open_targets.transcript

Python

In [1]:

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()

Out[1]:

	targetId	transcriptId	biotype	proteinId	uniprotSwissprotIds	uniprotTremblIds	uniprotIsoformIds	alphafoldIds	isEnsemblCanonical	chromosome	start	end	strand	transcriptionStartSite	flags	exons	version
0	ENSG00000290825	ENST00000832824	lncRNA	None	<NA>	<NA>	<NA>	<NA>	False	1	11121	14413	1	11121	[]	[{'exonId': 'ENSE00004248723', 'chromosome': '...	26.09
1	ENSG00000290825	ENST00000832825	lncRNA	None	<NA>	<NA>	<NA>	<NA>	False	1	11125	14405	1	11125	[]	[{'exonId': 'ENSE00004248721', 'chromosome': '...	26.09
2	ENSG00000290825	ENST00000832826	lncRNA	None	<NA>	<NA>	<NA>	<NA>	False	1	11410	14413	1	11410	[]	[{'exonId': 'ENSE00004248726', 'chromosome': '...	26.09
3	ENSG00000290825	ENST00000832827	lncRNA	None	<NA>	<NA>	<NA>	<NA>	False	1	11411	14413	1	11411	[]	[{'exonId': 'ENSE00004248710', 'chromosome': '...	26.09
4	ENSG00000290825	ENST00000832828	lncRNA	None	<NA>	<NA>	<NA>	<NA>	False	1	11426	14409	1	11426	[]	[{'exonId': 'ENSE00004248702', 'chromosome': '...	26.09

R

In [1]:

library(bedrockbio)

lf <- load_table("open_targets.transcript")
df <- head(lf, 5) |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 17 columns)
   targetId        | transcriptId    | biotype | proteinId | isEnsemblCanonical | chromosome | start | end
   --------------- | --------------- | ------- | --------- | ------------------ | ---------- | ----- | -----
0  ENSG00000290825 | ENST00000832824 | lncRNA  | —         | false              | 1          | 11121 | 14413
1  ENSG00000290825 | ENST00000832825 | lncRNA  | —         | false              | 1          | 11125 | 14405
2  ENSG00000290825 | ENST00000832826 | lncRNA  | —         | false              | 1          | 11410 | 14413
3  ENSG00000290825 | ENST00000832827 | lncRNA  | —         | false              | 1          | 11411 | 14413
4  ENSG00000290825 | ENST00000832828 | lncRNA  | —         | false              | 1          | 11426 | 14409

Description

Per-transcript index derived from GENCODE, including genomic coordinates, biotype, protein/UniProt identifiers, and curation flags (MANE, APPRIS, GENCODE Primary, Ensembl canonical) [Target]

Partitions

Not partitioned.

Schema

Column	Type	Description
targetId	TEXT	Ensembl gene identifier of the target the transcript belongs to [bioregistry:ensembl]
transcriptId	TEXT	Ensembl identifier of the transcript (ENST###) [bioregistry:ensembl]
biotype	TEXT	Biotype classification of the transcript
proteinId	TEXT	Ensembl protein identifier for the transcript (ENSP###); null for non-coding transcripts [bioregistry:ensembl]
uniprotSwissprotIds	TEXT[]	Reviewed (Swiss-Prot) UniProt identifiers for the protein translated from the transcript [bioregistry:uniprot]
uniprotTremblIds	TEXT[]	Unreviewed (TrEMBL) UniProt identifiers for the protein translated from the transcript [bioregistry:uniprot]
uniprotIsoformIds	TEXT[]	UniProt isoform identifiers for the protein translated from the transcript [bioregistry:uniprot]
alphafoldIds	TEXT[]	AlphaFold structure identifiers for the protein translated from the transcript
isEnsemblCanonical	BOOLEAN	Flag indicating if the transcript is the Ensembl canonical transcript for the gene
chromosome	TEXT	Chromosome on which the transcript is located
start	BIGINT	Genomic start position of the transcript
end	BIGINT	Genomic end position of the transcript
strand	INT	Strand orientation of the transcript: 1 for the forward strand, -1 for the reverse strand
transcriptionStartSite	INT	Transcription Start Site (TSS) genomic position, derived from the transcript’s strand and coordinates
flags	STRUCT(label TEXT, value TEXT)[]	List of curation flags describing the transcript (e.g. MANE, APPRIS, GENCODE Primary, Ensembl canonical)
exons	STRUCT(exonId TEXT, chromosome TEXT, start BIGINT, end BIGINT, strand INT)[]	List of exons that make up the transcript
version	TEXT	Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.