About evidence codes:
Every annotation must be attributed to a source, which may be a literature reference, another database or a computational analysis. The annotation must indicate what kind of evidence is found in the cited source to support the association between the gene product and the GO term. This helps users differentiate, for example, phylogenetically-inferred annotations from annotations confirmed in a wet lab. Although GO is confident in all statements made in annotations, some users might wish to examine only computational statements or otherwise filter based on evidence.
A simple controlled vocabulary is used to record evidence; the evidence codes in GAFs are simply the three-letter codes used to signify the type of evidence cited. In some GO files - including the GPAD - these three letter codes are mapped up to Evidence & Conclusion Ontology codes such as ECO:0000314.
More information on the meaning and use of the evidence codes can be found in the GO evidence codes documentation.