Table of contents

Summary

GAF summary

Found 273 annotations in 281 lines.

GAF Validation Summary Errors are reported first.

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 2 violations with type Warning.

GAF Prediction Summary

Found 12 predictions, see prediction file for details.

Used Ontology Summary

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

Report

Group: pamgo - Dataset: pamgo_ddadantii

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-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

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-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 #273 annotations in 281 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000008 No annotations should be made to uninformative high level terms Warning count: 2
73 GO_AR:0000008 Warning Do not annotate to: GO:0140110 'transcription regulator activity' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate ASAP ABF-0016089 pecS GO:0140110 PMID:18790868 IMP F DNA-binding transcriptional regulatory protein PecS gene taxon:198628 20080130 ASAP
245 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 ASAP ABF-0020512 gacA GO:0042710 PMID:18052890 IMP P "Response regulator of the two-component transcriptional regulatory system UvrY-BarA (ExpA-ExpS, GacA-GacS)" gene taxon:198628 20080222 ASAP
#------------

Predictions

GO:0010466 negative regulation of peptidase activity AnnotationPropagation P GO:0030414 peptidase inhibitor activity IDA
GO:0045944 positive regulation of transcription by RNA polymerase II AnnotationPropagation P GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IMP
GO:0034219 carbohydrate transmembrane transport AnnotationPropagation P GO:0033155 oligogalacturonide transmembrane transporter activity IGI
GO:0033156 oligogalacturonide transport AnnotationPropagation P GO:0033155 oligogalacturonide transmembrane transporter activity IGI
GO:0045944 positive regulation of transcription by RNA polymerase II AnnotationPropagation P GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific ISA
GO:0034219 carbohydrate transmembrane transport AnnotationPropagation P GO:0033155 oligogalacturonide transmembrane transporter activity IGI
GO:0033156 oligogalacturonide transport AnnotationPropagation P GO:0033155 oligogalacturonide transmembrane transporter activity IGI
GO:0034219 carbohydrate transmembrane transport AnnotationPropagation P GO:0033155 oligogalacturonide transmembrane transporter activity IGI
GO:0033156 oligogalacturonide transport AnnotationPropagation P GO:0033155 oligogalacturonide transmembrane transporter activity IGI
GO:0045944 positive regulation of transcription by RNA polymerase II AnnotationPropagation P GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IMP
GO:0006508 proteolysis AnnotationPropagation P GO:0008237 metallopeptidase activity IDA
GO:0045944 positive regulation of transcription by RNA polymerase II AnnotationPropagation P GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific ISA

Predictions (experimental)