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bedrock.bio

open_targets.evidence_cancer_gene_census

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
targetId id targetFromSourceId diseaseFromSourceMappedId datasourceId datatypeId diseaseFromSourceId literature mutatedSamples resourceScore studyId qualityControls diseaseId publicationDate evidenceDate score directionOnTrait directionOnTarget version
0 ENSG00000198053 02b6aea89d550e1563d283563456b855332444b0 ENSG00000198053 EFO_1000560 cancer_gene_census somatic_mutation None [24825865] [{'functionalConsequenceId': 'SO_0001583', 'nu... 0.50 NaN [] MONDO_0019468 2014-05-13 2014-05-13 0.50 risk NaN 26.09
1 ENSG00000118513 02c5f0c52bec051ca5d59ba10d4d3f67363e6ff6 ENSG00000118513 EFO_0000349 cancer_gene_census somatic_mutation None [25159823, 22138691, 24504440] [{'functionalConsequenceId': 'SO_0001583', 'nu... 0.75 416 [] MONDO_0005005 2011-12-04 2011-12-04 0.75 risk GoF 26.09
2 ENSG00000159216 030e5e71027310fa9095044016e9945705ed7935 ENSG00000159216 EFO_0002916 cancer_gene_census somatic_mutation None <NA> [{'functionalConsequenceId': 'SO_0001583', 'nu... 0.50 582 [] MONDO_0019086 NaN NaN 0.50 risk NaN 26.09
3 ENSG00000198822 042f57fe21792f879e689a64c3f3a9d1e4182784 ENSG00000198822 EFO_1000071 cancer_gene_census somatic_mutation None <NA> [{'functionalConsequenceId': 'SO_0001059', 'nu... 0.25 652 [] MONDO_0003185 NaN NaN 0.25 risk NaN 26.09
4 ENSG00000185920 0532333af0a779d0137dd5810bf3c06bd04c6072 ENSG00000185920 MONDO_0015686 cancer_gene_census somatic_mutation None [29162652] [{'functionalConsequenceId': 'SO_0001583', 'nu... 0.50 NaN [] MONDO_0015686 2017-11-21 2017-11-21 0.50 risk LoF 26.09

Description

Section titled “Description”

Disease-target evidence based on Cancer Gene Census provided by COSMIC [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
diseaseFromSourceId TEXT Disease identifier from the original source
literature TEXT[] List of PubMed or preprint reference identifiers
mutatedSamples STRUCT(functionalConsequenceId TEXT, numberMutatedSamples BIGINT, numberSamplesTested BIGINT, numberSamplesWithMutationType BIGINT)[] Samples with a given mutation tested
resourceScore DOUBLE Score provided by datasource indicating strength of target-disease association
studyId TEXT Identifier of the study generating the data
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.