v2.2.1

[MohammedFCIS]

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

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This discussion was created from the release v2.2.1.