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bedrock.bio

open_targets.evidence_gene2phenotype

import bedrock_bio as bb

rel = bb.load_table('open_targets.evidence_gene2phenotype')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
targetId id targetFromSourceId diseaseFromSourceMappedId literature studyId confidence allelicRequirements diseaseFromSourceId diseaseFromSource ... datasourceId datatypeId qualityControls diseaseId publicationDate evidenceDate score directionOnTrait directionOnTarget version
0 ENSG00000119888 6a8fea8a7fba511483d0297b6dcdd3cc31e5f654 EPCAM MONDO_0013184 [18572020, 19820410, 20034091, 21315192, 24048... DD definitive [biallelic_autosomal] MONDO:0013184 diarrhea with tufting enteropathy, congenital ... gene2phenotype genetic_literature [] MONDO_0013184 2008-05-15 2008-05-15 1.0 risk LoF 26.09
1 ENSG00000152104 b7c3ca2309b534137109d7efbf41c8c3c90e91c2 PTPN14 MONDO_0013324 [20826270] DD strong [biallelic_autosomal] MONDO:0013324 choanal atresia and lymphedema ... gene2phenotype genetic_literature [] MONDO_0013324 2010-09-01 2010-09-01 1.0 risk LoF 26.09
2 ENSG00000196586 f24e3ddb7ba109aca4ac489d69156e06d7cac8c3 MYO6 MONDO_0019497 [18348273, 23485424, 24105371, 25999546] Ear definitive [monoallelic_autosomal] NaN nonsyndromic genetic hearing loss ... gene2phenotype genetic_literature [] MONDO_0019497 2008-04-01 2008-04-01 1.0 risk NaN 26.09
3 ENSG00000100146 1b7bf11bf144659f55b70f17772db31c867991c2 SOX10 MONDO_0018094 [10077527, 17999358, 18348267, 18348274, 18627... DD; Eye; Skin definitive [monoallelic_autosomal] MONDO:0012698 Waardenburg syndrome ... gene2phenotype genetic_literature [] MONDO_0018094 1996-10-01 1996-10-01 1.0 risk LoF 26.09
4 ENSG00000132518 24e4bb703ccd99fc4d5889da680b87d9e41e34af GUCY2D MONDO_0018998 [12325031, 12623820, 29061346, 8944027] Eye definitive [biallelic_autosomal] MONDO:0008764 Leber congenital amaurosis ... gene2phenotype genetic_literature [] MONDO_0018998 1996-12-01 1996-12-01 1.0 risk LoF 26.09

Description

Section titled “Description”

Disease-target evidence curated by the Gene2Phenotype consortium [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
literature TEXT[] List of PubMed or preprint reference identifiers
studyId TEXT Identifier of the study generating the data
confidence TEXT Confidence qualifier on the reported evidence
allelicRequirements TEXT[] Inheritance patterns
diseaseFromSourceId TEXT Disease identifier from the original source
diseaseFromSource TEXT Disease label from the original source
variantFunctionalConsequenceId TEXT Sequence ontology (SO) identifier of the functional consequence of the variant [bioregistry:so]
datasourceId TEXT Identifer of the evidence source
datatypeId TEXT Type of the evidence
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.