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bedrock.bio

ensembl.xrefs

import bedrock_bio as bb

rel = bb.load_table('ensembl.xrefs')
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 transcript_id protein_id xref_db xref_subset xref_info_type xref_primary_accession xref_secondary_accession xref_identity source_identity linkage_type
0 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000003 FBtr0081624 None ena None None AE014297 None <NA> <NA> None
1 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000003 FBtr0081624 None ena None None NT_033777 None <NA> <NA> None
2 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000003 FBtr0081624 None ena None None 3R None <NA> <NA> None
3 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000003 FBtr0081624 None ena None None AE014297 None <NA> <NA> None
4 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000003 FBtr0081624 None ena None None NT_033777 None <NA> <NA> None

Description

Section titled “Description”

Cross-references from Ensembl gene/transcript/protein IDs to external databases (UniProt, RefSeq, Entrez, ENA).

One row per external cross-reference.

Always filter on genbank_assembly_accession.

Filter xref_db to the target database (e.g. uniprot) and use xref_primary_accession as the external identifier.

Join back to genes / transcripts / cds on the Ensembl IDs.

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_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_000027305.1'
    • 'GCA_000146045.2'
    • '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 Ensembl cross-reference file.
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 being cross-referenced.
transcript_id TEXT Ensembl transcript ID being cross-referenced.
protein_id TEXT Ensembl protein ID being cross-referenced. May be null when the cross-reference is not translation-level.
xref_db TEXT External database the cross-reference points to — uniprot, refseq, entrez, or ena.
xref_subset TEXT Normalized subset within the external database (e.g. swissprot, trembl, isoform, mrna, or peptide), if any. May be null.
xref_info_type TEXT How the cross-reference was derived (e.g. direct, sequence_match, dependent). May be null.
xref_primary_accession TEXT Primary accession in the external database.
xref_secondary_accession TEXT Secondary accession in the external database. May be null.
xref_identity INT Percent sequence identity supporting a sequence-match cross-reference. May be null.
source_identity INT Percent identity from the Ensembl side of a sequence-match cross-reference. May be null.
linkage_type TEXT Relationship type reported by Ensembl for the cross-reference. May be null.