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bedrock.bio

open_targets.target

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
id approvedSymbol biotype genomicLocation approvedName go hallmarks synonyms symbolSynonyms nameSynonyms ... subcellularLocations targetClass obsoleteSymbols obsoleteNames constraint proteinIds dbXrefs pathways tss version
0 ENSG00000083454 P2RX5 protein_coding {'chromosome': '17', 'start': 3669763, 'end': ... purinergic receptor P2X 5 [{'id': 'GO:0033198', 'source': 'GO_REF:000010... <NA> [{'label': 'P2X purinoceptor 5', 'source': 'un... [{'label': 'P2X5', 'source': 'uniprot'}, {'lab... [{'label': 'P2X purinoceptor 5', 'source': 'un... ... [{'location': 'Cell membrane ; Multi-pass memb... [{'id': 1047, 'label': 'Ligand-gated ion chann... [] [{'label': 'purinergic receptor P2X, ligand-ga... [{'constraintType': 'syn', 'score': 0.01620100... [{'id': 'Q93086', 'source': 'uniprot_swissprot... [{'id': '8536', 'source': 'HGNC'}, {'id': 'CHE... [{'pathwayId': 'R-HSA-418346', 'pathway': 'Pla... 3696155 26.09
1 ENSG00000087087 SRRT protein_coding {'chromosome': '7', 'start': 100875065, 'end':... serrate, RNA effector molecule [{'id': 'GO:0006355', 'source': 'GO_REF:000002... <NA> [{'label': 'Serrate RNA effector molecule homo... [{'label': 'SRRT', 'source': 'uniprot'}, {'lab... [{'label': 'Serrate RNA effector molecule homo... ... [{'location': 'Nucleus, nucleoplasm', 'source'... [{'id': 601, 'label': 'Unclassified protein', ... [] [{'label': 'serrate RNA effector molecule homo... [{'constraintType': 'syn', 'score': -2.1412999... [{'id': 'Q9BXP5', 'source': 'uniprot_swissprot... [{'id': '24101', 'source': 'HGNC'}, {'id': '5O... [{'pathwayId': 'R-HSA-9930044', 'pathway': 'Nu... 100875103 26.09
2 ENSG00000092201 SUPT16H protein_coding {'chromosome': '14', 'start': 21351289, 'end':... SPT16 homolog, facilitates chromatin remodelin... [{'id': 'GO:0005515', 'source': 'PMID:32814053... <NA> [{'label': 'FACT complex subunit SPT16', 'sour... [{'label': 'hSPT16', 'source': 'uniprot'}, {'l... [{'label': 'FACT complex subunit SPT16', 'sour... ... [{'location': 'Nucleus', 'source': 'uniprot', ... [{'id': 601, 'label': 'Unclassified protein', ... [] [{'label': 'suppressor of Ty (S.cerevisiae) 16... [{'constraintType': 'syn', 'score': 0.38003998... [{'id': 'Q9Y5B9', 'source': 'uniprot_swissprot... [{'id': '11465', 'source': 'HGNC'}, {'id': '4Z... [{'pathwayId': 'R-HSA-167246', 'pathway': 'Tat... 21384019 26.09
3 ENSG00000100567 PSMA3 protein_coding {'chromosome': '14', 'start': 58244740, 'end':... proteasome 20S subunit alpha 3 [{'id': 'GO:0005515', 'source': 'PMID:15225636... <NA> [{'label': 'Proteasome subunit alpha type-3', ... [{'label': 'alpha-7', 'source': 'uniprot'}, {'... [{'label': 'Proteasome subunit alpha type-3', ... ... [{'location': 'Cytoplasm', 'source': 'uniprot'... [{'id': 601, 'label': 'Unclassified protein', ... [] [{'label': 'proteasome (prosome, macropain) su... [{'constraintType': 'syn', 'score': -0.5937700... [{'id': 'P25788', 'source': 'uniprot_swissprot... [{'id': '9532', 'source': 'HGNC'}, {'id': '4R3... [{'pathwayId': 'R-HSA-5632684', 'pathway': 'He... 58244843 26.09
4 ENSG00000105707 HPN protein_coding {'chromosome': '19', 'start': 35040506, 'end':... hepsin [{'id': 'GO:0008233', 'source': 'PMID:19843851... <NA> [{'label': 'Serine protease hepsin', 'source':... [{'label': 'HPN', 'source': 'uniprot'}, {'labe... [{'label': 'Serine protease hepsin', 'source':... ... [{'location': 'Cell membrane ; Single-pass typ... [{'id': 1079, 'label': 'Enzyme', 'level': 'l1'... [] [] [{'constraintType': 'syn', 'score': 0.58762997... [{'id': 'P05981', 'source': 'uniprot_swissprot... [{'id': '5155', 'source': 'HGNC'}, {'id': '1O5... [{'pathwayId': 'R-HSA-6806942', 'pathway': 'ME... 35041721 26.09

Description

Section titled “Description”

Core annotation for drug targets (gene/proteins).

Targets are defined based on EMBL-EBI Ensembl database and uses the Ensembl gene ID as the primary identifier.

An Ensembl gene ID is considered potential drug target if included in the canonical assembly or if present alternative assemblies but encoding for a reviewed protein product according to the UniProt database [Target]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
id TEXT Unique identifier for the target [bioregistry:ensembl]
approvedSymbol TEXT Approved gene symbol of the target
biotype TEXT Biotype classification of the target gene, indicating if the gene is protein coding
genomicLocation STRUCT(chromosome TEXT, start BIGINT, end BIGINT, strand INT) Genomic location information of the target gene
approvedName TEXT Approved full name of the target gene
go STRUCT(id TEXT, source TEXT, evidence TEXT, aspect TEXT, geneProduct TEXT, ecoId TEXT)[] List of Gene Ontology (GO) annotations related to the target
hallmarks STRUCT(attributes STRUCT(pmid BIGINT, description TEXT, name TEXT)[], cancerHallmarks STRUCT(pmid BIGINT, description TEXT, impact TEXT, label TEXT)[]) Hallmarks related to the target gene sourced from COSMIC
synonyms STRUCT(label TEXT, source TEXT)[] List of synonyms for the target gene
symbolSynonyms STRUCT(label TEXT, source TEXT)[] List of symbol-based synonyms for the target gene
nameSynonyms STRUCT(label TEXT, source TEXT)[] List of name-based synonyms for the target gene
functionDescriptions TEXT[] Functional descriptions of the target gene sourced from UniProt
subcellularLocations STRUCT(location TEXT, source TEXT, termSL TEXT, labelSL TEXT, targetModifier TEXT)[] List of subcellular locations where the target protein is found
targetClass STRUCT(id BIGINT, label TEXT, level TEXT)[] Target classification categories from ChEMBL
obsoleteSymbols STRUCT(label TEXT, source TEXT)[] List of obsolete symbols previously used for the target gene
obsoleteNames STRUCT(label TEXT, source TEXT)[] List of obsolete names previously used for the target gene
constraint STRUCT(constraintType TEXT, score FLOAT, exp FLOAT, obs INT, oe FLOAT, oeLower FLOAT, oeUpper FLOAT, upperRank INT, upperBin INT, upperBin6 INT)[] Constraint scores for the target gene from gnomAD
proteinIds STRUCT(id TEXT, source TEXT)[] Protein identifiers associated with the target
dbXrefs STRUCT(id TEXT, source TEXT)[] Database cross-references for the target
pathways STRUCT(pathwayId TEXT, pathway TEXT, topLevelTerm TEXT)[] Pathway annotations for the target
tss BIGINT Transcription Start Site (TSS) information for the target
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.