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bedrock.bio

open_targets.pharmacogenomics

import bedrock_bio as bb

rel = bb.load_table('open_targets.pharmacogenomics')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
datasourceId datasourceVersion datatypeId directionality evidenceLevel genotype genotypeAnnotationText genotypeId haplotypeFromSourceId haplotypeId ... phenotypeText variantAnnotation studyId targetFromSourceId variantFunctionalConsequenceId variantRsId variantId isDirectTarget drugs version
0 clinpgx 2026-07-05 clinical_annotation NaN 4 Mediterranean, Dallas, Panama' Sassari, Caglia... Female patients with the heterozygous for the ... None NaN G6PD Mediterranean, Dallas, Panama' Sassari, C... ... varying degree of G6PD deficient red blood cel... <NA> 1183705226 ENSG00000160211 None None None False [{'drugFromSource': 'chloroquine', 'drugId': '... 26.09
1 clinpgx 2026-07-05 clinical_annotation No function 3 *6 Individuals with one *6 allele in combination ... None PA166128233 CYP3A5*6 ... metabolize atazanavir more rapidly [{'baseAlleleOrGenotype': '*3 + *6 + *7', 'com... 1185000451 ENSG00000106258 None None None False [{'drugFromSource': 'atazanavir', 'drugId': 'C... 26.09
2 clinpgx 2026-07-05 clinical_annotation Normal function 3 *1 Patients carrying the *1 allele in addition to... None PA165816576 CYP2D6*1 ... decreased risk of drug toxicity [{'baseAlleleOrGenotype': '*1/*2xN', 'comparis... 1449310414 ENSG00000272532 None None None False [{'drugFromSource': 'hydrocodone', 'drugId': '... 26.09
3 clinpgx 2026-07-05 clinical_annotation Decreased function 3 *10 Patients carrying the *10 allele in combinatio... None PA165816582 CYP2D6*10 ... NaN [{'baseAlleleOrGenotype': '*1/*3 + *1/*4 + *1/... 1451208340 ENSG00000283284 None None None False [{'drugFromSource': 'ketoprofen', 'drugId': 'C... 26.09
4 clinpgx 2026-07-05 clinical_annotation Decreased function 3 *28 Patients carrying the *28 allele in combinatio... None PA166115842 UGT1A1*28 ... increased likelihood of hyperbilirubinemia [{'baseAlleleOrGenotype': '*1/*28', 'compariso... 1451204520 ENSG00000241635 None None None False [{'drugFromSource': 'sorafenib', 'drugId': 'CH... 26.09

Description

Section titled “Description”

Genetic variants influencing individual drug responses.

Pharmacogenetics data is integrated from sources including ClinPGx [Target, Genetics]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
datasourceId TEXT Identifier for the data provider
datasourceVersion TEXT Data provider version number
datatypeId TEXT Classification of the type of pharmacogenomic data (e.g. clinical_annotation)
directionality TEXT Indicates wether the genetic variant increases or decreases drug response
evidenceLevel TEXT Strength of the scientific support for the variant/drug response
genotype TEXT Genetic variant configuration
genotypeAnnotationText TEXT Explanation of the genotype’s clinical significance
genotypeId TEXT Identifier for the specific genetic variant combination (e.g. 1_1500_A_A,T)
haplotypeFromSourceId TEXT Haplotype ID in the ClinPGx dataset
haplotypeId TEXT Combination of genetic variants that constitute a particular allele of a gene (e.g. CYP2C9*3)
literature TEXT[] List of PubMed or preprint reference identifiers
pgxCategory TEXT Classification of the drug response type (e.g. Toxicity)
phenotypeFromSourceId TEXT Open Targets disease identifier result of mapping phenotypeText
phenotypeText TEXT Drug response influenced by the variation
variantAnnotation STRUCT(baseAlleleOrGenotype TEXT, comparisonAlleleOrGenotype TEXT, directionality TEXT, effect TEXT, effectDescription TEXT, effectType TEXT, entity TEXT, id TEXT, literature TEXT)[] Metadata on the underlying variation
studyId TEXT Clinical Annotation ID in the ClinPGx dataset
targetFromSourceId TEXT Open Targets target identifier as provided by the data source
variantFunctionalConsequenceId TEXT The sequence ontology identifier of the consequence of the variant based on Ensembl VEP in the context of the transcript [bioregistry:so]
variantRsId TEXT Variant reference SNP cluster ID (Rsid)
variantId TEXT The unique identifier for the variant following schema: {chromosome}-{position}-{referenceAllele}-{alternateAllele}
isDirectTarget BOOLEAN Flag indicating whether the target overlapping the variation is directly targeted by the drug
drugs STRUCT(drugFromSource TEXT, drugId TEXT)[] List of drug references
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.