A very common question in using Scaffold is "how do I add GO terms?" Well, there are a couple ways to do this, and this article discusses them.
A common question is what is represented by GO terms that have filled in circles versus circles that are empty. Filled in circles are those terms that have been verified via experimentation and empty circles are those that have been inferred by computational means.
For organism-specific GOA, see this article.
NCBI web site:
http://www.ncbi.nlm.nih.gov/
UniProt GOA:
http://www.ebi.ac.uk/GOA
To configure GO annotation sources, go to Edit > Edit Annotation Options... Here, you can add as many as you want. Note that the "All Proteomes" may take roughly 6 hours to download and index and requires up to 120 GB of space on your local file system. This amount of space is also required on the drive that houses your Temp directory.
A resource for additional GOA databases:
https://www.ebi.ac.uk/GOA/downloads
If you find one of these that looks promising, find the link to the GAF.GZ version of the file, and add it in Scaffold per the above instructions, using the Other Web Site... option.
To save GO annotation files to your C drive you must run Scaffold as an administrator. We recommend saving to an alternative drive that you have read/write privileges for with ample room to store files up to 120 GB.
Our Help is very good and there are lots of great sections on how to use Scaffold. Just open Scaffold and go to Help > Help Contents and search for your topic.