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bedrock.bio

ensembl.genes

import bedrock_bio as bb

rel = bb.load_table('ensembl.genes')
rel = rel.filter("genbank_assembly_accession = 'GCA_000001215.4'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources release genbank_assembly_accession gene_id gene_version gene_symbol description analysis_name sequence_id start_position end_position is_forward_strand gene_source biotype gene_type
0 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000003 <NA> 7SLRNA:CR32864 Signal recognition particle 7SL RNA CR32864 flybase 3R 6822500 6822798 True FlyBase ncRNA ncRNA_gene
1 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000008 <NA> a arc flybase 2R 22136968 22172834 True FlyBase protein_coding gene
2 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000014 <NA> abd-A abdominal A flybase 3R 16807214 16830049 False FlyBase protein_coding gene
3 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000015 <NA> Abd-B Abdominal B flybase 3R 16927212 16972236 False FlyBase protein_coding gene
4 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000017 <NA> Abl Abl tyrosine kinase flybase 3L 16615866 16647882 False FlyBase protein_coding gene

Description

Section titled “Description”

Gene-level annotation (one row per Ensembl gene).

One row per gene.

Always filter on genbank_assembly_accession.

Join to transcripts, exons, cds, etc. on gene_id.

Look up gene_id by gene_symbol to translate a gene name to an Ensembl ID.

Partitions

Section titled “Partitions”
  • genbank_assembly_accession
    • 'GCA_000001215.4'
    • 'GCA_000001405.29'
    • 'GCA_000001635.9'
    • 'GCA_000001735.1'
    • 'GCA_000002035.4'
    • 'GCA_000002285.4'
    • 'GCA_000002525.1'
    • 'GCA_000002655.1'
    • 'GCA_000002765.3'
    • 'GCA_000002855.2'
    • 'GCA_000002945.2'
    • 'GCA_000002985.3'
    • 'GCA_000003025.6'
    • 'GCA_000003195.3'
    • 'GCA_000003625.1'
    • 'GCA_000004195.4'
    • 'GCA_000004515.4'
    • 'GCA_000005845.2'
    • 'GCA_000006565.2'
    • 'GCA_000006665.1'
    • 'GCA_000006745.1'
    • 'GCA_000006765.1'
    • 'GCA_000006845.1'
    • 'GCA_000006885.1'
    • 'GCA_000006925.2'
    • 'GCA_000006945.2'
    • 'GCA_000007545.1'
    • 'GCA_000007565.2'
    • 'GCA_000007785.1'
    • 'GCA_000008525.1'
    • 'GCA_000008765.1'
    • 'GCA_000008805.1'
    • 'GCA_000009045.1'
    • 'GCA_000009085.1'
    • 'GCA_000009205.2'
    • 'GCA_000011065.1'
    • 'GCA_000011325.1'
    • 'GCA_000013425.1'
    • 'GCA_000013465.1'
    • 'GCA_000015005.1'
    • 'GCA_000016305.1'
    • 'GCA_000025565.1'
    • 'GCA_000025985.1'
    • 'GCA_000027005.1'
    • 'GCA_000027305.1'
    • 'GCA_000146045.2'
    • 'GCA_000149245.3'
    • 'GCA_000151735.1'
    • 'GCA_000167675.2'
    • 'GCA_000174395.2'
    • 'GCA_000182965.3'
    • 'GCA_000196035.1'
    • 'GCA_000196095.1'
    • 'GCA_000215625.1'
    • 'GCA_000226075.1'
    • 'GCA_000237925.3'
    • 'GCA_000285655.3'
    • 'GCA_000306945.1'
    • 'GCA_000349665.1'
    • 'GCA_000409795.2'
    • 'GCA_000805365.1'
    • 'GCA_001433935.1'
    • 'GCA_001457595.1'
    • 'GCA_001704415.1'
    • 'GCA_001858045.3'
    • 'GCA_002263795.4'
    • 'GCA_002863925.1'
    • 'GCA_003339765.3'
    • 'GCA_003668045.2'
    • 'GCA_008728515.1'
    • 'GCA_011100615.1'
    • 'GCA_016699485.1'
    • 'GCA_016772045.2'
    • 'GCA_018294505.1'
    • 'GCA_036323735.1'
    • 'GCA_902167145.1'
    • 'GCA_905237065.2'

Schema

Section titled “Schema”
Column Type Description
sources STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] Provenance for the GFF3 feature records.
release TEXT Ensembl release number the annotation was drawn from.
genbank_assembly_accession TEXT Partition column. GenBank assembly accession.
gene_id TEXT Ensembl gene ID (e.g. ENSG00000123456).
gene_version INT Version suffix of the gene ID. May be null.
gene_symbol TEXT Gene symbol (e.g. HGNC symbol for human). May be null.
description TEXT Ensembl gene description. May be null.
analysis_name TEXT Ensembl analysis that produced the gene feature. May be null.
sequence_id TEXT GFF3 sequence ID the gene is located on.
start_position INT 1-based start coordinate of the gene on the assembly.
end_position INT 1-based end coordinate of the gene on the assembly.
is_forward_strand BOOLEAN Whether the gene is on the forward strand.
gene_source TEXT Per-gene annotation provider in GFF3 column 2 (e.g. ensembl, havana, ensembl_havana).
biotype TEXT Gene biotype (e.g. protein_coding, lncRNA, pseudogene).
gene_type TEXT Raw GFF3 gene feature type — gene, ncRNA_gene, or pseudogene.