Table of contents

Summary

GAF Parser Summary

There are 10 GAF parser warnings.

GAF summary

Found 1148 annotations in 1160 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.

For rule GO_AR:0000008 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000008) No annotations should be made to uninformative high level terms, there are 7 violations with type Warning.

GAF Prediction Summary

Found 81 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf    go/releases/2019-09-13/extensions/go-gaf.owl

Report

Group: gonuts - Dataset: gonuts

SUMMARY

This report generated on 2019-09-16

Header From Original Association File

!Project_name: Gene Ontology Normal Usage Tracking System (GONUTS)
!URL: http://gowiki.tamu.edu
!Contact Email: ecoliwiki@gmail.com
!Funding: NIGMS U24GM088849

Contents

gorule-0000008

gorule-0000016

gorule-0000018

gorule-0000020

gorule-0000027

gorule-0000029

gorule-0000033

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

gorule-0000033

Public Reference IDs (PMID, PMC, doi, or GO_REF) should be preferred over group specific Reference IDs

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
503 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P68871 HBB Contributes_to GO:0031720 PMID:19740759 IDA F protein taxon:9606 20101214 GONUTS
505 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P68871 HBB Contributes_to GO:0004601 PMID:19740759 IDA F protein taxon:9606 20101214 GONUTS
524 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P69905 HBA2 Contributes_to GO:0031720 PMID:19740759 IDA F protein taxon:9606 20101214 GONUTS
526 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P69905 HBA2 Contributes_to GO:0004601 PMID:19740759 IDA F protein taxon:9606 20101214 GONUTS
545 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P00738 HP Contributes_to GO:0004601 PMID:19740759 IDA F protein taxon:9606 20101214 GONUTS
838 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P14565 traI Contributes_to GO:0004520 PMID:7499339 IDA F protein taxon:83333 20110517 GONUTS
1005 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P76014 dhaL Contributes_to GO:0016740 PMID:11350937 IDA F protein taxon:83333 20110524 GONUTS
1008 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P37349 dhaM Contributes_to GO:0016740 PMID:11350937 IDA F protein taxon:83333 20110524 GONUTS
1009 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 #1148 annotations in 1160 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000007 IPI should not be used with catalytic activity molecular function terms Warning count: 1
534 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
#------------
# GO_AR:0000008 No annotations should be made to uninformative high level terms Warning count: 7
180 GO_AR:0000008 Warning Do not annotate to: GO:0005215 'transporter activity' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB P37409 btuB GO:0005215 PMID:1448622 IMP F protein taxon:90371 20110414 GONUTS
197 GO_AR:0000008 Warning Do not annotate to: GO:0006810 'transport' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB P0A261 tsx GO:0006810 PMID:9043137 IMP P protein taxon:90371 20110414 GONUTS
260 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate UniProtKB Q38845 PP2AA1 GO:0006950 PMID:18162590 IMP P protein taxon:3702 20101021 GONUTS
368 GO_AR:0000008 Warning Do not annotate to: GO:0040007 'growth' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB P36581 cal1 NOT GO:0040007 PMID:19351719 IMP P protein taxon:284812 20101123 GONUTS
894 GO_AR:0000008 Warning Do not annotate to: GO:0042710 'biofilm formation' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB P0A6A3 ackA GO:0042710 PMID:12753190 IMP P protein taxon:83333 20110923 GONUTS
989 GO_AR:0000008 Warning Do not annotate to: GO:0001101 'response to acid chemical' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate UniProtKB P0ACA3 sspA GO:0001101 PMID:15819627 IMP P protein taxon:83333 20110412 GONUTS
995 GO_AR:0000008 Warning Do not annotate to: GO:0008152 'metabolic process' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate UniProtKB P76085 paaK GO:0008152 PMID:9748275 IMP P protein taxon:83333 20110412 GONUTS
#------------

Predictions

GO:0098793 presynapse 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 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:0055114 oxidation-reduction process AnnotationPropagation P GO:0008940 nitrate reductase activity IGI
GO:0006508 proteolysis AnnotationPropagation P GO:0004175 endopeptidase activity IDA
GO:0016310 phosphorylation AnnotationPropagation P GO:0009029 tetraacyldisaccharide 4'-kinase activity IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008888 glycerol dehydrogenase [NAD+] activity IDA
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: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:0006470 protein dephosphorylation AnnotationPropagation P GO:0008138 protein tyrosine/serine/threonine phosphatase activity IDA
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: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:1903506 regulation of nucleic acid-templated transcription AnnotationPropagation P GO:0003712 transcription coregulator activity IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0004616 phosphogluconate dehydrogenase (decarboxylating) activity IMP
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:0055114 oxidation-reduction process AnnotationPropagation P GO:0008940 nitrate reductase activity IMP
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:0004497 monooxygenase activity EXP
GO:0016310 phosphorylation AnnotationPropagation P GO:0004618 phosphoglycerate kinase activity IMP
GO:0015904 tetracycline transmembrane transport AnnotationPropagation P GO:0008493 tetracycline transmembrane transporter 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:0022900 electron transport chain AnnotationPropagation P GO:0009055 electron transfer activity IMP
GO:0005829 cytosol AnnotationPropagation C GO:0045022 early endosome to late endosome transport IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0016491 oxidoreductase activity IDA
GO:0005929 cilium AnnotationPropagation C GO:0042073 intraciliary transport IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008137 NADH dehydrogenase (ubiquinone) 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:0097339 glycolate transmembrane transport AnnotationPropagation P GO:0043879 glycolate transmembrane transporter activity IGI
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008863 formate dehydrogenase (NAD+) 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:0016310 phosphorylation AnnotationPropagation P GO:0016301 kinase activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0008942 nitrite reductase [NAD(P)H] activity IMP
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: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:0006508 proteolysis AnnotationPropagation P GO:0008237 metallopeptidase activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0016491 oxidoreductase activity IMP
GO:0032259 methylation AnnotationPropagation P GO:0003908 methylated-DNA-[protein]-cysteine S-methyltransferase activity IMP
GO:0018106 peptidyl-histidine phosphorylation AnnotationPropagation P GO:0004673 protein histidine kinase activity IDA
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:0006508 proteolysis AnnotationPropagation P GO:0008235 metalloexopeptidase 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:0032508 DNA duplex unwinding AnnotationPropagation P GO:0003678 DNA helicase activity IDA
GO:0005623 cell AnnotationPropagation C GO:0035356 cellular triglyceride homeostasis IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0004450 isocitrate dehydrogenase (NADP+) activity IDA
GO:0016310 phosphorylation AnnotationPropagation P GO:0016301 kinase activity ISM
GO:0000160 phosphorelay signal transduction system AnnotationPropagation P GO:0000156 phosphorelay response regulator activity IDA
GO:0005623 cell AnnotationPropagation C GO:0035356 cellular triglyceride homeostasis IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0016491 oxidoreductase activity IMP
GO:0016310 phosphorylation AnnotationPropagation P GO:0016301 kinase activity IDA
GO:0097339 glycolate transmembrane transport AnnotationPropagation P GO:0043879 glycolate transmembrane transporter activity IGI
GO:0032259 methylation AnnotationPropagation P GO:0004851 uroporphyrin-III C-methyltransferase activity ISS
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:0006479 protein methylation AnnotationPropagation P GO:0008276 protein methyltransferase activity IMP
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0004345 glucose-6-phosphate dehydrogenase activity IMP
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:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity ISS
GO:0018106 peptidyl-histidine phosphorylation AnnotationPropagation P GO:0004673 protein histidine kinase activity IMP
GO:0098869 cellular oxidant detoxification AnnotationPropagation P GO:0016209 antioxidant activity IMP
GO:0071897 DNA biosynthetic process AnnotationPropagation P GO:0003887 DNA-directed DNA polymerase activity IDA

Predictions (experimental)