Access Open Target.
otargen
Tidy R interface to the Open Targets Platform GraphQL API.
Query genes, diseases, drugs, variants, and genetic evidence directly from R and receive analysis-ready tibbles — no manual JSON wrangling required.
Installation
CRAN (stable)
install.packages("otargen")
GitHub (development)
# install.packages("devtools")
devtools::install_github("amirfeizi/otargen")
Quick start
Every function takes a single identifier (gene, disease, drug, or variant) and returns a tidy tibble.
Drug safety & mechanisms (by ChEMBL ID)
library(otargen)
# Adverse events reported for imatinib
adverseEventsQuery(chemblId = "CHEMBL941")
# Mechanism of action for imatinib
mechanismsOfActionQuery(chemblId = "CHEMBL941")
# Drug indications with clinical stage info
indicationsQuery(chemblId = "CHEMBL941")
Gene-level queries (by Ensembl ID)
# Known drugs and clinical candidates targeting TP53
knownDrugsGeneQuery(ensgId = "ENSG00000141510")
# Cancer hallmarks for TP53
hallmarksQuery(ensgId = "ENSG00000141510")
# Protein-protein interactions for TP53
interactionsQuery(ensgId = "ENSG00000141510", size = 25)
# DepMap cancer cell-line essentiality for EGFR
depMapQuery(ensgId = "ENSG00000146648")
# Target safety liabilities for EGFR
safetyQuery(ensgId = "ENSG00000146648")
Gene + disease evidence (by Ensembl ID + EFO ID)
# ChEMBL evidence linking PARP1 to breast cancer
chemblQuery(ensemblId = "ENSG00000143799", efoId = "EFO_0000305")
# GWAS credible sets for PCSK9 and hyperlipidemia
gwasCredibleSetsQuery(ensemblId = "ENSG00000169174", efoId = "EFO_0004911")
# ClinVar evidence for BRCA1 and ovarian cancer
clinVarQuery(ensemblId = "ENSG00000012048", efoId = "EFO_0001075")
# Literature evidence from Europe PMC
europePMCQuery(ensemblId = "ENSG00000012048", efoId = "EFO_0001075")
Pharmacogenomics & variants
# Pharmacogenomics data for a drug
pharmacogenomicsChemblQuery(chemblId = "CHEMBL1016")
# UniProt variants
uniProtVariantsQuery(variantId = "4_1804392_G_A")
# Variant effect predictions
variantEffectPredictorQuery(variantId = "1_154453788_C_T")
Genetics & colocalisation
# Locus-to-gene predictions for a credible set
locus2GeneQuery(studyLocusId = "fa375739ca2a6b825ce5cc69d117e84b")
# GWAS colocalisation analysis
gwasColocalisation(study_locus_id = "5a86bfd40d2ebecf6ce97bbe8a737512")
Available functions (35)
| Category | Functions |
|---|---|
| Drug queries | adverseEventsQuery, indicationsQuery, knownDrugsChemblQuery, mechanismsOfActionQuery, pharmacogenomicsChemblQuery |
| Gene / target queries | compGenomicsQuery, depMapQuery, geneOntologyQuery, geneticConstraintQuery, hallmarksQuery, interactionsQuery, knownDrugsGeneQuery, mousePhenotypesQuery, pathwaysQuery, pharmacogenomicsGeneQuery, safetyQuery |
| Gene + disease evidence | chemblQuery, clinVarQuery, europePMCQuery, geneBurdenQuery, genomicsEnglandQuery, orphanetQuery, uniprotLiteratureQuery |
| Variant queries | pharmacogenomicsVariantQuery, uniProtVariantsQuery, variantEffectPredictorQuery, variantEffectQuery, variantsQuery |
| Genetics / GWAS | gwasColocalisation, gwasCredibleSet, gwasCredibleSetsQuery, locus2GeneQuery, overlapInfoForStudy, qtlCredibleSetsQuery, sharedTraitStudiesQuery |
Full documentation: https://amirfeizi.github.io/otargen/
What's new in 2.0.1
Bug fixes for HTTP 400 errors caused by upstream Open Targets API schema changes. Nine functions updated: chemblQuery, clinVarQuery, geneBurdenQuery, orphanetQuery, indicationsQuery, knownDrugsChemblQuery, knownDrugsGeneQuery, geneOntologyQuery, and interactionsQuery. See NEWS.md for details.
Citation
If you use otargen in your research, please cite:
Feizi A, Ray D (2023). otargen: an R package for accessing and visualizing Open Targets Genetics data. Bioinformatics, 39(7). https://doi.org/10.1093/bioinformatics/btad441
Contributing
Bug reports and feature requests: GitHub Issues
Contributions are welcome via pull requests on GitHub.
License
MIT.