Package: dbparser 2.2.3.9000

Mohammed Ali

dbparser: Drugs Databases Parser

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'.

Authors:Mohammed Ali [aut, cre], Ali Ezzat [aut], Hao Zhu [rev], Emma Mendelsohn [rev]

dbparser_2.2.3.9000.tar.gz
dbparser_2.2.3.9000.zip(r-4.7-any)dbparser_2.2.3.9000.zip(r-4.6-any)dbparser_2.2.3.9000.zip(r-4.5-any)
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dbparser_2.2.3.9000.tar.gz(r-4.7-any)dbparser_2.2.3.9000.tar.gz(r-4.6-any)
dbparser_2.2.3.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dbparser/json (API)

# Install 'dbparser' in R:
install.packages('dbparser', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #347

Bug tracker:https://github.com/ropensci/dbparser/issues

Pkgdown/docs site:https://docs.ropensci.org

On CRAN:

Conda:

10.10 score 67 stars 262 scripts 622 downloads 4 mentions 16 exports 22 dependencies

Last updated from:94ae3dd888 (on cran). Checks:10 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK143
pkgdown docsOK246
source / vignettesOK246
linux-releaseOK151
macos-releaseOK146
macos-oldrelOK124
windows-develOK109
windows-releaseOK91
windows-oldrelOK99
wasm-releaseOK107

Exports:add_database_infocett_nodes_optionsdrug_node_optionsget_genes_for_phenotypemerge_drugbank_hpomerge_drugbank_onsidesmerge_drugbank_twosidesparseDrugBankparseHPOparseOnSIDESparseTWOSIDESreferences_node_optionssearch_phenotypesshow_dvobject_metadatasubset_drugbank_dvobjectsubset_onsides_dvobject

Dependencies:clicrayondata.tabledplyrgenericsgluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6rlangtibbletidyselectutf8vctrswithrXML

Anticipating On-Target Drug Effects with HPO Gene-Phenotype Data
Introduction | Prerequisites | 1. Load the data | 1.1 HPO gene-phenotype associations | 1.2 DrugBank targets | 2. Link drug targets to phenotypes | 3. Keep the informative phenotypes | 4. Group phenotypes into clinical domains | 5. Interpret the phenotypes using the direction of drug action | Bivalirudin and F2: phenotypes predict the main adverse effect | Leuprolide and the GnRH axis: phenotypes predict the therapeutic effect | Calcitriol and VDR: the direction is reversed | 6. Compare the phenotype profiles | Conclusion
Rendered fromhpo_target_phenotypes.Rmdusingknitr::rmarkdown

Last update: 2026-10-10
Started: 2026-10-10

Drug Mechanism Profiling with CETT Actions
Introduction | Scientific case: finding a mechanistic substitute for lepirudin | Prerequisites | 1. Parse the DrugBank records | 2. Target actions now carry the drug | Why the drug link matters | 3. Map the targets to genes | 4. Find drugs that share lepirudin's mechanism | 5. Compare the wider interaction profiles | Summary
Rendered fromcett_mechanisms.Rmdusingknitr::rmarkdown

Last update: 2026-10-10
Started: 2026-10-10

Unlocking DrugBank: Parsing and Visualizing Mechanistic Data
Introduction | 1. Loading Data | The Parsing Workflow | Loading Sample Data | 2. Analysis: The Drug Landscape | 3. Analysis: Approval Status | 4. Analysis: Molecular Mechanisms | 5. Next Steps: Integrated Pharmacovigilance
Rendered fromdbparser.Rmdusingknitr::rmarkdown

Last update: 2026-01-08
Started: 2018-10-04

Introducing dbparser 2.2.0
The "Hub and Spoke" Architecture | Pipeline-Ready Pharmacovigilance | New Tools for Reproducibility | A Scientific Case Study | Availability
Rendered fromdbparser_2_2.Rmdusingknitr::rmarkdown

Last update: 2025-12-27
Started: 2025-12-27

Integrated Pharmacovigilance: Linking DrugBank, OnSIDES, and TWOSIDES
Introduction | Prerequisites | 1. Loading and Inspecting Data | 1.1 Load DrugBank (The Hub) | 1.2 Load OnSIDES (Single-Drug Labels) | 1.3 Load TWOSIDES (Drug Interactions) | 2. Merging the Databases (Chaining) | 3. Single Drug Analysis: Leuprolide (DB00007) | 3.1 Extract Baseline Adverse Events (OnSIDES) | 4. Single Drug Analysis: Calcitriol (DB00136) | 5. Polypharmacy Analysis: Drug-Drug Interactions | 5.1 Visualization of Interaction Risks | 6. Comparative Overview | 7. Conclusion
Rendered fromdrugbank_nside.Rmdusingknitr::rmarkdown

Last update: 2025-12-26
Started: 2025-12-09