[ensembl-dev] which version of Gene Ontology is used for my query in biomart

[James Allen]

Hello Anton,
The GO version is not available from BioMart - probably the easiest way to get 
it (and I appreciate that it's not very easy, and is certainly not obvious...) 
is by querying the ontology database on our public SQL server, e.g. on a command 
line:

mysql --host ensembldb.ensembl.org --user anonymous ensembl_ontology_102 -e 
'SELECT data_version FROM ontology WHERE namespace = "go"'

which gives the result "2020-06-01".

For the GO versions used in past releases, replace the '102' in the database 
name with the required version.


Regarding your second question, you can save a BioMart query in XML format, by 
clicking the appropriately labelled button in the menu bar along the top of the 
BioMart interface. This XML is independent of a release, so applying it to a 
future release might give different results - so if that's important, the XML 
will need to be cited alongside the appropriate Ensembl archive site, e.g. 
http://nov2020.archive.ensembl.org.

An alternative to the XML, for relatively simple queries, is a url, also 
generated by using the button in BioMart's menu bar. This generates something 
like: 
http://www.ensembl.org/biomart/martview/092cdd74b317beea2767dd0d8d3a3524?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.external_gene_name&FILTERS=hsapiens_gene_ensembl.default.filters.go_parent_term."GO:0050789"&VISIBLEPANEL=resultspanel

The long arbitrary identifier can be removed to make it a bit more readable, 
e.g. 
http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.external_gene_name&FILTERS=hsapiens_gene_ensembl.default.filters.go_parent_term."GO:0050789"&VISIBLEPANEL=resultspanel

And the url can, of course, be altered at the start to point to a specific 
archive site.

Hope that helps, please let us know if you have any further questions,
Cheers,
James
Ensembl Production


On 26/12/2020 05:33, Anton Kratz wrote:
> 1.) How can I know which version of Gene Ontology is used for a query that I do 
> in biomart?
> 
> Longer version: I am trying to get all genes annotated to a certain Gene 
> Ontology term. So I select Dataset --> Human genes (GRCh38.p13), Filter --> Gene 
> Ontology: GO Term Accession: GO:0050789, under "Attributes" I select what I want 
> to have back (I only want "Gene Symbol") and then "Results". I get the gene 
> symbols as expected. But I don't seem to find the information anywhere which 
> version of GO was used for the query. I want to put that information into the 
> methods of a manuscript that I am currently working on.
> 
> 2.) A related question, can I somehow save the query, or describe the query more 
> formally, to make my query more reproducible?
> 
> Thanks,
> 
> Anton
> 
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