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bedrock.bio

open_targets.association_by_datasource_direct

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
diseaseId targetId aggregationType aggregationValue associationScore evidenceCount timeseries currentNovelty version
0 EFO_0000180 ENSG00000020633 datasourceId europepmc 0.030415 1 [{'year': 2025, 'associationScore': 0.03041483... 0.000000e+00 26.09
1 EFO_0000180 ENSG00000081985 datasourceId europepmc 0.012166 1 [{'year': 2022, 'associationScore': 0.01216593... 1.450215e-03 26.09
2 EFO_0000180 ENSG00000086065 datasourceId europepmc 0.076037 2 [{'year': 2026, 'associationScore': 0.07603708... 6.697325e-02 26.09
3 EFO_0000180 ENSG00000091513 datasourceId europepmc 0.079417 16 [{'year': 2014, 'associationScore': 0.02281112... 8.253626e-04 26.09
4 EFO_0000180 ENSG00000102265 datasourceId europepmc 0.115069 3 [{'year': 2022, 'associationScore': 0.11506946... 2.234020e-08 26.09

Description

Section titled “Description”

Data source-specific metrics for direct target-disease associations and its development over time implying association novelty.

Dataset contains association scores calculated for each data source indepedently for the aggregation of all evidence supporting any given target-disease.

This dataset only contains direct associations, therefore no evidence is propagated across the disease or phenotype space using the Experimental Factor Ontology [Target-Disease]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
diseaseId TEXT Open Targets disease identifier
targetId TEXT Unique identifier for the target [bioregistry:ensembl]
aggregationType TEXT Evidence column used to aggregate data: datasourceId
aggregationValue TEXT Datasource identifier of the group: eg. gwas_credible_set
associationScore DOUBLE Current disease/target association score of evidence from the given datasource
evidenceCount BIGINT Total number of evidence supporting the disease/target association for a given datasource
timeseries STRUCT(year INT, associationScore DOUBLE, novelty DOUBLE, yearlyEvidenceCount INT)[] Timeseries describing the evolution of association
currentNovelty DOUBLE Novelty of the disease/target association
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.