GO version by wormbase version release.

Hello,

I was wondering…
How can I known which version of gene ontology terms GO, was used in a determined version of the wormbase?

I’m using wormbase version WS235, but I can not found on the files or in the description of WS235 release, which release of GO ontology was used.

Thanks,

I’m just looking around, and I don’t know the subject, but the headers to this file give a date and name the databases used. They don’t give a version number for them, but it seems a good place to start.

and here;

http://www.geneontology.org/GO.downloads.database.shtml

you can find the latest build of the full GO database;

http://archive.geneontology.org/latest-full/

or from the archive;

http://archive.geneontology.org/

Matching the GO build date with the wormbase release date should answer your question.

Hello guys,

Thanks for help me.

Unfortunately, just use the date to figure out which version of GO was used was not successful.
When I did the statistical test to find association between some groups of genes and their GO terms, the program told me that there were some GO terms that do not appear in the GO-tables supplied to it.

As I’m using the WS235 version of wormbase, which is dated (the gene GO relation obo file) 31:10:2012, I tried with the GO version dated on 2012-10-01.
Wherever, as the calculation don’t take to much time, I will repeat it with different releases of GO in order to minimize the number of non-founded GO terms.

Maybe, would be good to write the versions of the files used to build new versions of wormbase.

Take care guys, Amazing database is wormbase, I believe that is because the community that support it.

well well,

I have tried with GO versions released from sept 2011 to april 2013, looking which of them has less unrecognized GO terms with the WS235 wormbase release. The best was the GO release of august 2012.

The remainder unrecognized GO terms corresponds to OBSOLETE terms. The website of wormbase indicate when a GO terms is obsolete, but this is no explicit in the tab delimeted files that contains the association between genes and GO terms in the ftp site

End of the story