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bedrock.bio

open_targets.study

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
studyId geneId projectId studyType traitFromSource traitFromSourceMappedIds biosampleFromSourceId pubmedId publicationTitle publicationFirstAuthor ... qualityControls analysisFlags summarystatsLocation hasSumstats condition sumstatQCValues diseaseIds backgroundDiseaseIds biosampleId version
0 FINNGEN_R12_AUTOIMMUNE_HYPERTHYROIDISM None FINNGEN_R12 gwas Autoimmune hyperthyroidism [EFO_0004237] None 36653562 NaN NaN ... [Study has non empty or zero nCases, nControls... [] gs://finngen-public-data-r12/summary_stats/fin... True None <NA> [MONDO_0005364] [] None 26.09
1 FINNGEN_R12_CD2_BENIGN_LARYNX None FINNGEN_R12 gwas Benign neoplasm: Larynx [MONDO_0002354] None 36653562 NaN NaN ... [Study has non empty or zero nCases, nControls... [] gs://finngen-public-data-r12/summary_stats/fin... True None <NA> [MONDO_0002354] [] None 26.09
2 FINNGEN_R12_E4_ADRENAS None FINNGEN_R12 gwas Disorders of adrenal gland, other and/or unspe... [EFO_0005539] None 36653562 NaN NaN ... [Study has non empty or zero nCases, nControls... [] gs://finngen-public-data-r12/summary_stats/fin... True None <NA> [MONDO_0005495] [] None 26.09
3 FINNGEN_R12_H7_PRESBYOPIA None FINNGEN_R12 gwas Presbyopia [MONDO_0001330] None 36653562 NaN NaN ... [Study has non empty or zero nCases, nControls... [] gs://finngen-public-data-r12/summary_stats/fin... True None <NA> [MONDO_0001330] [] None 26.09
4 GCST000337_7 None GCST gwas Quantitative traits [EFO_0004611] None 19197348 Genome-wide association studies in an isolated... Lowe JK ... [Harmonized summary statistics are not availab... [] NaN <NA> None <NA> [EFO_0004611] [] None 26.09

Description

Section titled “Description”

Metadata for all complex trait GWAS and molecular QTL studies in the Platform.

The dataset includes study metadata, phenotype information, sample sizes, publication information and more.

Molecular QTL studies are split by their target trait (e.g. gene, splice junction, etc), biosample (tissue, cell type or cell line) and condition (e.g. stimulation, time period, etc), potentially leading to tens of thousands of studies derived from the same publication [Genetics]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
studyId TEXT Unique identifier of the GWAS or molQTL study.
geneId TEXT Ensembl identifier of the gene representing a specific gene whose molecular is being analysed in molQTL study [bioregistry:ensembl]
projectId TEXT Identifier of the source project collection that the study information is derived from
studyType TEXT Field specifying if study contains phenotype/disease or molecular genetic associations
traitFromSource TEXT Molecular or phenotypic trait, derived from source, analysed in the study
traitFromSourceMappedIds TEXT[] Phenotypic trait IDs that map to the analysed trait reported by study
biosampleFromSourceId TEXT Identifier of the referenced biological material
pubmedId TEXT PubMed identifier of the publication that references the study [bioregistry:pubmed]
publicationTitle TEXT Title of the publication that references the study
publicationFirstAuthor TEXT Last name and initials of the author of the publication that references the study
publicationDate TEXT Date of the publication that references the study
publicationJournal TEXT Abbreviated journal name where the publication referencing study was published
backgroundTraitFromSourceMappedIds TEXT[] Any background trait(s) shared by all individuals in the study
initialSampleSize TEXT Study initial sample size
nCases INT The number of cases in this broad ancestry group
nControls INT The number of controls in this broad ancestry group
nSamples INT The number of samples tested in GWAS analysis
cohorts TEXT[] List of cohort(s) represented in the discovery sample
ldPopulationStructure STRUCT(ldPopulation TEXT, relativeSampleSize DOUBLE)[] Collection of populations referenced by the study
discoverySamples STRUCT(sampleSize INT, ancestry TEXT)[] Collection of ancestries reported by the study discovery phase
replicationSamples STRUCT(sampleSize INT, ancestry TEXT)[] Collection of ancestries reported by the study replication phase
qualityControls TEXT[] Control metrics refining study validation
analysisFlags TEXT[] Collection of flags indicating the type of the analysis conducted in the association study
summarystatsLocation TEXT Path to the source study summary statistics (if exists at the source)
hasSumstats BOOLEAN Indication whether the summary statistics exist in the source
condition TEXT Reported sample conditions
sumstatQCValues STRUCT(QCCheckName TEXT, QCCheckValue FLOAT)[] Mapping of quality control flags
diseaseIds TEXT[] Disease identifier associated with a studied trait
backgroundDiseaseIds TEXT[] Any background disease(s) shared by all individuals in the study
biosampleId TEXT Biosample identifier that maps to the biosample reported by study [bioregistry:uberon]
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.