[ensembl-dev] Trouble finding display name in core schema

Stefano Giorgetti sgiorgetti at ebi.ac.uk
Tue Mar 1 07:26:13 GMT 2022

Hello Laura,

Thanks for your email.

The "display_name" is referenced to by the field "display_xref_id" in 
either gene or transcript table, and you can find the actual 
"display_name" in the xref table.

For example, let's assume we are interested in the gene identified by 
"ENSG00000139618", the following SQL query shows you the "display_name"

SELECT g.gene_id, g.stable_id, g.biotype, g.display_xref_id, 
x.external_db_id, e.db_name, x.display_label
    FROM gene g INNER JOIN xref x ON g.display_xref_id = x.xref_id
                INNER JOIN external_db e ON x.external_db_id = 
    WHERE g.stable_id = 'ENSG00000139618';

A similar query can work on transcripts; for example

SELECT t.gene_id, t.stable_id, t.biotype, t.display_xref_id, 
x.external_db_id, e.db_name, x.display_label
      FROM transcript t INNER JOIN xref x ON t.display_xref_id = x.xref_id
                        INNER JOIN external_db e ON x.external_db_id = 
      LIMIT 5;

In both the examples, I added in the "external_db" table to show where 
the "display_name" comes from.
This is entirely optional, and you can safely remove table and related 
field from the queries.

Hope this helps.

Best wishes,


On 01/03/2022 03:08, Luebbert, Laura wrote:
> Hi,
> I am having trouble finding the equivalent of the “display_name” (name 
> or identifier of a gene/transcript) in the Ensembl core schema. In 
> which table can I find this information for each stable ID?
> With best regards,
> Laura
> _______________________________________________
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