocran81 c2d4u

How downloads are counted

Repository

ropensci/dbparser ↗Organization: ropensci

67Stars

19Forks

9Open issues

0Open PRs

11Releases

648Commits

10Commit identities

648 commits · Last activity 2026-10-10 · 0% stars, 30d · Default branch at 2.2.3.9000, ahead of CRAN 2.2.1 (checked 2026-10-18) · Discussions: 5 posts

Responsiveness

How these are sampled

PRs merged (all time): 98%
Median days to close, 50 most recently updated closed issues: 126
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-16 · 622026-07-07 · 67

How these are measured

PracticesBeta

14 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/ropensci/dbparser on 2026-10-18.

Continuous integration (4)

GitHub ActionsR CMD check workflowTravis CI (config file)AppVeyor

The R CMD check workflow runs on macOS

Governance and community (3)

Code of conductContributing guideIssue templates

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-02-14

CRAN release process (1)

cran-comments.md

Show all practicesHide 2 practices

Research and citation (2)

codemeta.jsonJOSS paper

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing dbparser adds 22 packages (12 with compiled code, 12 MB of source tarballs). Heaviest: data.table 5.7 MB, vctrs 1.0 MB, XML 937 KB.

Depends (1)

R >= 3.5

Imports (8)

data.table dplyr progress purrr tibbletoolsutilsXML

LinkingTo (0)

none

Suggests (5)

canvasXpress knitr rmarkdown testthat tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (4)

Mohammed Ali

Author, Maintainer since 1.0.0 (2018)

Ali Ezzat

Author

Emma Mendelsohn

Reviewer · added in 1.1.0

Hao Zhu

Reviewer · added in 1.1.0

Releases (14)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.2.1Latest
record
2026-01-08 · current release · diff ↗ ·
added 7 exports
add_database_info, merge_drugbank_onsides, merge_drugbank_twosides, parseOnSIDES, parseTWOSIDES, subset_drugbank_dvobject, subset_onsides_dvobject
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.3
record
2024-04-20 · diff ↗
2.0.2
record
2024-02-16 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.0.1
record
2023-03-27 · diff ↗
2.0.0
record
2023-03-17 · diff ↗ ·
removed 91 exports
carriers, carriers_actions, carriers_articles, carriers_attachments, carriers_links, carriers_polypep_ex_ident, carriers_polypeptides, carriers_polypeptides_go, carriers_polypeptides_pfams, carriers_polypeptides_syn, carriers_textbooks, cett, drug_affected_organisms, drug_ahfs_codes, drug_atc_codes, drug_calc_prop, drug_categories, drug_classification, drug_dosages, drug_element, drug_element_options, drug_ex_identity, drug_exp_prop, drug_external_links, drug_food_interactions, drug_general_information, drug_groups, drug_interactions, drug_intern_brand, drug_manufacturers and 61 more

added 5 exports
cett_nodes_options, drug_node_options, parseDrugBank, references_node_options, show_dvobject_metadata
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.2.0
record
2020-08-26 · diff ↗ ·
removed 21 exports
carriers_polypeptide, carriers_polypeptide_ext_id, drug, drug_all, drug_articles, drug_books, drug_links, enzymes_polypeptide, enzymes_polypeptide_ext_ident, enzymes_polypeptide_go, enzymes_polypeptide_pfams, enzymes_polypeptide_syn, targets_polypeptide, targets_polypeptide_ext_ident, targets_polypeptide_go, targets_polypeptide_pfams, targets_polypeptide_syn, transporters_polypeptide, transporters_polypeptide_go, transporters_polypeptide_pfams, transporters_polypeptide_syn

added 30 exports
carriers_attachments, carriers_polypep_ex_ident, carriers_polypeptides, cett, drug_general_information, drug_pharmacology, drugs, drugs_articles, drugs_attachments, drugs_links, drugs_textbooks, enzymes_attachments, enzymes_polypep_ex_ident, enzymes_polypeptides, enzymes_polypeptides_go, enzymes_polypeptides_pfams, enzymes_polypeptides_syn, references, run_all_parsers, targets_attachments, targets_polypep_ex_ident, targets_polypeptides, targets_polypeptides_go, targets_polypeptides_pfams, targets_polypeptides_syn, transporters_attachments, transporters_polypeptides, transporters_polypeptides_go, transporters_polypeptides_pfams, transporters_polypeptides_syn
1.1.2
record
2020-06-08 · diff ↗
1.1.1
record
2020-05-10 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.0
record
2020-02-21 · diff ↗ ·
removed 82 exports
close_db, get_xml_db_rows, open_db, open_mdb, parse_drug, parse_drug_affected_organisms, parse_drug_ahfs_codes, parse_drug_all, parse_drug_articles, parse_drug_atc_codes, parse_drug_books, parse_drug_calculated_properties, parse_drug_carriers, parse_drug_carriers_actions, parse_drug_carriers_articles, parse_drug_carriers_links, parse_drug_carriers_polypeptides, parse_drug_carriers_polypeptides_external_identifiers, parse_drug_carriers_polypeptides_go_classifiers, parse_drug_carriers_polypeptides_pfams, parse_drug_carriers_polypeptides_synonyms, parse_drug_carriers_textbooks, parse_drug_categories, parse_drug_classification, parse_drug_dosages, parse_drug_element, parse_drug_element_options, parse_drug_enzymes, parse_drug_enzymes_actions, parse_drug_enzymes_articles and 52 more

added 79 exports
carriers, carriers_actions, carriers_articles, carriers_links, carriers_polypeptide, carriers_polypeptide_ext_id, carriers_polypeptides_go, carriers_polypeptides_pfams, carriers_polypeptides_syn, carriers_textbooks, drug, drug_affected_organisms, drug_ahfs_codes, drug_all, drug_articles, drug_atc_codes, drug_books, drug_calc_prop, drug_categories, drug_classification, drug_dosages, drug_element, drug_element_options, drug_ex_identity, drug_exp_prop, drug_external_links, drug_food_interactions, drug_groups, drug_interactions, drug_intern_brand and 49 more

Show 7 earlier eventsHide 7 earlier events

1.0.4
record
2019-08-28 · diff ↗ ·
added 1 export
open_mdb
1.0.3
record
2019-07-12 · diff ↗
1.0.2
record
2019-07-08 · diff ↗ ·
added 1 export
parse_drug_calculated_properties
R
R 3.6.0 released · 2019-04-26
1.0.1
record
2019-04-16 · diff ↗ ·
removed 1 export
parse_drug_classifications

added 3 exports
parse_drug_classification, parse_drug_international_brands, parse_drug_salts
1.0.0
record
2018-12-18
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-12-18
Total releases: 14 / 8 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Download size: 2.6 MB

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("dbparser")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for dbparser version 2.2.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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