• Summary (original)
• Report (original)
• OWLTools check (original)
• Predictions (original)
• Predictions (experimental) (original)

GAF summary

Found 1450 annotations in 1458 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 22 violations with type Warning.

GAF Prediction Summary

Found 107 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf

Group: sgn - Dataset: sgn

SUMMARY

This report generated on 2018-10-01

• Associations: 1450
• Lines in file (incl headers): 1458
• Lines skipped: 8

Contents

gorule-0000016

gorule-0000020

other

MESSAGES

gorule-0000016

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

• total: 6

Messages

• WARNING - Violates GO Rule: GORULE:0000016: All IC annotations should include a GO ID in the "With/From" column (GO:0009536) -- SGN 246 crtiso GO:0009536 PMID:11884678 IC C carotenoid isomerase tangerine|Solyc10g081650 gene taxon:4081 20070920 SGN
• WARNING - Violates GO Rule: GORULE:0000016: All IC annotations should include a GO ID in the "With/From" column (GO:0005634) -- SGN 8265 SlSK GO:0005634 PMID:19533382 IC C SlSK Solyc07g055200 gene taxon:4081 20090730 SGN
• WARNING - Violates GO Rule: GORULE:0000016: All IC annotations should include a GO ID in the "With/From" column (GO:0051607) -- SGN 1381 sw5 GO:0051607 PMID:11043474 IC NCBI_gi:15418708 P Spotted wilt resistance-5 Sw-5|Solyc09g098130.1.1 gene taxon:4081 20100107 SGN
• WARNING - Violates GO Rule: GORULE:0000016: All IC annotations should include a GO ID in the "With/From" column (GO:0016120) -- SGN 5583 tg1 GO:0016120 SGN_ref:861 IC P test gene tg2|tg gene taxon:4081 20121115 SGN
• WARNING - Violates GO Rule: GORULE:0000016: All IC annotations should include a GO ID in the "With/From" column (GO:0006281) -- SGN 8336 MSH2 GO:0006281 PMID:19690966 IC P DNA mismatch repair protein 2 gene taxon:4081 20100416 SGN
• WARNING - Violates GO Rule: GORULE:0000016: All IC annotations should include a GO ID in the "With/From" column (GO:0006281) -- SGN 8337 MSH7 GO:0006281 PMID:19690966 IC P DNA mismatch repair protein 7 gene taxon:4081 20100416 SGN

gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

• total: 4

Messages

• WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0004872) -- SGN 662 Gr GO:0004872 PMID:15834010 IMP F green ripe gr|DQ372895|Solyc01g104340 gene taxon:4081 20071005 SGN
• WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0004872) -- SGN 1046 Nr2 GO:0004872 PMID:15834010 IMP F Never ripe-2 Nr-2|Never-ripe|Solyc09g075440 gene taxon:4081 20071005 SGN
• WARNING - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0000988) -- SGN 8326 HSFA2 GO:0000988 PMID:19491106 IDA F heat stress transcription factor A2 gene taxon:4081 20120224 SGN
• WARNING - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0042965) -- SGN 43099 SlGRX1 GO:0042965 PMID:20862491 IDA P glutaredoxin gene gene taxon:4081 20101210 SGN

other

• total: 0

#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #1450 annotations in 1458 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000007 IPI should not be used with catalytic activity molecular function terms Warning count: 1
81 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: 22
10 GO_AR:0000008 Warning Do not annotate to: GO:0044428 'nuclear part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 364 c14 GO:0044428 PMID:11444695 IDA C cysteine protease CYP1 C14|tdi-65|Solyc12g088670 gene taxon:4081 20090612 SGN
11 GO_AR:0000008 Warning Do not annotate to: GO:0044434 'chloroplast part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 364 c14 GO:0044434 PMID:11444695 IDA C cysteine protease CYP1 C14|tdi-65|Solyc12g088670 gene taxon:4081 20090612 SGN
18 GO_AR:0000008 Warning Do not annotate to: GO:0044459 'plasma membrane part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 1027 LeST1-1 GO:0044459 PMID:12937983 IDA C sulfate transporter 1 THT1-3|THT7-1|THT1-4|Solyc10g047170 gene taxon:4081 20090929 SGN
29 GO_AR:0000008 Warning Do not annotate to: GO:0044459 'plasma membrane part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 5291 amt1 GO:0044459 PMID:8755617 IDA C AMT1 Solyc09g090730 gene taxon:4081 20090929 SGN
30 GO_AR:0000008 Warning Do not annotate to: GO:0044459 'plasma membrane part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 5389 LeST1-2 GO:0044459 PMID:12937983 IDA C sulfate transporter 2 AF347614|Solyc12g056930 gene taxon:4081 20090929 SGN
40 GO_AR:0000008 Warning Do not annotate to: GO:0044434 'chloroplast part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 17699 SlBCAT4 GO:0044434 PMID:20435740 IDA C SlBCAT4 Solyc03g043880 gene taxon:4081 20120131 SGN
42 GO_AR:0000008 Warning Do not annotate to: GO:0044429 'mitochondrial part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 110964 SlBCAT2 GO:0044429 PMID:20435740 IDA C SlBCAT2 Solyc07g021630 gene taxon:4081 20120130 SGN
297 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
329 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
433 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
539 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
858 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
897 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
1000 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
1043 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
1064 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
1108 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
1222 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
1374 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
1387 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
1397 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
1435 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
#------------

GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade 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:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045544 gibberellin 20-oxidase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0010951 negative regulation of endopeptidase activity AnnotationPropagation P GO:0004869 cysteine-type endopeptidase inhibitor activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0006508 proteolysis AnnotationPropagation P GO:0008234 cysteine-type peptidase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045552 dihydrokaempferol 4-reductase activity ISS
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0033744 L-methionine:thioredoxin-disulfide S-oxidoreductase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
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:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0010466 negative regulation of peptidase activity AnnotationPropagation P GO:0030414 peptidase inhibitor activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade 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:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0032259 methylation AnnotationPropagation P GO:0016206 catechol O-methyltransferase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0098869 cellular oxidant detoxification AnnotationPropagation P GO:0016209 antioxidant activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity IMP
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045544 gibberellin 20-oxidase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0006468 protein phosphorylation AnnotationPropagation P GO:0004672 protein kinase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA