OpenTargetsR

An enhanced R interface for querying the Open Targets Platform, providing user-friendly wrapper functions around the otargen package.

Overview

OpenTargetsR simplifies data retrieval from the Open Targets Platform by accepting human-readable gene symbols and disease names, automatically converting them to the required identifiers for API queries. This package provides a more intuitive interface compared to the original otargen package while maintaining full functionality.

Features

• User-friendly input: Use HGNC gene symbols and disease names instead of complex identifiers
• Automatic ID resolution: Seamlessly converts gene symbols to Ensembl IDs and disease names to EFO/MONDO IDs
• Comprehensive coverage: Access all major Open Targets data types including:
  • Gene-disease associations
  • Drug information and mechanisms
  • Genetic variant effects
  • Pathway and ontology data
  • Safety and pharmacogenomics information
• Consistent interface: All functions follow consistent naming and parameter conventions
• Rich documentation: Extensive examples and parameter descriptions for all functions

Installation

# Install from GitHub (once published)
# devtools::install_github("Zaoqu-Liu/OpenTargetsR")

# For now, install locally after downloading
# devtools::install_local("/path/to/OpenTargetsR")

Quick Start

library(OpenTargetsR)

# Get ChEMBL evidence for PSEN1 and Alzheimer disease
chembl_data <- ChemblGeneDiseaseQuery("PSEN1", "Alzheimer disease")

# Get adverse events for aspirin
adverse_events <- DrugAdverseEventsQuery("aspirin")

# Get gene ontology annotations for THBS2
go_data <- GeneOntologyGeneQuery("THBS2")

# Get variant effect predictions
vep_data <- VariantEffectPredictorVariantQuery("4_1804392_G_A")

Function Categories

Gene-Disease Queries

• ChemblGeneDiseaseQuery() - ChEMBL evidence data
• EuropePMCGeneDiseaseQuery() - Literature evidence
• GeneBurdenGeneDiseaseQuery() - Gene burden analysis
• GenomicsEnglandGeneDiseaseQuery() - Clinical genomics evidence
• GWASCredibleSetsTargetDiseaseQuery() - GWAS credible sets
• OrphanetGeneDiseaseQuery() - Rare disease evidence
• UniProtLiteratureGeneDiseaseQuery() - Protein literature evidence

Gene-Only Queries

• ComparativeGenomicsGeneQuery() - Evolutionary conservation
• DepMapEssentialityGeneQuery() - Gene essentiality scores
• GeneOntologyGeneQuery() - GO annotations
• GeneticConstraintGeneQuery() - Constraint metrics
• HallmarkGeneQuery() - Cancer hallmarks
• InteractionsGeneQuery() - Protein interactions
• KnownDrugsGeneQuery() - Targeting drugs
• MousePhenotypesGeneQuery() - Mouse model data
• PathwaysGeneQuery() - Pathway annotations
• GenePharmacogenomicsQuery() - Pharmacogenomics
• SafetyLiabilitiesGeneQuery() - Safety profiles

Drug Queries

• DrugAdverseEventsQuery() - Adverse events
• DrugIndicationsQuery() - Approved indications
• DrugKnownDrugsQuery() - Related compounds
• DrugMechanismsOfActionQuery() - Mechanisms of action
• DrugPharmacogenomicsQuery() - Genetic effects

Variant Queries

• VariantPharmacogenomicsQuery() - PGx associations
• QTLCredibleSetsVariantQuery() - QTL data
• UniProtVariantsVariantQuery() - Protein consequences
• VariantEffectPredictorVariantQuery() - VEP annotations
• VariantEffectVariantQuery() - General effects

Disease Queries

• SharedTraitStudiesDiseasesQuery() - Cross-trait genetics

Utility Functions

• get_chembl_id() - Resolve drug names to ChEMBL IDs
• get_trait_id() - Resolve disease names to EFO/MONDO IDs

Examples

Gene-Disease Analysis

# Comprehensive analysis of APOE and Alzheimer disease
gene <- "APOE"
disease <- "Alzheimer disease"

# Get multiple evidence types
chembl_evidence <- ChemblGeneDiseaseQuery(gene, disease)
literature_evidence <- EuropePMCGeneDiseaseQuery(gene, disease)
gwas_evidence <- GWASCredibleSetsTargetDiseaseQuery(gene, disease)
uniprot_evidence <- UniProtLiteratureGeneDiseaseQuery(gene, disease)

Drug Safety Analysis

# Analyze aspirin safety profile
drug <- "aspirin"

adverse_events <- DrugAdverseEventsQuery(drug)
mechanisms <- DrugMechanismsOfActionQuery(drug)
indications <- DrugIndicationsQuery(drug)
pharmacogenomics <- DrugPharmacogenomicsQuery(drug)

Gene Function Analysis

# Comprehensive gene function analysis
gene <- "TP53"

go_annotations <- GeneOntologyGeneQuery(gene)
pathways <- PathwaysGeneQuery(gene)
interactions <- InteractionsGeneQuery(gene, size = 100)
hallmarks <- HallmarkGeneQuery(gene)
constraint <- GeneticConstraintGeneQuery(gene)
safety <- SafetyLiabilitiesGeneQuery(gene)

Dependencies

• otargen: Core Open Targets API interface
• BioEnricher: Gene ID mapping
• dplyr, tibble, tidyr: Data manipulation
• httr, jsonlite: Web API access
• stringr, purrr, rlang: Utility functions

Author

Zaoqu Liu (liuzaoqu@163.com)

License

MIT License

Contributing

Please report issues and suggestions on the GitHub repository.