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bedrock.bio

open_targets.evidence_reactome

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
id targetFromSourceId diseaseFromSourceMappedId datasourceId datatypeId diseaseFromSource diseaseFromSourceId literature pathways reactionId reactionName targetModulation variantAminoacidDescriptions qualityControls diseaseId targetId publicationDate evidenceDate score version
0 3274096a8dcdc95e2f4d35f6138388ec94ce53b3 P63165 MONDO_0100096 reactome affected_pathway COVID-19 DOID:0080600 [15848177] [{'id': 'R-HSA-9694631', 'name': 'Maturation o... R-HSA-9729307 Nucleoprotein is SUMOylated up_or_down <NA> [] MONDO_0100096 ENSG00000116030 2005-04-01 2005-04-01 1.0 26.09
1 38e7319f2ff8ca7a4a168fda45cd1475491daf43 P36507 EFO_0000538 reactome affected_pathway hypertrophic cardiomyopathy DOID:11984 [24937142, 21779496] [{'id': 'R-HSA-9656223', 'name': 'Signaling by... R-HSA-9656209 Dissociation of RAS:RAF1 mutant complex gain_of_function <NA> [] MONDO_0005045 ENSG00000126934 2011-03-01 2011-03-01 1.0 26.09
2 4b1732611307d3cb0f0682da98cbf9a1bf33ea48 Q53GL7 EFO_0000694 reactome affected_pathway severe acute respiratory syndrome DOID:2945 [32029454, 29199039] [{'id': 'R-HSA-9683610', 'name': 'Maturation o... R-HSA-9686061 Nucleoprotein is ADP-ribosylated up_or_down <NA> [] MONDO_0005091 ENSG00000178685 2017-12-01 2017-12-01 1.0 26.09
3 960b1f149048ea0ad03951390189ec910b88e25c Q9H9A7 EFO_0000311 reactome affected_pathway cancer DOID:162 [16793542] [{'id': 'R-HSA-9709603', 'name': 'Impaired BRC... R-HSA-9709601 Defective recruitment of BRCA2 and RAD51 due t... partial_loss_of_function <NA> [] MONDO_0004992 ENSG00000178966 2006-06-01 2006-06-01 1.0 26.09
4 b516648915ed7d1680af870cd5902b14e04c9da2 P01116 EFO_0000311 reactome affected_pathway cancer DOID:162 [25907612, 22510884, 23352452, 15035987] [{'id': 'R-HSA-6802946', 'name': 'Signaling by... R-HSA-6802921 Activated MAP2Ks phosphorylate MAPKs downstrea... gain_of_function <NA> [] MONDO_0004992 ENSG00000133703 2004-03-01 2004-03-01 1.0 26.09

Description

Section titled “Description”

Manually curated disease-target evidence based on reaction pathways sourced from Reactome [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
diseaseFromSource TEXT Disease label from the original source
diseaseFromSourceId TEXT Disease identifier from the original source
literature TEXT[] List of PubMed or preprint reference identifiers
pathways STRUCT(id TEXT, name TEXT)[] List of pooled pathways
reactionId TEXT Pathway, gene set or reaction identifier in Reactome
reactionName TEXT Name of the reaction, patway or gene set in Reactome
targetModulation TEXT Description of target modulation event
variantAminoacidDescriptions TEXT[] Descriptions of variant consequences at protein level
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.