External references

This presentation shows you how to access links to Ensembl features in other databases, such as UniProt and RefSeq.

Exercise 6

Retrieve a list of GO term IDs and term names linked to the gene with stable ID ENSG00000139618.

  • Use get_all_DBLinks with an external database name argument to restrict the number of xrefs returned.
  • Ontology term data such as term name and definition are stored outside of the core database. Create an OntologyTerm Adaptor with the help of the Registry method get_adaptor using arguments: Multi (species), Ontology (database type), OntologyTerm (adaptor type).
  • For all xrefs returned by get_all_DBLinks use the OntologyTerm Adaptor to fetch the relevant term and print its accession and name (xref display_id is the same as term accession).
Magali explains the answers to these questions in this 3-minute video.
You can download her sample script and output