*GAF Parser Summary* There are 927 GAF parser warnings. *GAF summary* Found 400079 annotations in 400114 lines. *GAF Validation Summary* Errors are reported first. For rule GO_AR:0000001 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000001) Basic GAF checks, there are 788 violations with type Error. For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 82 violations with type Error. For rule GO_AR:0000003 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000003) Annotations to 'binding ; GO:0005488' and 'protein binding ; GO:0005515' should be made with IPI and an interactor in the 'with' field, there are 52 violations with type Warning. For rule GO_AR:0000006 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000006) IEP usage is restricted to terms from the Biological Process ontology, there are 5 violations with type Warning. For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 450 violations with type Warning. For rule GO_AR:0000018 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000018) IPI annotations require a With/From entry, there are 2 violations with type Warning. *GAF Prediction Summary* Found 3504 predictions, see prediction file for details. *Used Ontology Summary* go/extensions/go-gaf