Table of contents

Summary

GAF summary

Found 1470 annotations in 1485 lines.

GAF Validation Summary Errors are reported first.

For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 2 violations with type Error.

GAF Prediction Summary

Found 34 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf    go/releases/2019-05-09/extensions/go-gaf.owl

Report

Group: goa - Dataset: goa_human_complex

SUMMARY

This report generated on 2019-05-09

Header From Original Association File

!gaf-version: 2.1
!
!Note that the annotation set in this file is filtered in order to reduce redundancy; the full, unfiltered set can be found in
!ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz
!
!Generated: 2019-05-07 11:19
!GO-version: http://purl.obolibrary.org/obo/go/releases/2019-05-04/extensions/go-plus.owl
!

Contents

gorule-0000018

other

MESSAGES

gorule-0000018

IPI annotations require a With/From entry

Messages

other

OWLTools check

#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #1470 annotations in 1485 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000014 Valid GO term ID Error count: 2
128 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation ComplexPortal CPX-1120 abeta-40-42-oligomer_human GO:1902951 PMID:17360908 IMP UniProtKB:P05067:VAR_000023 P Amyloid-beta protein 40/42 oligomeric complex fibrillar amyloid-beta oligomer|Annular protofibril complex|Amyloid-beta fibrils|beta-amyloid protein 40/42 heterooligomer|beta-amyloid protein 40/42 complex|beta-amyloid-40/42 complex|beta amyloid protein 40/42 complex|amyloid-beta-40/42 complex|amyloid beta protein 40/42 complex|amyloid-beta protein 40/42 heterooligomer|amyloid-beta-40/42 heterooligomer|amyloid beta protein 40/42 heterooligomer|beta-amyloid-40/42 heterooligomer|beta amyloid protein 40/42 heterooligomer|Abeta protein 40/42 complex|APP oligomer|Type 1 amyloid-beta oligomer|ADDL complex|pre-fibrillar amyloid-beta oligomer|prefibrillar amyloid-beta oligomer|Type 2 amyloid-beta oligomer protein_complex taxon:9606 20170626 ARUK-UCL has_agent(GO:0097720),part_of(GO:0051826),regulates_o_occurs_in(CL:1001571)
193 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation ComplexPortal CPX-1134 abeta-42-oligomer_human GO:0032147 PMID:23386614 IGI UniProtKB:P04925 P Amyloid-beta protein 42 oligomeric complex pre-fibrillar amyloid-beta oligomer|prefibrillar amyloid-beta oligomer|Type 2 amyloid-beta oligomer|fibrillar amyloid-beta oligomer|Annular protofibril complex|Amyloid-beta fibrils|beta-amyloid protein 42 heterooligomer|beta-amyloid protein 42 complex|beta-amyloid-42 complex|beta amyloid protein 42 complex|amyloid-beta-42 complex|amyloid beta protein 42 complex|amyloid-beta protein 42 heterooligomer|amyloid-beta-42 heterooligomer|amyloid beta protein 42 heterooligomer|beta-amyloid-42 heterooligomer|beta amyloid protein 42 heterooligomer|Abeta protein 42 complex|APP oligomer|Type 1 amyloid-beta oligomer|ADDL complex protein_complex taxon:9606 20170626 ARUK-UCL has_agent(GO:0045121),has_regulation_target(UniProtKB:P06241)
#------------

Predictions

GO:0051170 import into nucleus AnnotationPropagation P GO:0061608 nuclear import signal receptor activity IDA
GO:0051726 regulation of cell cycle AnnotationPropagation P GO:0097472 cyclin-dependent protein kinase activity IDA
GO:0006468 protein phosphorylation AnnotationPropagation P GO:0097472 cyclin-dependent protein kinase activity IDA
GO:0051170 import into nucleus AnnotationPropagation P GO:0061608 nuclear import signal receptor activity IDA
GO:0010466 negative regulation of peptidase activity AnnotationPropagation P GO:0030414 peptidase inhibitor activity IDA
GO:0006915 apoptotic process AnnotationPropagation P GO:0008656 cysteine-type endopeptidase activator activity involved in apoptotic process IDA
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process AnnotationPropagation P GO:0008656 cysteine-type endopeptidase activator activity involved in apoptotic process IDA
GO:0051726 regulation of cell cycle AnnotationPropagation P GO:0097472 cyclin-dependent protein kinase activity IDA
GO:0006468 protein phosphorylation AnnotationPropagation P GO:0097472 cyclin-dependent protein kinase activity IDA
GO:0005623 cell AnnotationPropagation C GO:0051209 release of sequestered calcium ion into cytosol IDA
GO:0051726 regulation of cell cycle AnnotationPropagation P GO:0097472 cyclin-dependent protein kinase activity IDA
GO:0006468 protein phosphorylation AnnotationPropagation P GO:0097472 cyclin-dependent protein kinase activity IDA
GO:0006508 proteolysis AnnotationPropagation P GO:0008233 peptidase activity IDA
GO:0051726 regulation of cell cycle AnnotationPropagation P GO:0097472 cyclin-dependent protein kinase activity IDA
GO:0006468 protein phosphorylation AnnotationPropagation P GO:0097472 cyclin-dependent protein kinase activity IDA
GO:0043984 histone H4-K16 acetylation AnnotationPropagation P GO:0046972 histone acetyltransferase activity (H4-K16 specific) IDA
GO:0006259 DNA metabolic process AnnotationPropagation P GO:1990599 3' overhang single-stranded DNA endodeoxyribonuclease activity IMP
GO:0090305 nucleic acid phosphodiester bond hydrolysis AnnotationPropagation P GO:1990599 3' overhang single-stranded DNA endodeoxyribonuclease activity IMP
GO:0006479 protein methylation AnnotationPropagation P GO:0008276 protein methyltransferase activity IDA
GO:0005739 mitochondrion AnnotationPropagation C GO:1901029 negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway IDA
GO:0016311 dephosphorylation AnnotationPropagation P GO:0016791 phosphatase activity IDA
GO:0006508 proteolysis AnnotationPropagation P GO:0008233 peptidase activity IDA
GO:0000122 negative regulation of transcription by RNA polymerase II AnnotationPropagation P GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
GO:0005623 cell AnnotationPropagation C GO:1905665 positive regulation of calcium ion import across plasma membrane IGI
GO:1904356 regulation of telomere maintenance via telomere lengthening FoldBasedPredictor GO:0098505 G-rich strand telomeric DNA binding part_of GO:0051974 negative regulation of telomerase activity part_of GO:1904356 regulation of telomere maintenance via telomere lengthening IDA
GO:0051974 negative regulation of telomerase activity FoldBasedPredictor GO:0098505 G-rich strand telomeric DNA binding part_of GO:0051974 negative regulation of telomerase activity part_of GO:1904356 regulation of telomere maintenance via telomere lengthening IDA
GO:0007596 blood coagulation FoldBasedPredictor GO:0016485 protein processing has_direct_input UniProtKB:P00742 occurs_in CL:0002618 part_of GO:0007596 blood coagulation IDA
GO:0006303 double-strand break repair via nonhomologous end joining FoldBasedPredictor GO:1990599 3' overhang single-stranded DNA endodeoxyribonuclease activity occurs_at GO:0000784 nuclear chromosome, telomeric region part_of GO:0006303 double-strand break repair via nonhomologous end joining IMP
GO:0033554 cellular response to stress FoldBasedPredictor GO:2000363 positive regulation of prostaglandin-E synthase activity has_output CHEBI:15551 prostaglandin E2 occurs_in CL:0000243 glial cell (sensu Vertebrata) occurs_in UBERON:0001891 midbrain part_of GO:0033554 cellular response to stress regulates_o_occurs_in CL:0000243 glial cell (sensu Vertebrata) ISS
GO:0097458 neuron part FoldBasedPredictor GO:0098978 glutamatergic synapse part_of CL:0002608 hippocampal neuron IDA
GO:1905581 positive regulation of low-density lipoprotein particle clearance FoldBasedPredictor GO:1905602 positive regulation of receptor-mediated endocytosis involved in cholesterol transport has_direct_input GO:0034362 low-density lipoprotein particle part_of GO:0001921 positive regulation of receptor recycling part_of GO:0032385 positive regulation of intracellular cholesterol transport part_of GO:1905581 positive regulation of low-density lipoprotein particle clearance part_of GO:1905597 positive regulation of low-density lipoprotein particle receptor binding part_of GO:1905599 positive regulation of low-density lipoprotein receptor activity part_of GO:1905602 positive regulation of receptor-mediated endocytosis involved in cholesterol transport IDA
GO:1905599 positive regulation of low-density lipoprotein receptor activity FoldBasedPredictor GO:1905602 positive regulation of receptor-mediated endocytosis involved in cholesterol transport has_direct_input GO:0034362 low-density lipoprotein particle part_of GO:0001921 positive regulation of receptor recycling part_of GO:0032385 positive regulation of intracellular cholesterol transport part_of GO:1905581 positive regulation of low-density lipoprotein particle clearance part_of GO:1905597 positive regulation of low-density lipoprotein particle receptor binding part_of GO:1905599 positive regulation of low-density lipoprotein receptor activity part_of GO:1905602 positive regulation of receptor-mediated endocytosis involved in cholesterol transport IDA
GO:1905597 positive regulation of low-density lipoprotein particle receptor binding FoldBasedPredictor GO:1905602 positive regulation of receptor-mediated endocytosis involved in cholesterol transport has_direct_input GO:0034362 low-density lipoprotein particle part_of GO:0001921 positive regulation of receptor recycling part_of GO:0032385 positive regulation of intracellular cholesterol transport part_of GO:1905581 positive regulation of low-density lipoprotein particle clearance part_of GO:1905597 positive regulation of low-density lipoprotein particle receptor binding part_of GO:1905599 positive regulation of low-density lipoprotein receptor activity part_of GO:1905602 positive regulation of receptor-mediated endocytosis involved in cholesterol transport IDA
GO:0001921 positive regulation of receptor recycling FoldBasedPredictor GO:1905602 positive regulation of receptor-mediated endocytosis involved in cholesterol transport has_direct_input GO:0034362 low-density lipoprotein particle part_of GO:0001921 positive regulation of receptor recycling part_of GO:0032385 positive regulation of intracellular cholesterol transport part_of GO:1905581 positive regulation of low-density lipoprotein particle clearance part_of GO:1905597 positive regulation of low-density lipoprotein particle receptor binding part_of GO:1905599 positive regulation of low-density lipoprotein receptor activity part_of GO:1905602 positive regulation of receptor-mediated endocytosis involved in cholesterol transport IDA

Predictions (experimental)