Table of contents

Summary

GAF Parser Summary

There are 10 GAF parser warnings.

GAF summary

Found 1137 annotations in 1149 lines.

GAF Validation Summary Errors are reported first.

For rule GO_AR:0000007 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000007) IPI should not be used with catalytic activity molecular function terms, there is one violation with type Warning.

GAF Prediction Summary

Found 88 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf

Report

Group: gonuts - Dataset: gonuts

SUMMARY

This report generated on 2018-12-16

Contents

gorule-0000008

gorule-0000016

gorule-0000018

gorule-0000020

gorule-0000027

gorule-0000029

other

MESSAGES

gorule-0000008

No annotations should be made to uninformative high level terms

Messages

gorule-0000016

With/From: IC annotations require a With/From GO ID

Messages

gorule-0000018

IPI annotations require a With/From entry

Messages

gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

Messages

gorule-0000027

Each identifier in GAF is valid

Messages

gorule-0000029

All IEAs over a year old are removed

Messages

other

OWLTools check

#Line number RuleID ViolationType Message Line
#------------
# GAF Parser ERROR count: 0
#------------
# GAF Parser WARNING count: 10
19 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB Q08698 nrdE Contributes_to GO:0004748 PMID:7809142 IDA F protein taxon:90371 20100519 GONUTS
497 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P68871 HBB Contributes_to GO:0031720 PMID:19740759 IDA F protein taxon:9606 20101214 GONUTS
499 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P68871 HBB Contributes_to GO:0004601 PMID:19740759 IDA F protein taxon:9606 20101214 GONUTS
518 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P69905 HBA2 Contributes_to GO:0031720 PMID:19740759 IDA F protein taxon:9606 20101214 GONUTS
520 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P69905 HBA2 Contributes_to GO:0004601 PMID:19740759 IDA F protein taxon:9606 20101214 GONUTS
539 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P00738 HP Contributes_to GO:0004601 PMID:19740759 IDA F protein taxon:9606 20101214 GONUTS
830 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P14565 traI Contributes_to GO:0004520 PMID:7499339 IDA F protein taxon:83333 20110517 GONUTS
994 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P76014 dhaL Contributes_to GO:0016740 PMID:11350937 IDA F protein taxon:83333 20110524 GONUTS
997 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P37349 dhaM Contributes_to GO:0016740 PMID:11350937 IDA F protein taxon:83333 20110524 GONUTS
998 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P76015 dhaK Contributes_to GO:0016740 PMID:11350937 IDA F protein taxon:83333 20110524 GONUTS
#------------
#------------
# Validation for #1137 annotations in 1149 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000007 IPI should not be used with catalytic activity molecular function terms Warning count: 1
528 GO_AR:0000007 Warning IPI should not be used with catalytic activity molecular function terms UniProtKB Q9DBH0 Wwp2 GO:0004842 PMID:15047715 IPI UniProtKB:P20263 F protein taxon:10090 20101213 GONUTS
#------------

Predictions

GO:0005623 cell AnnotationPropagation C GO:0045022 early endosome to late endosome transport IMP
GO:0005829 cytosol AnnotationPropagation C GO:0045022 early endosome to late endosome transport IMP
GO:0098869 cellular oxidant detoxification AnnotationPropagation P GO:0016209 antioxidant activity IMP
GO:0006479 protein methylation AnnotationPropagation P GO:0008276 protein methyltransferase activity IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008940 nitrate reductase activity IGI
GO:0006412 translation AnnotationPropagation P GO:0003746 translation elongation factor activity ISA
GO:0006414 translational elongation AnnotationPropagation P GO:0003746 translation elongation factor activity ISA
GO:0006417 regulation of translation AnnotationPropagation P GO:0003746 translation elongation factor activity ISA
GO:0016310 phosphorylation AnnotationPropagation P GO:0004797 thymidine kinase activity IMP
GO:0009165 nucleotide biosynthetic process AnnotationPropagation P GO:0004797 thymidine kinase activity IMP
GO:0009157 deoxyribonucleoside monophosphate biosynthetic process AnnotationPropagation P GO:0004797 thymidine kinase activity IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0004497 monooxygenase activity EXP
GO:0046835 carbohydrate phosphorylation AnnotationPropagation P GO:0004340 glucokinase activity IDA
GO:0051156 glucose 6-phosphate metabolic process AnnotationPropagation P GO:0004340 glucokinase activity IDA
GO:0006412 translation AnnotationPropagation P GO:0003746 translation elongation factor activity IMP
GO:0006414 translational elongation AnnotationPropagation P GO:0003746 translation elongation factor activity IMP
GO:0006417 regulation of translation AnnotationPropagation P GO:0003746 translation elongation factor activity IMP
GO:0032259 methylation AnnotationPropagation P GO:0004851 uroporphyrin-III C-methyltransferase activity ISS
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008940 nitrate reductase activity IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0016491 oxidoreductase activity IMP
GO:0018106 peptidyl-histidine phosphorylation AnnotationPropagation P GO:0004673 protein histidine kinase activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0004345 glucose-6-phosphate dehydrogenase activity IMP
GO:1903506 regulation of nucleic acid-templated transcription AnnotationPropagation P GO:0003712 transcription coregulator activity IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008888 glycerol dehydrogenase [NAD+] activity IDA
GO:0097339 glycolate transmembrane transport AnnotationPropagation P GO:0043879 glycolate transmembrane transporter activity IGI
GO:0018108 peptidyl-tyrosine phosphorylation AnnotationPropagation P GO:0005006 epidermal growth factor-activated receptor activity IMP
GO:0007173 epidermal growth factor receptor signaling pathway AnnotationPropagation P GO:0005006 epidermal growth factor-activated receptor activity IMP
GO:1901998 toxin transport AnnotationPropagation P GO:0019534 toxin transmembrane transporter activity IMP
GO:0055085 transmembrane transport AnnotationPropagation P GO:0019534 toxin transmembrane transporter activity IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0016491 oxidoreductase activity IMP
GO:0046835 carbohydrate phosphorylation AnnotationPropagation P GO:0003872 6-phosphofructokinase activity IMP
GO:0061615 glycolytic process through fructose-6-phosphate AnnotationPropagation P GO:0003872 6-phosphofructokinase activity IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0004096 catalase activity IDA
GO:0098869 cellular oxidant detoxification AnnotationPropagation P GO:0004096 catalase activity IDA
GO:0006470 protein dephosphorylation AnnotationPropagation P GO:0008138 protein tyrosine/serine/threonine phosphatase activity IDA
GO:0006508 proteolysis AnnotationPropagation P GO:0004175 endopeptidase activity IDA
GO:0006508 proteolysis AnnotationPropagation P GO:0008235 metalloexopeptidase activity IDA
GO:0005623 cell AnnotationPropagation C GO:0042073 intraciliary transport IMP
GO:0005929 cilium AnnotationPropagation C GO:0042073 intraciliary transport IMP
GO:0015904 tetracycline transport AnnotationPropagation P GO:0008493 tetracycline transmembrane transporter activity ISS
GO:0006855 drug transmembrane transport AnnotationPropagation P GO:0008493 tetracycline transmembrane transporter activity ISS
GO:0098656 anion transmembrane transport AnnotationPropagation P GO:0008493 tetracycline transmembrane transporter activity ISS
GO:0032508 DNA duplex unwinding AnnotationPropagation P GO:0003678 DNA helicase activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0016491 oxidoreductase activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008942 nitrite reductase [NAD(P)H] activity ISS
GO:0006412 translation AnnotationPropagation P GO:0003746 translation elongation factor activity ISA
GO:0006414 translational elongation AnnotationPropagation P GO:0003746 translation elongation factor activity ISA
GO:0006417 regulation of translation AnnotationPropagation P GO:0003746 translation elongation factor activity ISA
GO:0000160 phosphorelay signal transduction system AnnotationPropagation P GO:0000156 phosphorelay response regulator activity IDA
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity ISS
GO:0015768 maltose transport AnnotationPropagation P GO:0005363 maltose transmembrane transporter activity IMP
GO:0034219 carbohydrate transmembrane transport AnnotationPropagation P GO:0005363 maltose transmembrane transporter activity IMP
GO:0022900 electron transport chain AnnotationPropagation P GO:0009055 electron transfer activity IMP
GO:0016310 phosphorylation AnnotationPropagation P GO:0009029 tetraacyldisaccharide 4'-kinase activity IMP
GO:0006412 translation AnnotationPropagation P GO:0003746 translation elongation factor activity IDA
GO:0006414 translational elongation AnnotationPropagation P GO:0003746 translation elongation factor activity IDA
GO:0006417 regulation of translation AnnotationPropagation P GO:0003746 translation elongation factor activity IDA
GO:0016310 phosphorylation AnnotationPropagation P GO:0004618 phosphoglycerate kinase activity IMP
GO:0016310 phosphorylation AnnotationPropagation P GO:0016301 kinase activity ISM
GO:0071897 DNA biosynthetic process AnnotationPropagation P GO:0003887 DNA-directed DNA polymerase activity IMP
GO:0006412 translation AnnotationPropagation P GO:0003746 translation elongation factor activity ISA
GO:0006414 translational elongation AnnotationPropagation P GO:0003746 translation elongation factor activity ISA
GO:0006417 regulation of translation AnnotationPropagation P GO:0003746 translation elongation factor activity ISA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008863 formate dehydrogenase (NAD+) activity IGI
GO:0046835 carbohydrate phosphorylation AnnotationPropagation P GO:0004340 glucokinase activity IMP
GO:0051156 glucose 6-phosphate metabolic process AnnotationPropagation P GO:0004340 glucokinase activity IMP
GO:0006508 proteolysis AnnotationPropagation P GO:0008237 metallopeptidase activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008137 NADH dehydrogenase (ubiquinone) activity ISS
GO:0018106 peptidyl-histidine phosphorylation AnnotationPropagation P GO:0004673 protein histidine kinase activity IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0004450 isocitrate dehydrogenase (NADP+) activity IDA
GO:0001172 transcription, RNA-templated AnnotationPropagation P GO:0003968 RNA-directed 5'-3' RNA polymerase activity IGI
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0004616 phosphogluconate dehydrogenase (decarboxylating) activity IMP
GO:0098793 presynapse AnnotationPropagation C GO:0051583 dopamine uptake involved in synaptic transmission IMP
GO:0005623 cell AnnotationPropagation C GO:0051583 dopamine uptake involved in synaptic transmission IMP
GO:0071897 DNA biosynthetic process AnnotationPropagation P GO:0003887 DNA-directed DNA polymerase activity IDA
GO:0032259 methylation AnnotationPropagation P GO:0003908 methylated-DNA-[protein]-cysteine S-methyltransferase activity IMP
GO:0097339 glycolate transmembrane transport AnnotationPropagation P GO:0043879 glycolate transmembrane transporter activity IGI
GO:0005623 cell AnnotationPropagation C GO:0035356 cellular triglyceride homeostasis IMP
GO:0005623 cell AnnotationPropagation C GO:0042073 intraciliary transport IDA
GO:0005929 cilium AnnotationPropagation C GO:0042073 intraciliary transport IDA
GO:0006259 DNA metabolic process AnnotationPropagation P GO:0004520 endodeoxyribonuclease activity IDA
GO:0090305 nucleic acid phosphodiester bond hydrolysis AnnotationPropagation P GO:0004520 endodeoxyribonuclease activity IDA
GO:0016310 phosphorylation AnnotationPropagation P GO:0016301 kinase activity IDA
GO:0016310 phosphorylation AnnotationPropagation P GO:0016301 kinase activity IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004709 MAP kinase kinase kinase activity IDA
GO:0000186 activation of MAPKK activity AnnotationPropagation P GO:0004709 MAP kinase kinase kinase activity IDA
GO:0005623 cell AnnotationPropagation C GO:0035356 cellular triglyceride homeostasis IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008942 nitrite reductase [NAD(P)H] activity IMP

Predictions (experimental)