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bedrock.bio

open_targets.association_overall_direct

import bedrock_bio as bb

rel = bb.load_table('open_targets.association_overall_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 ENSG00000009413 overall None 0.001480 1 [{'year': 2017, 'associationScore': 0.0, 'nove... 1.764322e-04 26.09
1 EFO_0000180 ENSG00000042832 overall None 0.009991 2 [{'year': 2002, 'associationScore': 0.00999067... 0.000000e+00 26.09
2 EFO_0000180 ENSG00000066422 overall None 0.026642 1 [{'year': 2023, 'associationScore': 0.0, 'nove... 2.616261e-02 26.09
3 EFO_0000180 ENSG00000076984 overall None 0.008141 2 [{'year': 2023, 'associationScore': 0.00814054... 1.280905e-05 26.09
4 EFO_0000180 ENSG00000082175 overall None 0.038020 3 [{'year': 2008, 'associationScore': 0.03700248... 3.102197e-08 26.09

Description

Section titled “Description”

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

Dataset contains the overall association score 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 How evidence data was aggregated: overall
aggregationValue TEXT For overall association this column is empty
associationScore DOUBLE Current disease/target association score of evidence from any datasource
evidenceCount BIGINT Total number of evidence supporting the disease/target association for any datasource
timeseries STRUCT(year INT, associationScore DOUBLE, novelty DOUBLE, yearlyEvidenceCount BIGINT)[] 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.