[ensembl-dev] ensembl_ontology_75 schema

mag mr6 at ebi.ac.uk
Mon Mar 17 16:53:44 GMT 2014


Hi Ryan,

Ontology terms are linked to ensembl translations as external references.
For a given GO xref, the display_label column in the xref table (in the 
core database) will correspond to the accession column in the term table 
in the ontology database.

You can also retrieve this information using the perl API:

my $go_xrefs = $gene->get_all_DBLinks('GO');
my $ontology_term_adaptor = $registry->get_adaptor( 'Multi', 'Ontology', 
'OntologyTerm' );
while (my $go_xref = shift @{$go_xrefs} ) {
   my $go_term = $ontology_term_adaptor->fetch_by_accession( 
$go_xref->display_id );
   print $go_term->accession, " ", $go_term->name, "\n";
}


Hope that helps,
Magali

On 17/03/2014 16:17, Ryan Brown wrote:
> Ensembl:
>
> I am interested in getting  information related to the Term table in 
> the ensembl_ontology_75 database. Can you describe how rows in this 
> table relate to tables and columns in the ensembl_core_75 database? My 
> goal is to have a query where I can specify the name field in the 
> ontology term table, perform a set of inner joins, and then get data 
> from other tables / databases.
>
> Thanks
> Ryan
>
> -- 
> *Ryan M. Brown
> XenoGen Biosystems*
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