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bedrock.bio

open_targets.evidence_intogen

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
targetId id targetFromSourceId diseaseFromSourceMappedId datatypeId datasourceId cohortId cohortShortName cohortDescription significantDriverMethods ... resourceScore literature qualityControls diseaseId publicationDate evidenceDate score directionOnTrait directionOnTarget version
0 ENSG00000105568 38ab91171f4572bc2aac710a43895ed7f9477b25 PPP2R1A MONDO_0011962 somatic_mutation intogen CPTAC_WXS_UCEC_2020 CPTAC_WXS_UCEC_2020 Endometrial Carcinoma from CPTAC [dndscv, smregions, mutpanning, hotmaps] ... 6.202246e-18 <NA> [] MONDO_0011962 NaN NaN 1.000000 risk GoF 26.09
1 ENSG00000157764 88024f55d6e1832370a593760c65db51eb895824 BRAF MONDO_0005105 somatic_mutation intogen STJUDE_WGS_D_CM_2018 STJUDE_WGS_D_CM_2018 Melanoma from STJUDE [smregions] ... 5.060343e-07 <NA> [] MONDO_0005105 NaN NaN 0.691318 risk GoF 26.09
2 ENSG00000141510 003580f5067f5c4a72ede70a315e29229aabb84b TP53 MONDO_0005008 somatic_mutation intogen PCAWG_WGS_COLORECT_ADENOCA PCAWG_WGS_COLORECT_ADENOCA Colorectal Adenocarcinoma from PCAWG [oncodrivefml, dndscv, smregions, cbase, mutpa... ... 5.440269e-40 [32025007] [] MONDO_0005008 2020-02-05 2020-02-05 1.000000 risk LoF 26.09
3 ENSG00000198793 35ea4b89591269c805753941ea5e25316394bfd5 MTOR MONDO_0005008 somatic_mutation intogen HARTWIG_WGS_COADREAD_2023 HARTWIG_WGS_COADREAD_2023 Colorectal Adenocarcinoma from Hartwig Medical... [combination] ... 3.127027e-03 <NA> [] MONDO_0005008 NaN NaN 0.375406 risk GoF 26.09
4 ENSG00000168702 4875b411fe6c52fda557c1d907312b853d81e97e LRP1B MONDO_0005036 somatic_mutation intogen CBIOP_WXS_EGC_TMUCIH_2015 CBIOP_WXS_EGC_TMUCIH_2015 Stomach Adenocarcinoma from TMUCIH, PNAS 2015 [combination] ... 2.244832e-02 [25583476] [] MONDO_0005036 2015-01-12 2015-01-12 0.304068 risk LoF 26.09

Description

Section titled “Description”

Cancer-driver gene evidence based on the analysis of large-scale mutational data from IntOGen [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
datatypeId TEXT Type of the evidence
datasourceId TEXT Identifer of the evidence source
cohortId TEXT Identifier of the studied cohort
cohortShortName TEXT Short name of the studied cohort
cohortDescription TEXT Description of the studied cohort
significantDriverMethods TEXT[] Methods to detect cancer driver genes producing significant results
mutatedSamples STRUCT(functionalConsequenceId TEXT, numberMutatedSamples BIGINT, numberSamplesTested BIGINT, numberSamplesWithMutationType BIGINT)[] Samples with a given mutation tested
diseaseFromSource TEXT Disease label from the original source
resourceScore DOUBLE Score provided by datasource indicating strength of target-disease association
literature TEXT[] List of PubMed or preprint reference identifiers
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.