Table of contents

Summary

GAF summary

Found 87637 annotations in 87656 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 are 3 violations 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 4 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 are 3 violations with type Warning.

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.

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 Warning.

GAF Prediction Summary

Found 22 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf    go/releases/2019-10-31/extensions/go-gaf.owl

Report

Group: goa - Dataset: goa_dog

SUMMARY

This report generated on 2019-11-02

Header From Original Association File

!gaf-version: 2.1
!
!The set of protein accessions included in this file is based on UniProt reference proteomes, which provide one protein per gene.
!They include the protein sequences annotated in Swiss-Prot or the longest TrEMBL transcript if there is no Swiss-Prot record.
!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.gz
!
!Generated: 2019-10-15 18:51
!GO-version: http://purl.obolibrary.org/obo/go/releases/2019-10-03/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-0000020

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

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-0000020

Automatic repair of annotations to merged or obsoleted terms

Messages

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 #87637 annotations in 87656 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000005 No ISS or ISS-related annotations to 'protein binding ; GO:0005515' Error count: 3
45595 GO_AR:0000005 Error No ISS or ISS-related annotations to 'protein binding ; GO:0005515' UniProtKB F1PI70 B9D2 GO:0005515 GO_REF:0000024 ISS UniProtKB:P01137 F Transforming growth factor beta B9D2 protein taxon:9615 20141202 AgBase
82030 GO_AR:0000005 Error No ISS or ISS-related annotations to 'protein binding ; GO:0005515' UniProtKB P54831 TGFB1 GO:0005515 GO_REF:0000024 ISS UniProtKB:P01137 F Transforming growth factor beta-1 proprotein TGFB1 protein taxon:9615 20141202 AgBase
83440 GO_AR:0000005 Error No ISS or ISS-related annotations to 'protein binding ; GO:0005515' UniProtKB Q28295 VWF GO:0005515 GO_REF:0000024 ISS UniProtKB:P04275 F von Willebrand factor VWF|F8VWF protein taxon:9615 20070328 UniProt
#------------
# GO_AR:0000014 Valid GO term ID Error count: 4
37073 GO_AR:0000014 Error The id 'GO:1990967' in the annotation is an obsolete class UniProtKB F1P9G2 RAB29 GO:1990967 GO_REF:0000107 IEA UniProtKB:O14966|ensembl:ENSP00000356107 P RAB29, member RAS oncogene family RAB29 protein taxon:9615 20190925 Ensembl
48078 GO_AR:0000014 Error The id 'GO:0052213' in the annotation is an obsolete class UniProtKB F1PL06 IL33 GO:0052213 GO_REF:0000107 IEA UniProtKB:O95760|ensembl:ENSP00000370842 P Interleukin-33 IL33 protein taxon:9615 20190925 Ensembl
62735 GO_AR:0000014 Error The id 'GO:0052213' in the annotation is an obsolete class UniProtKB F1Q421 PLG GO:0052213 GO_REF:0000107 IEA UniProtKB:P00747|ensembl:ENSP00000308938 P Plasminogen PLG protein taxon:9615 20190925 Ensembl
69820 GO_AR:0000014 Error The id 'GO:1990967' in the annotation is an obsolete class UniProtKB J9NU44 RAB40B GO:1990967 GO_REF:0000107 IEA UniProtKB:Q12829|ensembl:ENSP00000461785 P SOCS box domain-containing protein RAB40B protein taxon:9615 20190925 Ensembl
#------------
# 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: 3
45595 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 F1PI70 B9D2 GO:0005515 GO_REF:0000024 ISS UniProtKB:P01137 F Transforming growth factor beta B9D2 protein taxon:9615 20141202 AgBase
82030 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 P54831 TGFB1 GO:0005515 GO_REF:0000024 ISS UniProtKB:P01137 F Transforming growth factor beta-1 proprotein TGFB1 protein taxon:9615 20141202 AgBase
83440 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 Q28295 VWF GO:0005515 GO_REF:0000024 ISS UniProtKB:P04275 F von Willebrand factor VWF|F8VWF protein taxon:9615 20070328 UniProt
#------------
# GO_AR:0000008 No annotations should be made to uninformative high level terms Warning count: 2
5095 GO_AR:0000008 Warning Do not annotate to: GO:0072001 'renal system development' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB E2QX76 CEP55 GO:0072001 GO_REF:0000107 IEA UniProtKB:Q53EZ4|ensembl:ENSP00000360540 P EABR domain-containing protein CEP55 protein taxon:9615 20190925 Ensembl
71735 GO_AR:0000008 Warning Do not annotate to: GO:0072001 'renal system development' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB J9NXR3 J9NXR3 GO:0072001 GO_REF:0000107 IEA UniProtKB:P16144|ensembl:ENSP00000200181 P Uncharacterized protein protein taxon:9615 20190925 Ensembl
#------------
# GO_AR:0000014 Valid GO term ID Warning count: 12
6050 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB E2QY30 HMGB2 GO:0001158 GO_REF:0000024 ISS UniProtKB:P30681 F High mobility group box 2 HMGB2 protein taxon:9615 20150512 AgBase
6051 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB E2QY30 HMGB2 GO:0001158 GO_REF:0000024 ISS UniProtKB:Q3U566 F High mobility group box 2 HMGB2 protein taxon:9615 20150512 AgBase
14481 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB E2R919 FOXN4 GO:0001158 GO_REF:0000107 IEA UniProtKB:Q8K3Q3|ensembl:ENSMUSP00000047951 F Fork-head domain-containing protein FOXN4 protein taxon:9615 20190925 Ensembl
14482 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB E2R919 FOXN4 GO:0001158 GO_REF:0000107 IEA UniProtKB:Q96NZ1|ensembl:ENSP00000299162 F Fork-head domain-containing protein FOXN4 protein taxon:9615 20190925 Ensembl
15055 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB E2R9I9 ZNF395 GO:0001158 GO_REF:0000107 IEA UniProtKB:E9Q5N9|ensembl:ENSMUSP00000064422 F C2H2-type domain-containing protein ZNF395 protein taxon:9615 20190925 Ensembl
22135 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB E2RH17 LDB1 GO:0001158 GO_REF:0000107 IEA UniProtKB:P70662|ensembl:ENSMUSP00000118546 F LID domain-containing protein LDB1 protein taxon:9615 20190925 Ensembl
27121 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB E2RMA8 LHX1 GO:0001158 GO_REF:0000107 IEA UniProtKB:P63006|ensembl:ENSMUSP00000018842 F LIM homeobox 1 LHX1 protein taxon:9615 20190925 Ensembl
29785 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB E2RPT1 GATA3 GO:0001158 GO_REF:0000107 IEA UniProtKB:P23772|ensembl:ENSMUSP00000100041 F GATA binding protein 3 GATA3 protein taxon:9615 20190925 Ensembl
50550 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F1PP21 ISL1 GO:0001158 GO_REF:0000107 IEA UniProtKB:P61371|ensembl:ENSP00000230658 F ISL LIM homeobox 1 ISL1 protein taxon:9615 20190925 Ensembl
63563 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F6UNN7 ZBTB7B GO:0001158 GO_REF:0000107 IEA UniProtKB:Q64321|ensembl:ENSMUSP00000103058 F Zinc finger and BTB domain containing 7B ZBTB7B protein taxon:9615 20190925 Ensembl
67446 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB G1K277 HMGA1 GO:0001158 GO_REF:0000107 IEA UniProtKB:P17096|ensembl:ENSP00000399888 F High mobility group protein HMG-I/HMG-Y HMGA1 protein taxon:9615 20190925 Ensembl
85863 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB Q7YRJ7 SOX9 GO:0001158 GO_REF:0000024 ISS UniProtKB:Q04887 F Transcription factor SOX-9 SOX9 protein taxon:9615 20110708 UniProt
#------------

Predictions

GO:0070588 calcium ion transmembrane transport AnnotationPropagation P GO:1905060 calcium:cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration IMP
GO:0099566 regulation of postsynaptic cytosolic calcium ion concentration AnnotationPropagation P GO:1905060 calcium:cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration IMP
GO:0005623 cell AnnotationPropagation C GO:0047496 vesicle transport along microtubule ISS
GO:0005576 extracellular region AnnotationPropagation C GO:0060287 epithelial cilium movement involved in determination of left/right asymmetry IMP
GO:0005829 cytosol AnnotationPropagation C GO:0061502 early endosome to recycling endosome transport IDA
GO:0005623 cell AnnotationPropagation C GO:0051480 regulation of cytosolic calcium ion concentration IDA
GO:0036065 fucosylation AnnotationPropagation P GO:0046920 alpha-(1->3)-fucosyltransferase activity ISS
GO:0005623 cell AnnotationPropagation C GO:0097277 cellular urea homeostasis ISS
GO:0005623 cell AnnotationPropagation C GO:0051303 establishment of chromosome localization ISS
GO:0005829 cytosol AnnotationPropagation C GO:0042147 retrograde transport, endosome to Golgi ISS
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0101021 estrogen 2-hydroxylase activity ISS
GO:0005623 cell AnnotationPropagation C GO:0051209 release of sequestered calcium ion into cytosol ISS
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0101021 estrogen 2-hydroxylase activity ISS
GO:0005623 cell AnnotationPropagation C GO:0035356 cellular triglyceride homeostasis ISS
GO:0005623 cell AnnotationPropagation C GO:0097553 calcium ion transmembrane import into cytosol ISS
GO:0010452 histone H3-K36 methylation AnnotationPropagation P GO:0046975 histone methyltransferase activity (H3-K36 specific) ISS
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0070330 aromatase activity ISS
GO:0005623 cell AnnotationPropagation C GO:0030644 cellular chloride ion homeostasis ISS
GO:0055085 transmembrane transport AnnotationPropagation P GO:0140359 ABC-type transmembrane transporter activity ISS
GO:0005623 cell AnnotationPropagation C GO:0051482 positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway ISS
GO:0005789 endoplasmic reticulum membrane FoldBasedPredictor GO:1990381 ubiquitin-specific protease binding occurs_in GO:0005789 endoplasmic reticulum membrane IPI
GO:0005789 endoplasmic reticulum membrane FoldBasedPredictor GO:0051117 ATPase binding occurs_in GO:0005789 endoplasmic reticulum membrane IPI

Predictions (experimental)