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bedrock.bio

open_targets.evidence_expression_atlas

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
id targetFromSourceId diseaseFromSourceMappedId biosamplesFromSource confidence contrast datasourceId datatypeId literature log2FoldChangePercentileRank ... resourceScore studyId studyOverview qualityControls diseaseId targetId publicationDate evidenceDate score version
0 004d367fcd96b78e7f6aee4fe97931783d57e8c4 ENSG00000144354 EFO_0003060 [UBERON_0002048] low 'squamous cell carcinoma' vs 'normal tissue ad... expression_atlas rna_expression <NA> 99 ... 0.02500 E-MTAB-5231 Gene expression analysis of lung cancer sample... [] MONDO_0005233 ENSG00000144354 NaN NaN 0.036479 26.09
1 013d9098597c3ce61e6948dbf3981652540d6aad ENSG00000150551 EFO_0000519 [UBERON_0000955] high 'glioblastoma' vs 'normal' expression_atlas rna_expression <NA> 96 ... 0.00259 E-MEXP-567 Transcription profiling of human grade II astr... [] MONDO_0018177 ENSG00000150551 NaN NaN 0.054631 26.09
2 014833379cd681a67c2733ec9c1d3157f7a0f6b6 ENSG00000155966 EFO_0000384 [UBERON_0001159] medium 'Crohn's disease' vs 'normal' in 'sigmoid colon' expression_atlas rna_expression [29031501] 98 ... 0.03530 E-MTAB-5464 RNA sequencing of purified intestinal epitheli... [] MONDO_0005011 ENSG00000155966 2017-10-12 2017-10-12 0.018501 26.09
3 01cce20b9023cb98dfb08af4fc33b5553f8cdc92 ENSG00000166482 EFO_0000702 [UBERON_0002048] high 'small cell lung carcinoma' vs 'normal' expression_atlas rna_expression [27093186] 98 ... 0.00002 E-GEOD-60052 RNA-seq of primary tumors from 79 small cell l... [] MONDO_0008433 ENSG00000166482 2016-04-19 2016-04-19 0.133607 26.09
4 01f086ec5e9126b03f62cf8e4103788308e6de29 ENSG00000182240 EFO_0003778 [UBERON_0001090] medium 'psoriatic arthritis' vs 'healthy' in 'synovia... expression_atlas rna_expression <NA> 96 ... 0.01380 E-MTAB-3201 GENE EXPRESSION ANALYSIS  OF SYNOVIAL BIOPSIES... [] MONDO_0011849 ENSG00000182240 NaN NaN 0.023214 26.09

Description

Section titled “Description”

Disease-target evidence based on differential expression data provided by Expression Atlas [Target-Disease]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
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
biosamplesFromSource TEXT[] Identifier of the referenced biological material
confidence TEXT Confidence qualifier on the reported evidence
contrast TEXT Experiment contrast
datasourceId TEXT Identifer of the evidence source
datatypeId TEXT Type of the evidence
literature TEXT[] List of PubMed or preprint reference identifiers
log2FoldChangePercentileRank BIGINT Percentile of top differentially regulated genes (transcripts) within experiment
log2FoldChangeValue DOUBLE Log 2 fold expression change in contrast experiment
resourceScore DOUBLE Score provided by datasource indicating strength of target-disease association
studyId TEXT Identifier of the study generating the data
studyOverview TEXT Description of the study
qualityControls TEXT[] Evidence quality flags
diseaseId TEXT Open Targets disease identifier
targetId TEXT Open Targets target 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
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.