Hi. I would like to know how to work with a set of gene ontology terms that I have. I really need to know how can I make a graph or a conceptual map, with all my GO-terms obtained, and make all relation between them. I hope there is some tools with R programming or something. Thanks!
A good software representing a network between GO terms is Bingo. It's a Cytoscape plugin that you can specify your desired gene list and receive the network of GO terms that are significantly linked to your gene list. Although it does not match exactly with your question, but I think is one of the best choices for you.
You can see several tools for GO term visualization here. I would recommend to use Ontologizer 2.0 and integrated function to do both your enrichment and generate a graph (directed acyclic graph of GO terms) as you required.