open_targets.target_essentiality

Python

In [1]:

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()

Out[1]:

	targetId	isEssential	depMapEssentiality	version
0	ENSG00000109851	False	[{'tissueId': 'UBERON_0002097', 'tissueName': ...	26.09
1	ENSG00000138640	False	[{'tissueId': 'UBERON_0002367', 'tissueName': ...	26.09
2	ENSG00000180228	True	[{'tissueId': 'UBERON_0002113', 'tissueName': ...	26.09
3	ENSG00000165672	False	[{'tissueId': 'UBERON_0000473', 'tissueName': ...	26.09
4	ENSG00000127366	False	[{'tissueId': None, 'tissueName': 'other', 'sc...	26.09

R

In [1]:

library(bedrockbio)

lf <- load_table("open_targets.target_essentiality")
df <- head(lf, 5) |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 3 of 4 columns)
   targetId        | isEssential | version
   --------------- | ----------- | -------
0  ENSG00000109851 | false       | 26.09
1  ENSG00000138640 | false       | 26.09
2  ENSG00000180228 | true        | 26.09
3  ENSG00000165672 | false       | 26.09
4  ENSG00000127366 | false       | 26.09

Description

Target essentiality assessments based on dependencies exhibited when knocking-out genes in cancer cellular models using CRISPR screenings as reported in by the Cancer DepMap Project.

Gene effects below -1 can be considered dependencies [Target]

Partitions

Not partitioned.

Schema

Column	Type	Description
targetId	TEXT	Target identifier the essentiality was measured on [bioregistry:ensembl]
isEssential	BOOLEAN	Boolean flag indicating whether the tested gene is considered essential in the given context
depMapEssentiality	STRUCT(tissueId TEXT, tissueName TEXT, screens STRUCT(depmapId TEXT, cellLineName TEXT, diseaseFromSource TEXT, diseaseCellLineId TEXT, mutation TEXT, geneEffect FLOAT, expression FLOAT)[])[]	Essentiality measurements extraced from DepMap, stratified by tissue or anatomical units
version	TEXT	Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.