Table of contents

Summary

GAF summary

Found 102071 annotations in 102090 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 4 violations with type Error.

For rule GO_AR:0000011 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000011) ND annotations to root nodes only, there is one violation with type Warning.

GAF Prediction Summary

Found 13 predictions, see prediction file for details.

Used Ontology Summary

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

Report

Group: goa - Dataset: goa_human_isoform

SUMMARY

This report generated on 2019-11-18

Header From Original Association File

!gaf-version: 2.1
!
!The set of protein accessions included in this file is based on UniProt complete proteomes, which may provide more than one protein per gene.
!They include all Swiss-Prot entries for the species plus any TrEMBL entries that have an Ensembl DR line. The TrEMBL entries are likely to overlap with the Swiss-Prot entries or their isoforms.
!If a particular protein accession is not annotated with GO, then it will not appear in this file.
!
!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: 2019-11-11 16:05
!GO-version: http://purl.obolibrary.org/obo/go/releases/2019-11-09/extensions/go-plus.owl
!

Contents

gorule-0000002

gorule-0000006

gorule-0000007

gorule-0000008

gorule-0000011

gorule-0000013

gorule-0000015

gorule-0000016

gorule-0000017

gorule-0000018

gorule-0000027

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

gorule-0000008

No annotations should be made to uninformative high level terms

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

Messages

gorule-0000016

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

gorule-0000017

IDA annotations must not have a With/From entry

gorule-0000018

IPI annotations require a With/From entry

gorule-0000027

Each identifier in GAF is valid

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.

Messages

gorule-0000050

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

other

OWLTools check

#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #102071 annotations in 102090 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000014 Valid GO term ID Error count: 4
86040 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB P05067 APP GO:0000185 PMID:15190117 IGI ComplexPortal:CPX-1134 P Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20170614 ARUK-UCL has_agent(GO:0106003),occurs_in(UBERON:0002421),part_of(GO:0045666) UniProtKB:P05067:PRO_0000000092
86265 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB P05067 APP GO:0043410 PMID:15190117 IGI ComplexPortal:CPX-1134 P Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20170614 ARUK-UCL has_agent(GO:0106003),occurs_in(UBERON:0002421),part_of(GO:0045666) UniProtKB:P05067:PRO_0000000092
86273 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB P05067 APP GO:0045666 PMID:15190117 IGI ComplexPortal:CPX-1134 P Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20170614 ARUK-UCL has_agent(GO:0106003),occurs_in(UBERON:0002421) UniProtKB:P05067:PRO_0000000092
86305 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB P05067 APP GO:0061098 PMID:15190117 IGI ComplexPortal:CPX-1134 P Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20170614 ARUK-UCL has_agent(GO:0106003),occurs_in(UBERON:0002421),part_of(GO:0045666) UniProtKB:P05067:PRO_0000000092
#------------
# GO_AR:0000011 ND annotations to root nodes only Warning count: 1
99782 GO_AR:0000011 Warning ND annotations to root require reference ID UniProtKB Q9Y4H5 GPSM3 GO:0003674 PMID:2259622 ND F G-protein-signaling modulator 3 GPSM3|G18.1a protein taxon:9606 20061026 UniProt UniProtKB:Q9Y4H5
#------------

Predictions

GO:0007186 G protein-coupled receptor signaling pathway AnnotationPropagation P GO:0016520 growth hormone-releasing hormone receptor activity NAS
GO:0007186 G protein-coupled receptor signaling pathway AnnotationPropagation P GO:0016520 growth hormone-releasing hormone receptor activity NAS
GO:0007186 G protein-coupled receptor signaling pathway AnnotationPropagation P GO:0016520 growth hormone-releasing hormone receptor activity NAS
GO:0005623 cell AnnotationPropagation C GO:0051303 establishment of chromosome localization IMP
GO:0005739 mitochondrion AnnotationPropagation C GO:0042407 cristae formation IMP
GO:0045202 synapse AnnotationPropagation C GO:0098942 retrograde trans-synaptic signaling by trans-synaptic protein complex IDA
GO:0005623 cell AnnotationPropagation C GO:0051481 negative regulation of cytosolic calcium ion concentration 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:0016311 dephosphorylation AnnotationPropagation P GO:0046030 inositol trisphosphate phosphatase activity IDA
GO:0016311 dephosphorylation AnnotationPropagation P GO:0106018 phosphatidylinositol-3,5-bisphosphate phosphatase activity IDA
GO:0006869 lipid transport AnnotationPropagation P GO:0120017 ceramide transfer activity IDA
GO:0007186 G protein-coupled receptor signaling pathway AnnotationPropagation P GO:0016520 growth hormone-releasing hormone receptor activity NAS
GO:0006508 proteolysis AnnotationPropagation P GO:0008236 serine-type peptidase activity IDA

Predictions (experimental)