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bedrock.bio

open_targets.evidence_gene_burden

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
targetId id targetFromSourceId diseaseFromSourceMappedId datasourceId datatypeId allelicRequirements diseaseFromSource pValueMantissa pValueExponent ... sex diseaseFromSourceId qualityControls diseaseId publicationDate evidenceDate score directionOnTrait directionOnTarget version
0 ENSG00000118137 0bdbe6c6679238e3e2663beaeba8873d1ad1bf88 APOA1 EFO_0022282 gene_burden genetic_association [dominant] 23642#Free Cholesterol to Total Lipids in Medi... 1.677 -15 ... <NA> NaN [] EFO_0022282 2021-08-10 2021-08-10 0.833165 protect LoF 26.09
1 ENSG00000176170 165eacc862da8e145ff0eac2d7f2505b2b69a0ab ENSG00000176170 OBA_0002272 gene_burden genetic_association <NA> Immature reticulocyte fraction 1.921 -15 ... <NA> 30280 [] OBA_0002272 2022-08-15 2022-08-15 0.828743 protect LoF 26.09
2 ENSG00000015520 16aae75ef7071a2ad438c31a2ac707d8b841ea8e ENSG00000015520 EFO_0004574 gene_burden genetic_association <NA> Total cholesterol 9.701 -16 ... <NA> NaN [] EFO_0004574 2026-05-24 2026-05-24 0.850990 NaN LoF 26.09
3 ENSG00000084674 18d5ddf659af027733eb74b4466b75418eae1f91 APOB EFO_0022270 gene_burden genetic_association [dominant] 23577#NMR Free Cholesterol in Small HDL 3.475 -20 ... <NA> NaN [] EFO_0022270 2021-08-10 2021-08-10 1.000000 protect LoF 26.09
4 ENSG00000155657 1cfb603ff0f4daa12ef09e27b74545d846e4f029 TTN EFO_0011011 gene_burden genetic_association <NA> Sitting height (20015) 5.250 -13 ... <NA> NaN [] EFO_0011011 2021-10-18 2021-10-18 0.645988 protect LoF 26.09

Description

Section titled “Description”

Disease-target evidence based on testing aggregated effect of variants, curated from the literature by the Open Targets team [Target-Disease]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
targetId TEXT Open Targets target identifier
id TEXT Identifer of the disease/target evidence
targetFromSourceId TEXT Target ID in resource of origin (accepted sources include Ensembl gene ID, Uniprot ID, gene symbol), only capital letters are accepted
diseaseFromSourceMappedId TEXT Mapped Open Targets disease identifier
datasourceId TEXT Identifer of the evidence source
datatypeId TEXT Type of the evidence
allelicRequirements TEXT[] Inheritance patterns
diseaseFromSource TEXT Disease label from the original source
pValueMantissa DOUBLE Mantissa of the p-value
pValueExponent BIGINT Exponent of the p-value
beta DOUBLE Effect size of numeric traits
betaConfidenceIntervalLower DOUBLE Lower value of the confidence interval
betaConfidenceIntervalUpper DOUBLE Upper value of the confidence interval
oddsRatio DOUBLE Size of effect captured as odds ratio
oddsRatioConfidenceIntervalLower DOUBLE Lower value of the confidence interval for odds ratio
oddsRatioConfidenceIntervalUpper DOUBLE Upper value of the confidence interval for odds ratio
resourceScore DOUBLE Score provided by datasource indicating strength of target-disease association
ancestry TEXT Genetic origin of a population
ancestryId TEXT Identifier of the ancestry in the HANCESTRO ontology [bioregistry:hancestro]
literature TEXT[] List of PubMed or preprint reference identifiers
projectId TEXT The identifer of the project that generated the data
cohortId TEXT Identifier of the studied cohort
releaseVersion TEXT Open Targets data release version
studySampleSize BIGINT Sample size of study
studyCases BIGINT Number of cases in case-control study
studyCasesWithQualifyingVariants BIGINT Number of cases in case-control study that carry at least one allele of the qualifying variant
statisticalMethod TEXT Statistical method used to calculate the association
statisticalMethodOverview TEXT Overview of the statistical method used to calculate the association
urls STRUCT(niceName TEXT, url TEXT)[] Reference to linked external resource (e.g. clinical trials, studies, package inserts, reports, etc.)
sex TEXT[] Sex of the samples/population included in the analysis
diseaseFromSourceId TEXT Disease identifier from the original source
qualityControls TEXT[] Evidence quality flags
diseaseId TEXT Open Targets disease identifier
publicationDate TEXT Date of the earliest publication supporting the evidence
evidenceDate TEXT Earliest data for the evidence
score DOUBLE Score of the evidence reflecting the strength of the disease/target relationship
directionOnTrait TEXT Predicted direction of effect on the trait
directionOnTarget TEXT Gain or loss of function effect of the evidence on the target resulting from genetic variants, pharmacological modulation, or other perturbations
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.