Table of contents

Summary

GAF summary

Found 36258 annotations in 36277 lines.

GAF Validation Summary Errors are reported first.

For rule GO_AR:0000005 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000005) No ISS or ISS-related annotations to 'protein binding ; GO:0005515', there is one violation with type Error.

For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 12 violations with type Error.

For rule GO_AR:0000003 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000003) Annotations to 'binding ; GO:0005488' and 'protein binding ; GO:0005515' should be made with IPI and an interactor in the 'with' field, there is one violation with type Warning.

GAF Prediction Summary

Found 5 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_cow_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 16:01
!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-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

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-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.

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 #36258 annotations in 36277 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000005 No ISS or ISS-related annotations to 'protein binding ; GO:0005515' Error count: 1
29936 GO_AR:0000005 Error No ISS or ISS-related annotations to 'protein binding ; GO:0005515' UniProtKB E1BNK3 TGFB1 GO:0005515 GO_REF:0000024 ISS UniProtKB:P01137 F Transforming growth factor beta TGFB1 protein taxon:9913 20141202 AgBase UniProtKB:E1BNK3
#------------
# GO_AR:0000014 Valid GO term ID Error count: 12
28520 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:0010867 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001013),has_agent(UBERON:0002107),occurs_in(UBERON:0001911) UniProtKB:B0FPG4
28520 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:0010867 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001013),has_agent(UBERON:0002107),occurs_in(UBERON:0001911) UniProtKB:B0FPG4
28527 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:0045542 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001013),has_agent(UBERON:0002107),occurs_in(UBERON:0001911) UniProtKB:B0FPG4
28527 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:0045542 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001013),has_agent(UBERON:0002107),occurs_in(UBERON:0001911) UniProtKB:B0FPG4
28529 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:0045723 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001911),has_agent(UBERON:0002107),occurs_in(UBERON:0001013) UniProtKB:B0FPG4
28529 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:0045723 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001911),has_agent(UBERON:0002107),occurs_in(UBERON:0001013) UniProtKB:B0FPG4
28530 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:0045723 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001013),has_agent(UBERON:0002107),occurs_in(UBERON:0001911) UniProtKB:B0FPG4
28530 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:0045723 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001013),has_agent(UBERON:0002107),occurs_in(UBERON:0001911) UniProtKB:B0FPG4
28534 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:0071073 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001911),has_agent(UBERON:0002107),occurs_in(UBERON:0001013) UniProtKB:B0FPG4
28534 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:0071073 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001911),has_agent(UBERON:0002107),occurs_in(UBERON:0001013) UniProtKB:B0FPG4
28535 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:1900482 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001013),has_agent(UBERON:0002107),occurs_in(UBERON:0001911) UniProtKB:B0FPG4
28535 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB B0FPG4 GH1 GO:1900482 PMID:2731415 IDA P Growth hormone GH1 protein taxon:9913 20150522 AgBase happens_during(GO:0007595),has_agent(UBERON:0001013),has_agent(UBERON:0002107),occurs_in(UBERON:0001911) UniProtKB:B0FPG4
#------------
# GO_AR:0000003 Annotations to 'binding ; GO:0005488' and 'protein binding ; GO:0005515' should be made with IPI and an interactor in the 'with' field Warning count: 1
29936 GO_AR:0000003 Warning Annotations to 'binding' (GO:0005488) and 'protein binding' (GO:0005515) should be made with an IPI evidence code and the interactor in the 'with' field UniProtKB E1BNK3 TGFB1 GO:0005515 GO_REF:0000024 ISS UniProtKB:P01137 F Transforming growth factor beta TGFB1 protein taxon:9913 20141202 AgBase UniProtKB:E1BNK3
#------------

Predictions

GO:0005623 cell AnnotationPropagation C GO:0097277 cellular urea homeostasis ISS
GO:0009967 positive regulation of signal transduction AnnotationPropagation P GO:0030160 GKAP/Homer scaffold activity ISS
GO:0005737 cytoplasm AnnotationPropagation C GO:0030970 retrograde protein transport, ER to cytosol ISS
GO:0016020 membrane AnnotationPropagation C GO:0032596 protein transport into membrane raft IMP
GO:0045121 membrane raft FoldBasedPredictor GO:0051117 ATPase binding occurs_in CL:0000019 sperm occurs_in GO:0045121 membrane raft IPI

Predictions (experimental)