ABSTRACT
The Gene Ontology (GO) filled a crucial gap in the life sciences by providing a controlled and structured vocabulary that allowed computers to start processing genomics-related data in an automated way. Once this gap was filled, a swath of software tools have sprouted almost overnight, performing all sorts of analyses involving GO (see Chapter 25 for a review of such tools). Also, GO annotations have become a great reference for researchers across the entire spectrum of life sciences. But, as in most cases, lots of uses come with a few abuses, as well. The much sought after ability to automate the data analysis involved in this step led to the implementation of tens of tools able to perform a GO analysis at the click of a button. Unfortunately, by automating the process and thus removing the human labor from this step these tools also remove the human intelligence from the loop. And this, as always, is much needed here as well.
