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bedrock.bio

open_targets.evidence_eva_somatic

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
targetId id targetFromSourceId diseaseFromSourceMappedId alleleOrigins allelicRequirements clinicalSignificances cohortPhenotypes confidence datasourceId ... variantId variantRsId qualityControls diseaseId publicationDate evidenceDate score directionOnTrait directionOnTarget version
0 ENSG00000112038 095fd1e3faf52f440389b85a677b49eb0d9758e9 ENSG00000112038 EFO_0022041 [somatic] <NA> [drug response] [Tramadol response, Ultram response] no assertion criteria provided eva_somatic ... 6_154087846_GT_G rs1583463133 [] EFO_0022041 None 2020-03-29 0.90 NaN None 26.09
1 ENSG00000121879 336f95de3cfd9eebaccef7dac7e16ed70e22fed3 ENSG00000121879 MONDO_0008170 [somatic] <NA> [pathogenic] [Neoplasm of ovary, Ovarian Neoplasms, Ovarian... no assertion criteria provided eva_somatic ... 3_179204536_G_A rs1064793732 [] MONDO_0008170 None 2019-06-17 0.90 risk None 26.09
2 ENSG00000105976 0f30b8b5d34dcb14e18cdfab05fbcf88b62b1afe ENSG00000105976 MONDO_0005072 [somatic] [Somatic mutation] [other] [Neuroblastoma] no assertion criteria provided eva_somatic ... 7_116700069_C_A rs1554378983 [] MONDO_0005072 None 2017-09-26 0.30 NaN None 26.09
3 ENSG00000122008 40c46617d726124828b8f916aafc81dd0a6ccb24 ENSG00000122008 MONDO_0008315 [somatic] <NA> [pathogenic] [Malignant tumor of prostate, Prostate cancer] criteria provided, single submitter eva_somatic ... 5_75596885_T_A rs863225456 [] MONDO_0008315 None 2015-05-23 0.92 risk None 26.09
4 ENSG00000159184 45d473803cfb442fe2c35ad67e0ea5cb7a646b2c ENSG00000159184 Orphanet_1331 [somatic] <NA> [uncertain significance] [Prostate cancer, hereditary, 1] no assertion criteria provided eva_somatic ... 17_48728662_C_A rs1597935698 [] Orphanet_1331 None 2019-11-21 0.30 NaN None 26.09

Description

Section titled “Description”

Disease-target evidence based on somatic variation from ClinVar, provided by the European Variation Archive [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
alleleOrigins TEXT[] Origin of the variant allele
allelicRequirements TEXT[] Inheritance patterns
clinicalSignificances TEXT[] Standard terms to define clinical significance
cohortPhenotypes TEXT[] Clinical features/phenotypes observed in studied individuals
confidence TEXT Confidence qualifier on the reported evidence
datasourceId TEXT Identifer of the evidence source
datatypeId TEXT Type of the evidence
diseaseFromSource TEXT Disease label from the original source
diseaseFromSourceId TEXT Disease identifier from the original source
literature TEXT[] List of PubMed or preprint reference identifiers
releaseDate TEXT Date of the release of the data in a ‘YYYY-MM-DD’ format
studyId TEXT Identifier of the study generating the data
variantFromSourceId TEXT Identifier of the disease-causing variant at source
variantFunctionalConsequenceId TEXT Sequence ontology (SO) identifier of the functional consequence of the variant [bioregistry:so]
variantHgvsId TEXT Identifier in HGVS notation of the disease-causing variant
variantId TEXT Identifier in CHROM_POS_REF_ALT notation of the disease-causing variant
variantRsId TEXT Variant reference SNP cluster ID (Rsid)
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 Effect of direction on target
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.