Table of contents

Summary

GAF summary

Found 22931 annotations in 22950 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.

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 3 violations with type Warning.

GAF Prediction Summary

Found 10 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_chicken_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 16:00
!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

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

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

Messages

OWLTools check

#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #22931 annotations in 22950 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000014 Valid GO term ID Error count: 2
1424 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB A0A1D5P1B0 CLASP2 GO:0010717 PMID:23940118 IMP P Uncharacterized protein CLASP2 protein taxon:9031 20170214 UniProt happens_during(GO:0007369),has_agent(GO:0043256),occurs_in(CL:0000352) UniProtKB:A0A1D5P1B0
1426 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB A0A1D5P1B0 CLASP2 GO:1904261 PMID:23940118 IMP P Uncharacterized protein CLASP2 protein taxon:9031 20170214 UniProt happens_during(GO:0001837),happens_during(GO:0007369),has_agent(GO:0043256),occurs_in(CL:0000352) UniProtKB:A0A1D5P1B0
#------------
# GO_AR:0000008 No annotations should be made to uninformative high level terms Warning count: 3
3605 GO_AR:0000008 Warning Do not annotate to: GO:0005622 'intracellular' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB A0A1D5PFN2 PALM GO:0005622 PMID:9813098 IDA C Paralemmin-1 PALM protein taxon:9031 20170202 AgBase part_of(UBERON:0000955) UniProtKB:A0A1D5PFN2
22641 GO_AR:0000008 Warning Do not annotate to: GO:0005622 'intracellular' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB Q9YGL6 PALM GO:0005622 PMID:9813098 IDA C Paralemmin-1 PALM protein taxon:9031 20170202 AgBase part_of(UBERON:0000955) UniProtKB:Q9YGL6-2
22642 GO_AR:0000008 Warning Do not annotate to: GO:0005622 'intracellular' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB Q9YGL6 PALM GO:0005622 PMID:9813098 IDA C Paralemmin-1 PALM protein taxon:9031 20170202 AgBase part_of(UBERON:0000955) UniProtKB:Q9YGL6-3
#------------

Predictions

GO:0005829 cytosol AnnotationPropagation C GO:0042147 retrograde transport, endosome to Golgi ISS
GO:0006259 DNA metabolic process AnnotationPropagation P GO:0004531 deoxyribonuclease II activity IDA
GO:0090305 nucleic acid phosphodiester bond hydrolysis AnnotationPropagation P GO:0004531 deoxyribonuclease II activity IDA
GO:0044295 axonal growth cone FoldBasedPredictor GO:2000009 negative regulation of protein localization to cell surface occurs_in GO:0044295 axonal growth cone transports_or_maintains_localization_of UniProtKB:F1N8P1 IMP
GO:0072348 sulfur compound transport FoldBasedPredictor GO:0055085 transmembrane transport transports_or_maintains_localization_of CHEBI:8927 S-(2,4-dinitrophenyl)glutathione ISS
GO:0071705 nitrogen compound transport FoldBasedPredictor GO:0055085 transmembrane transport transports_or_maintains_localization_of CHEBI:8927 S-(2,4-dinitrophenyl)glutathione ISS
GO:0015711 organic anion transport FoldBasedPredictor GO:0055085 transmembrane transport transports_or_maintains_localization_of CHEBI:8927 S-(2,4-dinitrophenyl)glutathione ISS
GO:0098656 anion transmembrane transport FoldBasedPredictor GO:0055085 transmembrane transport transports_or_maintains_localization_of CHEBI:8927 S-(2,4-dinitrophenyl)glutathione ISS
GO:0005829 cytosol FoldBasedPredictor GO:0031072 heat shock protein binding occurs_in GO:0005829 cytosol occurs_in UBERON:0000993 oviduct IPI
GO:0008144 drug binding FoldBasedPredictor GO:1990239 steroid hormone binding has_input CHEBI:17026 progesterone occurs_in UBERON:0000993 oviduct ISS

Predictions (experimental)