mappings

Identifier

ensembl.mappings

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 taxonomy_id (partition column).

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.

Related tables: ensembl.genes (join on gene_id); ensembl.transcripts (join on transcript_id); ensembl.cds (join on protein_id).

Partitions

• release
  • '116'
• taxonomy_id
  • '10090'
  • '10116'
  • '7955'
  • '9541'
  • '9544'
  • '9606'
  • '9615'
  • '9823'
  • '9986'

Schema

Column	Type	Description
release	TEXT	Partition column. Ensembl release number the annotation was drawn from.
taxonomy_id	INT	Partition column. NCBI taxonomy ID for the species (partition column).
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.
xref_db	TEXT	External database the cross-reference points to — uniprot, refseq, entrez, or ena.
xref_subset	TEXT	Sub-collection within the external database, 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.