In certain cases, annotations are correct, but the incorrect co-annotation is due to an inference based on the ontology structure. For example, ‘protein citrullination’ (GO:0018101) used to be placed under ‘citrulline biosynthetic process’ (GO:0019240). The faulty relationship was removed since protein citrullination describes the modification of an amino acid residue in a protein by citrulline, and ‘citrulline biosynthetic process’ describes the synthesis of free citrulline.
