ErmineJ uses the Gene Ontology RDF XML* file to obtain a complete set of data about GO terms and their definitions. This file is created by the Gene Ontology Consortium.
As of ErmineJ 3.0, the software automatically downloads the latest version of the file if one is not found in your ermineJ.data directory. If this doesn’t happen when you start the software the first time, the most recent version of the GO file should be available from the GO web site here. This file should be placed in your ermineJ.data directory for convenience. There is no need to unzip the file.
Older versions of the GO files should be available as well. Please report problems with broken links on the GO web site to the GO web site maintainers or the go-database mailing list.
If you want ErmineJ to fetch a new copy of the file, delete the one in your ermineJ.data directory and restart ErmineJ.
Note that the annotation file you use is not assured to be ‘in synch’ with the GO XML file you download. This matters because the GO terms change, and it is possible for an annotation file to have terms which are newer than the GO XML file you use.
If you are using an annotation file provided by a third party, or which you made yourself, we advise that you try to use the same version of GO that was used to created the annotations.
Note that currently the GO XML files is required, even if you are not using GO in your analysis. We may change this in a future version of ErmineJ.
*If you don’t know what RDF or XML mean, don’t worry, you don’t need to know.