ErmineJ uses the Gene Ontology OBO 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 OBO 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. Note that support for XML formats of GO have been removed from ErmineJ as of 3.2.
You can also use “subset” files such as GO slims or GO-basic, as long as your input is OBO format.
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 changing the GO file may change analysis results. We recommend using a single GO file and a similarly consistent annotation file for any important analyses to ensure reproducibility.
Note that the annotation file you use is not assured to be ‘in synch’ with the GO 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 file you use. You can use GOtrack to get gene annotations for popular organisms for specific dates.
If you are using an annotation file provided by a third party, or which you made yourself, we advise that you use the same version of GO that was used to created the annotations.
Note that currently the GO file 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 OBO is, don’t worry, you don’t need to know.