Entering edit mode
7.9 years ago
Louis Kok
▴
30
Hi all. I have a question about the gene ontology ranking. For example, GO:0004672 is named as protein kinase activity. From the Tree view, I found that it can be linked to different higher level, such as macromolecule modification, protein metabolic process and others at level 5. I would like classify the particular GO at level 5 or higher but it practically overlaps. I am not sure which one to choose to consider. Any advice is appreciated.
Example as below: http://amigo.geneontology.org/amigo/term/GO:0004672
By the way, is there any download link for GO hierarchical ranking of all ontology in text format? I could not find it so far.
Thank you.
I am not sure I understand what you're trying to achieve. In my experience, there's not much use for grouping GO terms by level in the hierarchy because a term can be at different levels in different branches (I think that's what you're describing) but also for a given level the terms can have different level of biological specificity. If you're trying to get a reduced ontology, consider using a GO slim.
Well yes, I agree with Jean. Your Go term can be found in the branch biological_process as well as molecular_function (at top level). This is just how it is. You can not really choose one and ignore the rest - at least none of us can tell you a general approach for it. Many Go terms overlap, so yes, I don't really understand what you try to accomplish.
Of course you can download the ontology. But this is not gonna be a text file but rather something like an owl file, which of course you can open with a txt editor but it's more than 100 MB and well, it is not just plain text. So what do you want to accomplish the the raw file?