Table of contents

Summary

GAF summary

Found 1362 annotations in 1370 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 15 violations with type Warning.

GAF Prediction Summary

Found 22 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf    go/releases/2019-11-16/extensions/go-gaf.owl

Report

Group: sgn - Dataset: sgn

SUMMARY

This report generated on 2019-11-18

Header From Original Association File

Contents

gorule-0000002

gorule-0000006

gorule-0000007

gorule-0000008

gorule-0000011

gorule-0000013

gorule-0000015

gorule-0000016

gorule-0000017

gorule-0000018

gorule-0000020

gorule-0000028

gorule-0000029

gorule-0000030

gorule-0000033

gorule-0000037

gorule-0000039

gorule-0000042

gorule-0000043

gorule-0000046

gorule-0000050

other

MESSAGES

gorule-0000002

No 'NOT' annotations to 'protein binding ; GO:0005515'

gorule-0000006

IEP and HEP usage is restricted to terms from the Biological Process ontology

gorule-0000007

IPI should not be used with catalytic activity molecular function terms

Messages

gorule-0000008

No annotations should be made to uninformative high level terms

Messages

gorule-0000011

ND annotations to root nodes only; and only root nodes can have the evidence code ND.

gorule-0000013

Taxon-appropriate annotation check

gorule-0000015

Dual species taxon check

gorule-0000016

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

Messages

gorule-0000017

IDA annotations must not have a With/From entry

gorule-0000018

IPI annotations require a With/From entry

gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

Messages

gorule-0000028

Aspect can only be one of C, P, F and should be repaired using the GO term

gorule-0000029

All IEAs over a year old are removed

gorule-0000030

Deprecated GO_REFs are not allowed

gorule-0000033

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

Messages

gorule-0000037

IBA annotations should ONLY be assigned_by GO_Central and have PMID:21873635 as a reference

gorule-0000039

Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants

gorule-0000042

Qualifier: IKR evidence code requires a NOT qualifier

gorule-0000043

Check for valid combination of evidence code and GO_REF

gorule-0000046

The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms.

gorule-0000050

Annotations to ISS, ISA and ISO should not be self-referential

other

OWLTools check

#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #1362 annotations in 1370 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000007 IPI should not be used with catalytic activity molecular function terms Warning count: 1
74 GO_AR:0000007 Warning IPI should not be used with catalytic activity molecular function terms SGN 5257 pmt GO:0030750 PMID:17221359 IPI NCBI_gi:86438859 F putrescine N-methyltransferase Solyc06g053510 gene taxon:4081 20090625 SGN
#------------
# GO_AR:0000008 No annotations should be made to uninformative high level terms Warning count: 15
290 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 SGN 68 SlIAA3 GO:0006950 PMID:22314799 IDA P auxin-regulated IAA3 LeIAA3|IAA3|Solyc09g065850 gene taxon:4081 20141120 SGN
322 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 SGN 463 e GO:0006950 PMID:22314799 IEP P entire b|SlIAA9|iaa9|LeIAA4|IAA4|ctd1|Solyc04g076850|SlIAA4 gene taxon:4081 20141120 SGN
426 GO_AR:0000008 Warning Do not annotate to: GO:0009628 'response to abiotic stimulus' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 4506 Asr2 GO:0009628 PMID:17602312 IEP P Abscicic acid stress ripening 2 Solyc04g071580 gene taxon:4081 20080215 SGN
528 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 SGN 9403 SlMAPKKK1 GO:0006950 PMID:25036993 IDA P MAP kinase kinase kinase 1 Solyc01g005030|MAPKKK1 gene taxon:4081 20141103 SGN
820 GO_AR:0000008 Warning Do not annotate to: GO:0009628 'response to abiotic stimulus' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 20062 iaa14 GO:0009628 PMID:22314799 IDA P auxin-regulated IAA14 Solyc03g121060|SlIAA14 gene taxon:4081 20141121 SGN
854 GO_AR:0000008 Warning Do not annotate to: GO:0009628 'response to abiotic stimulus' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 22083 Asr_2 GO:0009628 PMID:17602312 IEP P Abscicic acid stress ripening 2 Solyc04g071580|Asr2 gene taxon:4081 20120509 SGN
950 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 SGN 26635 SlC3H43 GO:0006950 PMID:24870401 ISS P Zinc finger transcription factor 43 Solyc06g054620|C3H43 gene taxon:4081 20150304 SGN
988 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 SGN 27917 SlC3H48 GO:0006950 PMID:24870401 ISS P Zinc finger transcription factor 48 24870401|C3H48|Solyc06g082010 gene taxon:4081 20150304 SGN
1009 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 SGN 28803 SlIAA20 GO:0006950 PMID:22314799 IDA P auxin-regulated IAA20 SlIAA20|iaa20|Solyc07g019450 gene taxon:4081 20141121 SGN
1052 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 SGN 29921 SlC3H50 GO:0006950 PMID:24870401 ISS P Zinc finger transcription factor 50 Solyc07g053750|C3H50 gene taxon:4081 20150304 SGN
1161 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 SGN 35249 SlIAA1 GO:0006950 PMID:22314799 IDA P auxin-regulated IAA1 IAA1|Solyc09g083280 gene taxon:4081 20141124 SGN
1296 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 SGN 40630 SlMAPKKK83 GO:0006950 PMID:25036993 IEP P MAP kinase kinase kinase 83 MAPKKK83|Solyc12g005360 gene taxon:4081 20141111 SGN
1307 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 SGN 40851 SlC3H73 GO:0006950 PMID:24870401 ISS P Zinc finger transcription factor 73 Solyc12g008660|C3H73 gene taxon:4081 20150304 SGN
1315 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 SGN 40914 SlMAPKKK84 GO:0006950 PMID:25036993 IEP P MAP kinase kinase kinase 84 MAPKKK84|Solyc12g009340 gene taxon:4081 20141111 SGN
1348 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 SGN 42691 SlC3H80 GO:0006950 PMID:24870401 ISS P Zinc finger transcription factor 80 C3H80|Solyc12g089260 gene taxon:4081 20150304 SGN
#------------

Predictions

GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0010466 negative regulation of peptidase activity AnnotationPropagation P GO:0030414 peptidase inhibitor activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045544 gibberellin 20-oxidase activity IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0006508 proteolysis AnnotationPropagation P GO:0008234 cysteine-type peptidase activity IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0010951 negative regulation of endopeptidase activity AnnotationPropagation P GO:0004869 cysteine-type endopeptidase inhibitor activity IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045552 dihydrokaempferol 4-reductase activity ISS
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0004784 superoxide dismutase activity IDA
GO:0019430 removal of superoxide radicals AnnotationPropagation P GO:0004784 superoxide dismutase activity IDA
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity IMP
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity IDA
GO:0006468 protein phosphorylation AnnotationPropagation P GO:0004672 protein kinase activity IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045544 gibberellin 20-oxidase activity IDA
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0033744 L-methionine:thioredoxin-disulfide S-oxidoreductase activity IDA
GO:0098869 cellular oxidant detoxification AnnotationPropagation P GO:0016209 antioxidant activity IDA
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045544 gibberellin 20-oxidase activity IDA

Predictions (experimental)