Question

GeneOntology is a nice project to provide a standard terminology for genes and gene functions, to help avoid the use of synonyms and wrong spelling when describing a gene.

I have been using the GeneOntology for a while, but honestly I think that it contains many errors and that many terms have not enough terms associated. Moreover, the terminology they use is not always clear and there are some duplications.

It is frequent to read in article or in slideshows charts were the GO classification is used to infer the properties of a set of genes... But I wonder if the authors check the GO annotations that they use.

What is your experience about GO?

Answer 1

In my experience it's case by case. In other words just because you are getting significant p-values, does not mean the results are biologically significant. I once submitted clusters of microarray data and received a bunch of hits that were significant by p-value, but really didn't have a theme. The GO terms I saw were from many different processes without an overall term (besides biological process) which linked them together. When I've looked at published GO terms searches I generally see a strong theme among many of the terms (however that doesn't necessarily mean it has biological significance until tested empirically). So seeing themes among your terms may suggest higher significance, but it should make biological sense too.

Answer 2

The GO terms and classifications are primarily an based on opinions and a human interpretation of a small group of people of what the current state of the knowledge is.Thus are more subjective than say experimental measurements would be.

In fact it is surprising that it works at all; and it does indeed. We just need to becareful not too read to much into it.