[ensembl-dev] G.O.

[Emily Perry]

Hi Joseph

The GO terms are stored in the xref table. They are linked to the transcripts via the object_xref table. The schema is here:
http://www.ensembl.org/info/docs/api/core/core_schema.html <http://www.ensembl.org/info/docs/api/core/core_schema.html>

It is not our job to write your MySQL queries for you, but we can point you to the appropriate tables if it is not obvious. I agree that in the case of GO terms, it is not obvious which tables contain this information, but it is up to you to craft a suitable query.

Just like many of the other tasks you have asked about, MySQL is not a great way to do this. Any MySQL query you do will not be ontology aware - only the most specific GO terms will be linked to the transcripts in the tables. This means that a query for all associations for a GO term with daughter terms will not return associations with the daughter terms, which would be an incomplete dataset. BioMart and our APIs are written to be ontology aware, which means that a similar query with those would return the associations with the daughter terms too – we recommend using one of those for a query like this.

All the best

Emily

> On 27 Jan 2020, at 14:20, Joseph Steinberger <joseph.steinberger at weizmann.ac.il> wrote:
> 
> Hello All,
> 
> What query will get me all the genes of a given GO annotation from a given species from the Ensembl MySQL database?
> 
> Sincerely,
> Joseph Steinberger
> 
> PhD student, laboratory of Naama Barkai, Weizmann Institute
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--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader 
(she/her)

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory 
Wellcome Genome Campus
Hinxton
Cambridge
CB10 1SD
UK 

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