I want to assign GO slim terms to some plant genes in non-model plants. So far as I know the only plant genomes relatively accurately annotated with GO slims are rice and Arabidopsis. So I am thinking of using best blast hit in rice or Arabidopsis (depends on whether the genome under study is monocot or dicot) to assign the GO slims. I'm working on genome scale dataset so cannot do manual curations, but I want be set up a reasonably accurate procedure. I'm new to this area and would appreciate if somebody can let me know if there are better ways to do this, or things other than blast similarity that I should take into account.
Thanks avilella, this is a very good point indeed.