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bedrock.bio

open_targets.evidence_cancer_biomarkers

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
id targetFromSourceId diseaseFromSourceMappedId datasourceId datatypeId drugFromSource drugId drugResponse diseaseFromSource confidence ... literature urls biomarkers qualityControls diseaseId targetId publicationDate evidenceDate score version
0 8f4586585642f889be1e83b21c64f9133fd9ea1b MET EFO_0000571 cancer_biomarkers affected_pathway Rociletinib CHEMBL3545308 EFO_0020001 Lung adenocarcinoma Case report ... [27252416] <NA> {'geneExpression': None, 'geneticVariation': [... [] MONDO_0005061 ENSG00000105976 2016-06-01 2016-06-01 1.0 26.09
1 e10df7ab627a7e5a2bf20b48d77321b7d01f00f9 BRAF EFO_0000389 cancer_biomarkers affected_pathway Braf Inhibitors NaN EFO_0020001 Cutaneous melanoma Early trials ... <NA> <NA> {'geneExpression': None, 'geneticVariation': [... [] MONDO_0005012 ENSG00000157764 NaN NaN 1.0 26.09
2 4b3688b44b75c63c16cec5ed66bda97b8796226d TPMT EFO_0000311 cancer_biomarkers affected_pathway Mercaptopurine CHEMBL1200751 EFO_0007053 Any cancer type FDA guidelines ... <NA> [{'niceName': 'Food and Drug Administration gu... {'geneExpression': None, 'geneticVariation': [... [] MONDO_0004992 ENSG00000137364 NaN NaN 1.0 26.09
3 1250fc37679fb429fcbe79cdd57171f021cd59bb CCND3 EFO_0000311 cancer_biomarkers affected_pathway Cdk4/6 Inhibitors NaN GO_0042493 Any cancer type Pre-clinical ... [22471707] <NA> {'geneExpression': None, 'geneticVariation': [... [] MONDO_0004992 ENSG00000112576 2012-01-01 2012-01-01 1.0 26.09
4 c322cfa4a90d3d65940b2ba06942b8b4d7c4ad42 TSC1 EFO_0000272 cancer_biomarkers affected_pathway Everolimus CHEMBL1908360 GO_0042493 Giant cell astrocytoma FDA guidelines ... <NA> [{'niceName': 'Food and Drug Administration gu... {'geneExpression': None, 'geneticVariation': [... [] MONDO_0019781 ENSG00000165699 NaN NaN 1.0 26.09

Description

Section titled “Description”

Disease-target evidence based on cancer biomarkers from the Cancer Genome Interpreter [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
datasourceId TEXT Identifer of the evidence source
datatypeId TEXT Type of the evidence
drugFromSource TEXT Drug name/family in resource of origin
drugId TEXT Open Targets drug identifier [bioregistry:chembl]
drugResponse TEXT Observed patterns of drug response
diseaseFromSource TEXT Disease label from the original source
confidence TEXT Confidence qualifier on the reported evidence
biomarkerName TEXT Altered characteristics that influences the disease process
literature TEXT[] List of PubMed or preprint reference identifiers
urls STRUCT(niceName TEXT, url TEXT)[] Reference to linked external resource (e.g. clinical trials, studies, package inserts, reports, etc.)
biomarkers STRUCT(geneExpression STRUCT(id TEXT, name TEXT)[], geneticVariation STRUCT(functionalConsequenceId TEXT, id TEXT, name TEXT)[]) List of biomarkers
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.