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bedrock.bio

open_targets.baseline_expression

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
celltypeBiosampleId tissueBiosampleId targetId datasourceId datatypeId unit celltypeBiosampleFromSource min q1 median q3 max distribution_score specificity_score tissueBiosampleFromSource targetFromSourceId tissueBiosampleParentId celltypeBiosampleParentId qualityControls version
0 CL_0000097 UBERON_0001832 ENSG00000000003 tabula_sapiens scrna-seq CPM(pseudobulk sum[counts]) mast cell 0.000000 0.000000 0.000000 0.000000 0.000000 0.443141 0.0 sublingual gland None UBERON_0001044 CL_0000766 [] 26.09
1 CL_0000232 UBERON_0000947 ENSG00000000003 tabula_sapiens scrna-seq CPM(pseudobulk sum[counts]) erythrocyte 0.000000 0.000000 0.000000 0.000000 0.000000 0.443141 0.0 aorta None UBERON_0001981 CL_0000764 [] 26.09
2 CL_0000235 UBERON_0004222 ENSG00000000003 tabula_sapiens scrna-seq CPM(pseudobulk sum[counts]) macrophage 0.000000 0.000000 0.000000 0.000000 0.000000 0.443141 0.0 stomach smooth muscle None UBERON_0000945 CL_0000766 [] 26.09
3 CL_0000359 UBERON_0001736 ENSG00000000003 tabula_sapiens scrna-seq CPM(pseudobulk sum[counts]) vascular associated smooth muscle cell 5.871992 5.871992 5.871992 5.871992 5.871992 0.443141 0.0 submandibular gland None UBERON_0001044 CL_0000183 [] 26.09
4 CL_0000576 UBERON_0002107 ENSG00000000003 tabula_sapiens scrna-seq CPM(pseudobulk sum[counts]) monocyte 0.000000 0.000000 0.864546 4.009778 8.959365 0.443141 0.0 liver None UBERON_0002107 CL_0000766 [] 26.09

Description

Section titled “Description”

Aggregated expression data generated from RNA-seq and mass spectrometry proteomic data [Target]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
celltypeBiosampleId TEXT Cell type identifier that maps to the cell type reported by study [bioregistry:cell ontology]
tissueBiosampleId TEXT Tissue identifier that maps to the tissue reported by study [bioregistry:uberon]
targetId TEXT Unique identifier for the target
datasourceId TEXT Origin of expression data
datatypeId TEXT Type of expression data
unit TEXT Unit for the target expression
celltypeBiosampleFromSource TEXT Tissue or cell type reported by study
min DOUBLE Minimum value of expression
q1 DOUBLE First quantile of expression
median DOUBLE Median value of expression
q3 DOUBLE Third quantile of expression
max DOUBLE Maximum value of expression
distribution_score DOUBLE Proportion of biosamples, within the dataset, that display median expression above a threshold
specificity_score DOUBLE Measure of how specific expression is to a biosample
tissueBiosampleFromSource TEXT Cell type reported by study
targetFromSourceId TEXT Target identifier from the source
tissueBiosampleParentId TEXT Broad tissue identifier that maps to the tissue reported by study [bioregistry:uberon]
celltypeBiosampleParentId TEXT Broad cell type identifier that maps to the cell type reported by study [bioregistry:cell ontology]
qualityControls TEXT[] Quality control flags or notes for baseline expression
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.